Contacts of the strand formed by residues 26 - 35 (chain A) in PDB entry 4HXG


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 LEU 26 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  THR*     2.8    22.6    +      -       -      -
     23A  ARG*     2.8    21.9    +      -       +      +
     24A  LYS*     5.7     2.9    -      -       +      -
     25A  ASN*     1.3    81.8    -      -       +      +
     27A  VAL*     1.3    62.7    +      -       -      +
     47A  ILE*     3.8    21.3    -      -       +      -
     48A  GLU      3.7     7.4    -      -       -      +
     49A  ASN*     4.6    15.0    -      -       +      +
     56A  LYS*     4.5    12.3    -      -       -      +
     66A  ILE*     4.6    13.2    -      -       +      -
     70A  GLY*     4.1     9.0    -      -       -      +
     92A  LEU*     3.4    41.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 27 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  ARG      3.3     3.8    -      -       -      +
     22A  THR*     3.5    13.0    -      -       -      +
     26A  LEU*     1.3    79.9    -      -       -      +
     28A  ALA*     1.3    63.8    +      -       -      +
     29A  TYR*     4.4     4.2    -      -       +      -
     46A  VAL      3.8     0.3    -      -       -      +
     47A  ILE*     3.5     2.8    -      -       -      -
     48A  GLU*     2.6    48.7    +      -       +      +
     50A  LEU*     3.6    30.5    -      -       +      -
     66A  ILE*     5.0     0.7    -      -       -      -
    313A  ILE*     3.4    40.6    -      -       +      -
    325A  LEU*     3.8    22.4    -      -       +      -
    335A  LEU*     5.4     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 28 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  ASP      3.8     0.7    -      -       -      +
     20A  PRO*     3.6     0.5    -      -       -      +
     21A  ARG*     2.9    35.9    +      -       +      +
     27A  VAL*     1.3    76.3    -      -       -      +
     29A  TYR*     1.3    64.4    +      -       -      +
     45A  ILE*     4.6     0.7    -      -       +      -
     46A  VAL      3.3     9.9    -      -       -      +
     47A  ILE*     3.8    20.9    -      -       +      -
     64A  PRO*     4.3    20.4    -      -       +      -
     66A  ILE*     4.3    17.1    -      -       +      +
     73A  ILE*     4.5     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 29 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  LEU*     4.3    18.4    -      -       +      -
     18A  SER      3.8     9.0    -      -       -      +
     19A  ASP      3.8     8.1    -      -       -      -
     20A  PRO*     4.2    12.3    -      -       +      -
     27A  VAL*     4.4     2.7    -      -       +      -
     28A  ALA*     1.3    80.0    -      -       -      +
     30A  VAL*     1.3    75.2    +      -       -      +
     31A  LEU*     4.8     1.1    -      -       +      -
     45A  ILE*     3.6     6.1    -      -       -      +
     46A  VAL*     3.0    52.8    +      -       +      +
     48A  GLU*     2.9    32.5    +      -       +      -
     55A  ARG*     3.8     0.2    +      -       -      -
     64A  PRO*     4.6     2.5    -      -       -      -
    315A  LEU*     5.4     4.9    -      -       +      -
    325A  LEU*     3.8    29.8    -      -       +      -
    336A  THR*     4.0     4.6    -      -       +      +
    338A  TYR*     2.6    43.8    +      +       -      -
----------------------------------------------------------
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Residues in contact with VAL 30 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  TYR      3.4     2.6    -      -       -      +
     17A  LEU*     3.2     7.3    -      -       -      -
     18A  SER*     2.8    56.2    +      -       -      +
     19A  ASP*     4.2     4.7    -      -       +      -
     29A  TYR*     1.3    79.6    -      -       -      +
     31A  LEU*     1.3    65.0    +      -       -      +
     32A  THR*     3.7    18.6    -      -       -      +
     43A  ASN*     4.2    16.2    -      -       +      +
     44A  THR      3.8     5.8    -      -       -      +
