Contacts of the strand formed by residues 273 - 288 (chain A) in PDB entry 6Q2J


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with CYS 273 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244A  CYS*     4.1     3.6    -      -       -      -
    258A  LYS*     5.5     1.2    -      -       -      +
    271A  ALA      4.4     7.2    -      -       -      -
    272A  PRO*     1.3    75.4    -      -       -      +
    274A  CYS*     1.3    63.6    +      -       -      +
    275A  VAL*     3.5    12.8    +      -       +      +
    307A  CYS*     3.4     0.5    -      -       -      -
    308A  ILE      2.9    34.0    +      -       -      +
    273B  CYS*     2.0    54.3    -      -       +      -
    275B  VAL*     4.9     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 274 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211A  CYS*     2.0    55.9    -      -       +      -
    240A  CYS*     3.7    23.9    -      -       -      +
    241A  ILE      5.0     1.3    -      -       -      -
    242A  GLY      5.2    12.1    -      -       -      +
    243A  ALA      5.3     0.4    -      -       -      +
    244A  CYS*     3.9     9.6    -      -       -      -
    273A  CYS*     1.3    72.2    -      -       -      +
    275A  VAL*     1.3    61.5    +      -       -      +
    276A  PRO*     4.7     0.9    -      -       -      +
    305A  CYS*     3.7    12.1    -      -       -      -
    306A  HIS      3.5     5.2    -      -       -      -
    258B  LYS*     4.5    13.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 275 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    273A  CYS*     4.1    13.9    -      -       +      +
    274A  CYS*     1.3    79.1    -      -       -      +
    276A  PRO*     1.3    79.0    -      -       +      +
    305A  CYS*     3.3     4.8    -      -       -      -
    306A  HIS*     2.9    40.8    +      -       +      +
    308A  ILE*     3.7    23.8    -      -       +      -
    258B  LYS*     5.8     2.0    -      -       -      +
    273B  CYS*     5.0     1.3    -      -       +      -
    275B  VAL*     3.8    27.8    -      -       +      -
    308B  ILE*     4.2    23.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 276 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240A  CYS*     5.1     2.7    -      -       +      +
    274A  CYS      4.7     1.3    -      -       -      +
    275A  VAL*     1.3    99.4    -      -       +      +
    277A  ALA*     1.3    60.5    +      -       -      +
    278A  SER      4.5     2.5    -      -       -      +
    279A  TYR*     3.6    46.6    +      -       +      +
    302A  ALA*     3.9    22.7    -      -       +      -
    304A  ASP      3.5     7.4    -      -       -      +
    305A  CYS*     3.6     8.7    -      -       -      -
    306A  HIS*     4.4     2.5    +      -       -      -
    254B  HIS*     4.4    13.9    -      -       +      +
    258B  LYS*     5.5     5.2    -      -       -      +
    308B  ILE*     5.0    10.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 277 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    276A  PRO*     1.3    75.1    -      -       -      +
    278A  SER*     1.3    60.0    +      -       -      +
    279A  TYR*     4.9     6.2    -      -       -      -
    304A  ASP*     2.9    28.0    +      -       -      +
    306A  HIS*     3.5    28.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 278 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    276A  PRO*     4.5     0.5    -      -       -      +
    277A  ALA*     1.3    81.5    +      -       -      +
    279A  TYR*     1.3    69.5    +      -       -      +
    302A  ALA*     3.9     1.0    -      -       -      -
    303A  LYS*     3.0    44.7    +      -       -      +
    304A  ASP*     3.3    15.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 279 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    276A  PRO*     3.6    40.8    +      -       +      +
    277A  ALA      4.9     6.1    -      -       -      -
    278A  SER*     1.3    81.7    -      -       -      +
    280A  ASN*     1.3    65.5    +      -       -      +
    281A  PRO*     4.1     4.5    -      -       -      +
    298A  ASP      4.2    17.5    -      -       -      +
    299A  ASP*     4.3    19.5    -      -       +      -
    301A  LEU      3.3    17.9    -      -       -      +
    302A  ALA*     3.9     7.4    -      -       -      -
    303A  LYS*     4.7     2.3    -      -       -      +
    252B  ASN*     2.9    31.9    +      -       +      -
    254B  HIS*     4.1    15.2    -      +       +      -
    308B  ILE*     3.3    20.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 280 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279A  TYR*     1.3    77.8    -      -       -      +
    281A  PRO*     1.3    73.9    -      -       +      +
    298A  ASP      4.8     1.1    -      -       -      -
    300A  LEU      3.9     2.9    +      -       -      -
    301A  LEU*     2.5    50.5    +      -       +      +
    302A  ALA      3.9     8.5    +      -       -      -
    303A  LYS*     3.8    37.3    -      -       -      +
    146C  ALA*     6.5     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 281 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279A  TYR      4.1     4.9    -      -       -      +
    280A  ASN*     1.3    96.2    -      -       +      +
    282A  MET*     1.3    62.6    +      -       -      +
    296A  THR*     4.0    16.4    -      -       +      -
    297A  TYR      3.2    15.5    -      -       -      +
    298A  ASP*     4.3    14.5    -      -       -      +
    301A  LEU*     4.3     5.5    -      -       -      +
    146C  ALA*     5.4     5.0    -      -       -      +
    149C  ALA*     3.9    24.6    -      -       +      +
