Contacts of the strand formed by residues 210 - 223 (chain A) in PDB entry 4LL4


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 VAL 210 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208A  ILE*     5.1     4.0    -      -       +      +
    209A  VAL*     1.3    78.9    -      -       -      +
    211A  PRO*     1.3    76.5    -      -       +      +
    212A  LYS*     4.1    18.3    -      -       -      +
    238A  ARG*     3.8    33.0    -      -       +      +
    239A  GLY      3.8    13.9    -      -       -      +
    241A  HIS*     4.2    16.6    -      -       +      +
    280A  VAL*     4.1     2.5    -      -       -      -
    281A  SER*     2.8    42.7    +      -       -      +
    283A  PRO*     6.2     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 211 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201A  PHE*     3.4    40.2    -      -       +      -
    210A  VAL*     1.3    88.5    -      -       +      +
    212A  LYS*     1.3    64.4    +      -       -      +
    239A  GLY*     2.8    38.2    +      -       -      +
    240A  ASN      3.4    22.2    -      -       -      +
    242A  ILE*     3.4    21.8    -      -       +      -
    248A  ALA*     6.2     0.7    -      -       +      -
    250A  TRP*     4.0    10.1    -      -       +      +
    279A  TYR      3.4     6.1    -      -       -      +
    280A  VAL*     4.1     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 212 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210A  VAL*     4.1    20.9    -      -       +      +
    211A  PRO*     1.3    79.9    -      -       -      +
    213A  ALA*     1.3    66.3    +      -       -      +
    237A  VAL      3.6    12.1    -      -       -      +
    238A  ARG*     4.3    25.6    -      -       +      +
    250A  TRP*     3.8     6.6    -      -       -      -
    278A  ILE*     3.4     6.4    -      -       -      +
    279A  TYR*     2.8    70.7    +      -       +      +
    281A  SER*     4.0    24.2    +      -       -      -
    287A  LYS*     6.2     0.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 213 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197A  ILE*     4.3    15.5    -      -       +      -
    212A  LYS*     1.3    79.4    -      -       -      +
    214A  ALA*     1.3    63.1    +      -       -      +
    236A  SER*     3.1    22.2    -      -       -      -
    237A  VAL*     3.0    25.9    +      -       +      +
    250A  TRP*     3.8    19.7    -      -       +      -
    255A  LEU*     4.3     5.8    -      -       +      -
    276A  LEU*     4.4     0.7    -      -       +      -
    277A  LEU      3.0    11.9    -      -       -      +
    278A  ILE*     4.3     4.7    -      -       +      -
    279A  TYR*     4.3     3.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 214 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213A  ALA*     1.3    77.9    -      -       -      +
    215A  ILE*     1.3    67.8    +      -       -      +
    216A  VAL*     3.9     3.5    +      -       +      -
    233A  LYS*     4.3     7.4    -      -       +      -
    235A  SER      3.5    12.1    -      -       -      +
    236A  SER*     3.9     8.7    -      -       -      +
    255A  LEU*     4.3     1.3    -      -       -      -
    275A  SER      3.7     0.2    -      -       -      +
    276A  LEU*     3.6     4.6    -      -       -      +
    277A  LEU*     2.7    38.9    +      -       +      +
    279A  TYR*     4.4     5.6    -      -       +      +
     83C  THR*     4.2    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 215 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195A  ILE*     3.6    31.4    -      -       +      -
    214A  ALA*     1.3    74.1    -      -       -      +
    216A  VAL*     1.3    68.6    +      -       -      +
    234A  LEU*     2.9    49.5    +      -       +      +
    235A  SER*     3.2    16.2    +      -       -      +
    255A  LEU*     4.0    20.4    -      -       +      +
    256A  ARG      3.6    24.7    -      -       -      +
    257A  VAL*     4.3    12.3    -      -       +      -
    274A  TYR*     4.6     9.0    -      -       +      -
    275A  SER      3.2     9.9    -      -       -      +
    276A  LEU*     4.3     3.8    -      -       +      -
    294A  LEU*     4.3     9.0    -      -       +      -
    296A  ILE*     5.0     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 216 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214A  ALA*     4.4     4.5    -      -       +      +
    215A  ILE*     1.3    83.2    -      -       -      +
    217A  ALA*     1.3    63.1    +      -       -      +
    218A  ARG*     3.8    15.9    -      -       -      +
    231A  THR*     4.4     7.2    -      -       +      -
    232A  GLN      3.3    11.4    -      -       -      +
    233A  LYS*     4.2     6.3    -      -       -      -
    273A  GLU      3.8     0.2    -      -       -      +
    274A  TYR*     3.2     9.5    -      -       -      -
    275A  SER*     2.8    51.1    +      -       -      +
    277A  LEU*     3.7    33.2    -      -       +      -
     82C  PRO      4.2     1.6    -      -       -      +