     45A  ILE*     4.6     2.5    -      -       +      -
     61A  ALA      4.6     1.1    -      -       -      +
     62A  SER*     4.3    12.1    -      -       -      -
     63A  MET      4.3     7.9    -      -       -      +
     64A  PRO*     3.6    27.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 31 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  ALA*     3.6    32.3    -      -       +      -
     16A  TYR      3.8     1.3    -      -       -      -
     17A  LEU*     3.8    16.6    -      -       +      -
     29A  TYR*     4.0     4.0    +      -       +      -
     30A  VAL*     1.3    72.4    -      -       -      +
     32A  THR*     1.3    66.9    +      -       -      +
     33A  LYS*     4.7     7.4    -      -       +      -
     42A  GLU      3.8     0.3    -      -       -      +
     43A  ASN*     3.6     2.8    -      -       -      -
     44A  THR*     2.9    48.1    +      -       -      +
     46A  VAL*     4.1    17.0    -      -       +      -
    338A  TYR*     4.2    12.6    -      -       +      -
     98B  LYS*     4.0    12.8    -      -       +      +
    160B  GLU      4.0     8.1    -      -       -      +
    161B  GLY      6.0     0.2    -      -       -      +
    162B  GLU*     3.7    25.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 32 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  ALA*     4.1     0.2    -      -       -      -
     16A  TYR*     2.8    54.3    +      -       +      +
     18A  SER*     4.7     4.0    +      -       -      -
     30A  VAL*     3.7    10.6    +      -       -      +
     31A  LEU*     1.3    76.1    -      -       -      +
     33A  LYS*     1.3    68.8    +      -       -      +
     41A  TYR*     4.0    28.3    -      -       +      -
     42A  GLU      3.3     4.7    -      -       -      +
     43A  ASN*     2.7    24.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 33 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  THR      3.7     7.1    +      -       -      -
     13A  LYS      4.6     0.2    -      -       -      -
     14A  PHE      3.3    26.9    -      -       -      +
     15A  ALA*     4.0     8.5    -      -       +      -
     16A  TYR*     5.0     0.9    -      -       -      -
     31A  LEU*     4.4    10.7    +      -       +      -
     32A  THR*     1.3    80.9    -      -       -      +
     34A  ALA*     1.3    64.7    +      -       -      +
     35A  ASN*     3.7     1.0    +      -       -      -
     41A  TYR*     3.5     6.7    -      -       -      -
     42A  GLU*     2.9    48.3    +      -       +      +
    161B  GLY      2.8    27.1    -      -       -      +
    162B  GLU*     3.6    24.4    +      -       -      +
    163B  GLU*     2.9    31.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 34 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  PHE*     4.4    11.9    -      -       +      +
     12A  THR*     3.3    50.9    +      -       +      +
     14A  PHE      5.1     2.0    +      -       -      -
     16A  TYR*     5.2     5.9    -      -       +      -
     33A  LYS*     1.3    76.6    +      -       -      +
     35A  ASN*     1.3    62.3    +      -       -      +
     36A  LEU      3.5     1.0    +      -       -      -
     40A  LYS      4.3     0.4    -      -       -      -
     41A  TYR*     4.1    24.5    -      -       +      -
    586A  PRO*     4.3     8.7    -      -       +      -
    589A  ARG*     5.2     0.7    -      -       -      +
    163B  GLU*     5.5     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  LYS*     3.7     2.0    +      -       +      -
     34A  ALA*     1.3    70.3    -      -       -      +
     36A  LEU*     1.3    57.8    +      -       -      +
     37A  GLU*     2.9    15.7    +      -       -      +
     38A  SER*     2.7    43.4    +      -       -      +
     39A  ASN*     3.0    20.6    +      -       -      -
     40A  LYS      3.0    24.1    +      -       -      +
     42A  GLU*     2.9    33.0    +      -       -      +
    586A  PRO*     3.5     4.0    -      -       -      +
----------------------------------------------------------
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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