    150C  SER*     5.4     2.7    -      -       -      +
    153C  LYS*     5.0    17.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 282 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  PRO*     4.0    23.1    -      -       +      -
    235A  VAL*     3.8    28.0    -      -       +      -
    236A  GLN      4.7     5.2    -      -       -      +
    281A  PRO*     1.3    76.2    -      -       -      +
    283A  VAL*     1.3    66.5    +      -       -      +
    284A  LEU*     3.9    14.0    +      -       +      +
    296A  THR*     3.6     0.8    -      -       -      -
    297A  TYR*     2.9    34.8    +      -       -      +
    300A  LEU*     3.7    37.2    -      -       +      +
    301A  LEU*     3.9    22.0    -      -       +      -
    139C  VAL      5.4     0.4    -      -       -      +
    145C  ASN*     3.4    30.1    -      -       -      +
    149C  ALA*     4.8     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 283 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  PRO*     4.3     1.2    -      -       -      +
    282A  MET*     1.3    78.5    -      -       -      +
    284A  LEU*     1.3    75.2    +      -       -      +
    285A  ILE*     5.4     0.2    -      -       +      -
    294A  LEU*     4.3     8.7    -      -       +      -
    295A  GLN      3.2    10.3    -      -       -      +
    296A  THR*     3.4    21.3    -      -       -      +
    139C  VAL*     3.3    25.6    -      -       +      +
    145C  ASN*     3.5    13.4    +      -       -      +
    148C  LEU*     4.1    15.5    -      -       +      +
    149C  ALA*     3.6    31.2    -      -       +      +
    152C  LEU*     3.8    23.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 284 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220A  LEU*     5.8     0.2    -      -       +      -
    225A  TRP*     3.7    28.3    -      -       +      -
    228A  TRP*     4.5     0.4    -      -       +      -
    229A  VAL*     3.7    30.1    -      -       +      -
    231A  SER      3.7     4.9    -      -       -      +
    232A  PRO*     4.5     7.4    -      -       +      -
    282A  MET*     4.0    22.7    -      -       +      +
    283A  VAL*     1.3    82.7    -      -       -      +
    285A  ILE*     1.3    66.5    +      -       -      +
    286A  GLN*     4.1     6.9    +      -       +      +
    294A  LEU*     3.6     3.1    -      -       -      -
    295A  GLN*     2.9    33.1    +      -       -      +
    297A  TYR*     4.5    21.8    -      -       +      -
    300A  LEU*     3.9    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 285 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229A  VAL*     3.3     4.9    -      -       -      -
    230A  LEU*     2.6    51.1    +      -       +      -
    231A  SER*     2.9    36.9    +      -       -      +
    283A  VAL*     5.4     0.4    -      -       +      -
    284A  LEU*     1.3    77.5    -      -       -      +
    286A  GLN*     1.3    59.2    +      -       -      +
    292A  VAL*     3.7    27.6    -      -       +      -
    293A  SER      3.4     3.8    -      -       -      +
    294A  LEU*     3.7    24.0    -      -       +      -
    132C  LEU*     5.7     2.7    -      -       +      -
    135C  ALA*     3.9    36.3    -      -       +      +
    136C  GLU*     4.7     2.5    -      -       +      +
    139C  VAL*     4.6     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 286 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228A  TRP*     3.3    23.9    -      -       +      +
    229A  VAL*     5.4     0.2    -      -       -      -
    284A  LEU*     4.8     5.5    -      -       +      +
    285A  ILE*     1.3    77.7    -      -       -      +
    287A  LYS*     1.3    61.3    +      -       -      +
    288A  THR*     3.3    18.8    +      -       +      +
    292A  VAL*     3.4     4.4    -      -       -      +
    293A  SER*     2.9    35.2    +      -       -      +
    295A  GLN*     3.3    34.5    -      -       +      +
    297A  TYR*     2.4    40.2    +      -       -      -
    551E  ILE*     3.3    23.6    -      -       +      +
    594E  HIS      3.5     8.6    +      -       -      +
    595E  GLU*     5.2     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 287 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226A  ALA      5.3     6.8    +      -       -      +
    227A  ASP      4.8    15.9    -      -       -      +
    228A  TRP*     3.7     8.2    +      -       -      -
    229A  VAL      5.2     3.8    -      -       -      +
    230A  LEU*     4.1    35.4    -      -       +      +
    285A  ILE      4.2     0.4    +      -       -      -
    286A  GLN*     1.3    69.2    -      -       -      +
    288A  THR*     1.3    67.2    +      -       -      +
    291A  GLY      3.6     6.5    -      -       -      +
    292A  VAL*     4.7    11.2    -      -       +      +
    549E  LYS      5.0     1.4    -      -       -      +
    550E  GLY*     4.8     4.3    -      -       -      -
    551E  ILE*     4.1    16.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 288 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    286A  GLN*     3.3    31.1    +      -       +      +
    287A  LYS*     1.3    79.7    -      -       -      +
    289A  ASP*     1.3    65.4    +      -       -      +
    290A  THR*     3.6    10.8    +      -       -      -
    291A  GLY*     2.9    31.3    +      -       -      +
    292A  VAL*     4.2     1.2    +      -       -      -
    293A  SER*     4.3    17.0    -      -       -      -
    549E  LYS      5.3     2.5    -      -       -      +
    551E  ILE*     3.9    18.6    -      -       +      -
    595E  GLU*     4.3    20.6    -      -       -      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il