     83C  THR*     4.1    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 217 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216A  VAL*     1.3    74.7    -      -       -      +
    218A  ARG*     1.3    61.6    +      -       -      +
    219A  HIS*     3.9    11.8    -      -       -      +
    230A  LEU      3.4     1.7    -      -       -      +
    231A  THR*     3.3     3.5    -      -       -      +
    232A  GLN*     2.7    46.5    +      -       +      +
    234A  LEU*     4.3     6.3    -      -       +      +
    260A  ILE*     4.1    15.5    -      -       +      -
    272A  VAL*     3.9    18.6    -      -       +      -
    273A  GLU      3.5     3.4    -      -       -      -
    274A  TYR*     4.2     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 218 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216A  VAL*     3.8    19.0    -      -       -      +
    217A  ALA*     1.3    75.2    -      -       -      +
    219A  HIS*     1.3    62.1    +      -       -      +
    220A  THR*     3.4     5.2    +      -       -      -
    229A  VAL*     3.8    16.8    -      -       +      -
    230A  LEU      3.3     4.5    -      -       -      -
    231A  THR*     4.3    19.8    +      -       +      +
    271A  ARG      3.7     0.2    -      -       -      +
    272A  VAL*     3.4     3.0    -      -       -      +
    273A  GLU*     2.6    56.8    +      -       +      +
    274A  TYR      4.4     3.4    +      -       -      -
    275A  SER*     2.9    32.7    +      -       -      +
    277A  LEU*     4.2     4.2    -      -       -      +
    291A  ASP*     3.1    22.1    +      -       -      -
     82C  PRO*     4.8     7.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 219 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217A  ALA*     4.0     6.4    -      -       -      +
    218A  ARG*     1.3    71.2    -      -       -      +
    220A  THR*     1.3    60.6    +      -       -      +
    221A  TYR*     3.7     5.0    -      -       +      -
    228A  LYS      3.5     1.0    -      -       -      +
    229A  VAL*     2.9     5.2    -      -       -      -
    230A  LEU*     2.7    72.4    +      -       +      +
    232A  GLN*     3.1    34.1    +      -       +      +
    260A  ILE*     4.1    16.8    -      -       +      -
    269A  ILE*     4.3    23.5    -      -       +      +
    271A  ARG      3.5     7.4    -      -       -      +
    272A  VAL*     3.7    26.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 220 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218A  ARG*     3.9     5.4    +      -       -      +
    219A  HIS*     1.3    73.5    -      -       -      +
    221A  TYR*     1.3    59.0    +      -       -      +
    227A  THR*     5.7     2.2    -      -       -      -
    228A  LYS      3.0    15.9    -      -       -      +
    229A  VAL*     4.2    10.3    -      -       +      +
    269A  ILE*     3.4     4.3    -      -       -      +
    270A  LEU*     2.8    35.4    +      -       +      -
    271A  ARG*     2.9    59.0    +      -       -      +
    273A  GLU*     4.4     3.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 221 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219A  HIS*     3.7    11.9    -      -       +      -
    220A  THR*     1.3    75.0    -      -       -      +
    222A  LEU*     1.3    65.8    +      -       -      +
    223A  ALA*     3.6    28.9    +      -       +      -
    226A  GLN      3.6     0.5    -      -       -      +
    227A  THR      3.5     4.3    +      -       -      -
    228A  LYS*     2.6    83.2    +      -       +      +
    229A  VAL      4.1     0.4    -      -       -      -
    230A  LEU*     3.9    27.2    -      -       +      +
    268A  ASN*     3.4     7.6    -      -       +      +
    269A  ILE*     3.5    24.5    -      -       +      +
    270A  LEU*     4.2     3.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 222 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  ARG*     3.8    42.8    -      -       +      +
    221A  TYR*     1.3    73.5    -      -       -      +
    223A  ALA*     1.3    62.7    +      -       -      +
    226A  GLN      3.1     7.0    -      -       -      +
    227A  THR      4.2     6.1    -      -       -      +
    268A  ASN*     2.6    48.4    +      -       -      +
    270A  LEU*     4.1    28.3    -      -       +      -
    224C  ASN*     3.8    13.7    -      -       +      +
    225C  GLY*     3.4    38.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 223 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221A  TYR*     3.6    29.9    +      -       +      -
    222A  LEU*     1.3    74.8    -      -       -      +
    224A  ASN*     1.3    73.1    +      -       +      +
    225A  GLY      3.4     2.0    -      -       -      -
    226A  GLN*     2.7    39.5    +      -       -      +
    228A  LYS*     4.6     9.4    -      -       +      +
    224C  ASN*     4.5     5.2    -      -       -      -
    225C  GLY*     4.4     0.6    -      -       -      -
----------------------------------------------------------
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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