Contacts of the strand formed by residues 259 - 267 (chain A) in PDB entry 3Q29


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 PHE 259 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  GLU      4.0     6.1    -      -       -      +
    113A  ALA*     4.1     6.6    -      -       -      -
    114A  LEU*     6.2     0.4    -      -       -      +
    156A  TYR*     4.2    24.8    +      +       +      +
    159A  TRP*     3.3    53.3    -      +       +      +
    160A  PRO*     5.2     0.8    -      -       -      +
    169A  ALA*     3.9    22.4    -      -       +      -
    257A  LYS      3.6     1.2    +      -       -      -
    258A  PRO*     1.3    81.5    -      -       -      +
    260A  VAL*     1.3    60.6    +      -       -      +
    261A  GLY      4.0     0.6    +      -       -      -
    329A  GLU*     3.3    22.0    -      -       +      -
    330A  ILE      4.7     2.0    -      -       -      -
    331A  MET*     3.3    37.7    -      -       +      -
    332A  PRO*     4.2     8.7    -      -       +      -
    337A  MET*     4.9     0.2    -      -       +      -
    340A  PHE*     4.3     4.0    -      +       -      -
    341A  TRP*     3.3    37.5    -      +       -      -
----------------------------------------------------------
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Residues in contact with VAL 260 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  HIS*     3.1     8.3    -      -       -      -
     93A  PHE*     4.6    16.6    -      -       +      -
    111A  VAL*     3.7    28.5    -      -       +      -
    112A  GLU      3.5     5.8    -      -       -      +
    113A  ALA*     4.9     0.4    -      -       +      -
    258A  PRO      4.2     1.8    -      -       -      +
    259A  PHE*     1.3    77.0    -      -       -      +
    261A  GLY*     1.3    64.1    +      -       -      +
    262A  VAL*     5.3     0.4    -      -       +      -
    325A  ALA*     3.5    38.4    -      -       +      +
    328A  GLY      4.4     0.2    -      -       -      -
    329A  GLU      2.8    27.1    +      -       -      +
    330A  ILE*     3.8    10.2    -      -       +      +
    331A  MET*     3.1    23.5    +      -       -      +
    379C  LEU*     4.7     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 261 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  ALA*     4.7     4.0    -      -       -      -
     65A  HIS*     3.6     0.7    -      -       -      -
    111A  VAL*     3.4     4.2    -      -       -      +
    112A  GLU*     2.7    48.8    +      -       -      +
    156A  TYR*     5.0     2.5    +      -       -      -
    259A  PHE      4.0     1.4    +      -       -      -
    260A  VAL*     1.3    74.8    -      -       -      +
    262A  VAL*     1.3    64.3    +      -       -      +
    263A  LEU      3.9     1.1    -      -       -      -
    331A  MET*     3.4    21.6    -      -       -      +
      1B  GLC      5.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 262 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  ALA*     4.2     0.9    -      -       -      -
     65A  HIS*     2.8    37.5    +      -       +      +
     93A  PHE*     4.3    22.0    -      -       +      -
     94A  THR*     4.4     7.9    -      -       -      -
     97A  ALA*     3.5    28.5    -      -       +      -
    108A  PRO*     3.8    24.9    -      -       +      -
    109A  ILE      4.3     0.4    -      -       -      +
    110A  ALA      3.2    14.4    -      -       -      +
    111A  VAL*     4.4     8.1    -      -       +      -
    260A  VAL*     5.3     1.1    -      -       +      -
    261A  GLY*     1.3    77.3    -      -       -      +
    263A  LEU*     1.3    69.5    +      -       -      +
    264A  SER*     2.8    21.9    +      -       -      +
    330A  ILE*     5.2     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 263 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  ILE*     5.0     7.0    -      -       +      -
     16A  LYS*     4.4    22.9    -      -       +      -
     62A  PHE*     4.4    21.3    -      -       +      +
     63A  TRP*     3.8    27.1    -      -       -      +
     64A  ALA*     4.2     5.8    -      -       -      +
    109A  ILE*     2.7    44.1    +      -       +      +
    110A  ALA*     2.8    17.7    +      -       +      +
    112A  GLU*     3.7    24.3    +      -       -      +
    261A  GLY      3.9     1.8    -      -       -      -
    262A  VAL*     1.3    70.5    -      -       -      +
    264A  SER*     1.3    56.8    +      -       -      +
    300A  LEU*     3.6    31.0    -      -       +      -
      1B  GLC      5.6     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 264 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  ILE      3.5     0.9    -      -       -      +
     62A  PHE*     3.1     7.6    -      -       -      -
     63A  TRP      2.8    36.8    +      -       -      -
     65A  HIS*     3.9     3.3    -      -       -      +
     68A  PHE*     3.7    11.6    -      -       -      -
     98A  VAL*     3.1    30.4    -      -       -      +
    106A  ALA*     4.1     8.7    -      -       -      -
    107A  TYR      3.2    10.5    -      -       -      -
    108A  PRO*     4.1     0.2    -      -       -      +
    109A  ILE*     4.2     3.4    -      -       -      -
    262A  VAL*     2.8    21.7    +      -       -      +
    263A  LEU*     1.3    73.3    +      -       -      +
    265A  ALA*     1.3    61.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 265 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  ILE*     4.1     5.6    -      -       +      -
     61A  ILE      3.3     4.3    -      -       -      -
     62A  PHE*     3.6    35.2    -      -       +      -
    106A  ALA*     3.3     3.8    -      -       -      +
    107A  TYR*     2.8    45.5    +      -       +      +
    109A  ILE*     4.4     3.4    -      -       +      -
    264A  SER*     1.3    73.1    -      -       -      +
    266A  GLY*     1.3    59.9    +      -       -      +
    267A  ILE      4.3     0.2    +      -       -      -
    281A  LEU*     4.1    20.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 266 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  ILE*     3.2     6.3    -      -       -      +
     61A  ILE*     2.8    35.4    +      -       -      +
     68A  PHE*     3.6    20.3    -      -       -      -
     77A  LEU*     4.1     9.9    -      -       -      -
    105A  ILE      4.2     2.0    -      -       -      -
    106A  ALA*     3.8     8.1    -      -       -      -
    265A  ALA*     1.3    75.6    -      -       -      +
    267A  ILE*     1.3    63.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 267 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  ASP      3.3    10.3    -      -       -      +
     60A  ILE*     4.6     1.1    -      -       +      -
     77A  LEU*     3.4     7.9    -      -       -      +
     78A  ALA*     2.8    41.2    +      -       +      +
     79A  GLU      6.1     0.2    -      -       -      +
     80A  ILE*     4.2    24.3    -      -       +      +
    105A  ILE      5.0     2.0    +      -       -      -
    107A  TYR*     4.3     6.5    -      -       +      -
    265A  ALA      5.3     0.2    -      -       -      +
    266A  GLY*     1.3    73.9    -      -       -      +
    268A  ASN*     1.3    70.8    +      -       -      +
    271A  SER*     4.7     2.7    -      -       -      -
    274A  LYS*     4.0    32.8    -      -       +      +
    277A  ALA*     4.2    13.7    -      -       +      -
    278A  LYS*     4.1    30.1    -      -       +      +
    281A  LEU*     4.4    10.5    -      -       +      -
----------------------------------------------------------
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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