Contacts of the strand formed by residues 314 - 326 (chain A) in PDB entry 3NBN


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 TRP 314 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175A  LEU*     3.8    21.1    -      -       +      -
    176A  PHE      3.5    23.6    -      -       -      +
    177A  ASN*     3.7    18.4    -      -       +      -
    187A  ARG      4.2     2.7    -      -       -      -
    188A  TYR      4.5     0.4    -      -       -      -
    189A  LEU*     3.8    37.0    -      -       +      -
    198A  ALA*     5.2     0.4    -      -       +      -
    270A  HIS      3.6     0.7    -      -       -      +
    271A  LYS*     3.1     6.4    -      -       -      -
    272A  CYS*     2.9    41.0    +      -       -      +
    274A  PHE*     4.5    17.7    -      +       +      -
    284A  LEU*     3.6    34.6    +      -       +      +
    286A  LEU*     4.4     7.0    -      -       +      -
    291A  ILE*     3.5    33.4    -      -       +      -
    311A  GLY      3.8    14.9    +      -       -      -
    312A  ALA      3.9    13.9    -      -       -      -
    313A  SER*     1.3    72.1    -      -       -      +
    315A  THR*     1.3    66.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 315 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175A  LEU*     3.2     4.9    -      -       -      +
    176A  PHE*     2.8    72.2    +      -       +      -
    178A  ARG      5.6     1.0    +      -       -      -
    269A  LEU*     3.9    34.8    -      -       +      +
    270A  HIS      3.6     5.6    -      -       -      +
    271A  LYS*     3.2    33.8    +      -       -      +
    313A  SER      4.3     0.7    +      -       -      -
    314A  TRP*     1.3    73.2    -      -       -      +
    316A  ILE*     1.3    61.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 316 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167A  ILE*     4.5    17.1    -      -       +      +
    173A  VAL*     3.6    35.2    -      -       +      -
    174A  ALA      4.4     0.2    -      -       -      +
    175A  LEU*     3.6    31.4    -      -       +      -
    208A  ILE*     5.1     5.8    -      -       +      -
    266A  VAL*     4.1    24.2    -      -       +      -
    268A  GLN*     4.7     0.5    -      -       -      -
    269A  LEU*     3.1    24.2    +      -       -      -
    270A  HIS*     3.2    19.7    +      -       +      +
    272A  CYS*     4.8    13.2    -      -       +      -
    274A  PHE*     5.4     2.7    -      -       +      -
    315A  THR*     1.3    76.0    -      -       -      +
    317A  ILE*     1.3    61.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 317 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  ALA*     3.8    10.5    -      -       +      -
     41A  VAL*     3.9    31.2    -      -       +      +
     55A  PRO*     3.4    32.1    -      -       +      -
    167A  ILE*     5.2     0.4    -      -       -      -
    173A  VAL*     3.3     5.3    -      -       -      +
    174A  ALA*     2.9    43.2    +      -       +      +
    176A  PHE*     4.6     6.7    -      -       +      -
    268A  GLN*     3.5    29.2    -      -       +      +
    269A  LEU*     4.0    25.6    -      -       +      -
    316A  ILE*     1.3    78.6    -      -       -      +
    318A  SER*     1.3    70.7    +      -       -      +
    319A  THR*     4.6     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 318 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  ALA*     3.9     0.2    -      -       -      -
     40A  LYS*     3.1    38.6    +      -       -      +
    167A  ILE*     4.0     9.1    -      -       -      +
    171A  THR*     2.7    31.2    +      -       -      +
    173A  VAL*     3.5    11.9    -      -       -      +
    268A  GLN*     2.6    32.3    +      -       -      -
    317A  ILE*     1.3    79.2    -      -       -      +
    319A  THR*     1.3    60.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 319 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  LEU*     5.1     2.5    -      -       +      -
     38A  HIS      2.7    27.7    +      -       -      -
     39A  ALA*     3.6     3.9    +      -       -      +
     40A  LYS*     3.1    27.1    +      -       -      -
     55A  PRO*     5.8     0.9    -      -       -      +
    172A  LYS*     2.9    42.5    +      -       +      +
    173A  VAL      4.6     0.2    -      -       -      +
    174A  ALA*     4.5    12.2    -      -       -      +
    203A  TRP*     3.8    16.8    -      -       +      -
    205A  ALA*     3.8    21.5    -      -       +      -
    317A  ILE*     3.8     1.6    +      -       -      +
    318A  SER*     1.3    74.8    -      -       -      +
    320A  ASP*     1.3    68.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 320 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  LEU*     3.6     6.3    -      -       -      +
     38A  HIS*     2.9    49.4    +      -       +      +
     40A  LYS*     3.7    24.4    +      -       +      +
    145A  LYS*     3.4    38.3    +      -       -      +
    172A  LYS*     3.9    20.6    +      -       -      +
    319A  THR*     1.3    83.0    -      -       -      +
    321A  LYS*     1.3    69.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 321 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  LEU*     4.4    13.2    -      -       +      -
     36A  ILE      3.4     7.2    -      -       -      +
     37A  LEU*     3.8    18.4    -      -       +      -
     38A  HIS*     4.5     1.6    -      -       -      -
    145A  LYS*     3.3    30.1    +      -       -      +
    172A  LYS*     4.0    22.0    -      -       -      +
    320A  ASP*     1.3    79.8    +      -       -      +
    322A  ALA*     1.3    63.7    +      -       -      +
    323A  GLU*     3.8    29.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 322 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  LEU*     3.7     1.6    -      -       -      +
     36A  ILE*     2.8    35.3    +      -       +      +
     38A  HIS*     4.9     0.9    -      -       +      -
    143A  LEU      3.6    23.8    -      -       -      +
    144A  SER*     4.1    13.0    -      -       -      -
    145A  LYS*     4.2    14.6    -      -       +      +
    321A  LYS*     1.3    77.0    -      -       -      +
    323A  GLU*     1.3    66.0    +      -       -      +
    324A  TYR*     3.3    13.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 323 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  THR*     4.4     7.2    +      -       -      +
     34A  VAL      4.2     6.5    -      -       -      +
     35A  LEU*     3.8    32.9    -      -       +      +
    145A  LYS*     5.8     0.6    -      -       -      +
    321A  LYS*     3.8    30.8    +      -       -      +
    322A  ALA*     1.3    71.2    -      -       -      +
    324A  TYR*     1.3    83.3    +      -       -      +
    325A  THR*     4.7    11.3    -      -       +      +
    342A  VAL*     5.1     8.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 324 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  THR*     3.4     2.2    -      -       -      -
     34A  VAL*     3.3    30.7    +      -       +      -
     36A  ILE*     4.9     1.6    -      -       +      -
    142A  PHE*     3.8    31.0    -      +       +      -
    143A  LEU*     2.7    48.7    +      -       -      +
    322A  ALA*     3.3    20.0    -      -       +      +
    323A  GLU*     1.3    94.8    -      -       -      +
    325A  THR*     1.3    63.9    +      -       -      +
    326A  PHE*     4.0     4.2    -      -       -      -
    340A  VAL*     3.4    45.3    -      -       +      -
    342A  VAL*     4.6     8.7    -      -       +      -
    363A  ASN*     4.5    12.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 325 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  ASP*     3.9     9.1    +      -       -      +
     32A  GLN      3.8     6.5    -      -       -      -
     33A  THR*     3.7    23.6    -      -       +      +
    323A  GLU*     4.7    12.1    -      -       +      +
    324A  TYR*     1.3    79.2    -      -       -      +
    326A  PHE*     1.3    67.8    +      -       -      +
    340A  VAL*     3.6    14.0    -      -       -      +
    341A  PRO      5.4     0.2    -      -       -      +
    422A  TYR*     3.8    10.8    -      -       -      +
    423A  SER*     3.5    32.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 326 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  ASP*     3.9     3.9    +      -       -      -
     32A  GLN*     3.2    65.2    +      -       +      +
     33A  THR*     4.1     7.0    -      -       -      -
     34A  VAL      4.4     6.5    -      -       -      -
     66A  TRP*     4.7    10.5    -      +       -      -
    131A  MET*     5.8     0.4    -      -       +      -
    139A  ILE*     5.3     6.7    -      -       +      -
    142A  PHE*     4.4    20.6    -      +       -      -
    324A  TYR      4.0     6.1    -      -       -      -
    325A  THR*     1.3    83.4    +      -       -      +
    327A  TYR*     1.3    60.5    +      -       -      +
    328A  GLU*     5.9     2.9    -      -       +      -
    337A  VAL*     3.3    47.8    -      -       +      -
    340A  VAL*     5.0     5.4    -      -       +      -
    420A  ILE*     4.4     3.6    -      -       +      -
    421A  ILE      3.5     9.6    -      -       -      -
    422A  TYR*     3.7    20.0    -      +       +      -
----------------------------------------------------------
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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