Contacts of the strand formed by residues 129 - 137 (chain A) in PDB entry 1AHF


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 ARG 129 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125A  VAL*     3.7     7.5    -      -       -      +
    126A  LYS*     1.3   115.3    -      -       -      +
    133A  VAL*     1.3    68.5    +      -       -      +
    134A  TRP*     2.9    40.4    -      -       +      +
    152A  LEU*     5.0     0.2    -      -       -      -
    154A  GLU*     3.2    25.7    +      -       +      +
    156A  ARG*     3.9    24.7    -      -       +      +
    179A  GLU      4.4     5.9    +      -       -      -
    181A  GLN*     2.8    32.9    -      -       -      +
    184A  ASP*     3.0    28.0    +      -       -      +
    185A  VAL      3.1    24.1    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 133 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119A  LEU*     5.4     0.9    -      -       +      -
    125A  VAL*     4.9     0.2    -      -       +      -
    129A  ARG*     1.3    78.0    -      -       -      +
    134A  TRP*     1.3    63.6    +      -       -      +
    135A  VAL*     3.8    19.4    +      -       +      -
    147A  PHE*     3.9    33.2    -      -       +      -
    152A  LEU*     3.9    28.7    -      -       +      -
    154A  GLU      2.5    14.6    +      -       -      +
    155A  VAL*     3.2     7.8    -      -       +      +
    156A  ARG      2.7    31.4    +      -       -      +
    185A  VAL*     3.3    28.5    -      -       +      +
    187A  LEU*     4.4     7.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 134 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  ARG*     2.9    18.8    -      -       +      +
    133A  VAL*     1.3    74.0    -      -       -      +
    135A  VAL*     1.3    61.0    +      -       -      +
    156A  ARG*     3.2    47.8    -      -       +      -
    157A  GLU      3.5    28.7    -      -       -      -
    158A  TYR*     3.3    22.4    -      -       +      -
    176A  SER*     4.1    13.0    -      -       -      -
    177A  LEU*     4.3     3.6    -      -       +      -
    179A  GLU*     3.2    42.0    -      -       +      -
    180A  ALA*     3.7    12.7    -      -       +      +
    184A  ASP*     2.6    33.0    +      -       +      -
    185A  VAL      2.7    20.9    +      -       -      +
    186A  VAL*     4.0    13.0    -      -       +      -
    187A  LEU*     3.0    26.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 135 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133A  VAL*     4.2    13.7    -      -       +      -
    134A  TRP*     1.3    78.4    -      -       -      +
    136A  SER*     1.3    75.5    +      -       -      +
    139A  SER*     4.2    15.7    -      -       -      +
    143A  HIS*     4.3    20.6    -      -       +      +
    144A  LYS*     4.3     9.4    -      -       -      -
    147A  PHE*     4.8     3.6    -      -       +      -
    155A  VAL*     3.7    29.2    -      -       +      -
    156A  ARG      2.7     8.7    +      -       -      +
    157A  GLU*     3.1    11.5    -      -       +      -
    158A  TYR*     3.1    20.8    +      -       -      -
    187A  LEU*     4.3    15.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 136 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  VAL*     1.3    82.9    -      -       -      +
    137A  ASN*     1.3    60.6    +      -       -      +
    138A  PRO      2.8     8.1    +      -       -      -
    139A  SER*     2.9    28.7    +      -       -      -
    157A  GLU*     4.5     1.9    -      -       -      +
    158A  TYR*     3.3    39.6    +      -       -      -
    160A  TYR*     4.0    11.9    -      -       -      -
    187A  LEU*     4.5     1.6    +      -       -      +
    189A  HIS*     4.6     2.6    -      -       -      -
    193A  HIS*     2.8    31.8    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 137 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  SER*     1.3    77.7    -      -       -      +
    138A  PRO*     1.3    69.5    -      -       -      +
    157A  GLU*     3.3    31.9    +      -       +      +
    158A  TYR      3.1    15.3    +      -       -      +
    159A  ALA*     5.1     3.7    -      -       -      -
    160A  TYR*     3.3    23.5    +      -       -      +
    161A  TYR*     3.8     2.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 138 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  SER*     2.8    18.7    +      -       -      -
    137A  ASN*     1.3    93.7    -      -       -      +
    139A  SER*     1.3    61.0    +      -       -      +
    160A  TYR*     5.0     0.7    -      -       +      -
    161A  TYR*     3.9    14.6    -      -       +      -
    193A  HIS*     3.1    14.6    -      -       +      -
    195A  PRO*     3.8    12.8    -      -       +      -
    196A  THR*     3.7    23.1    -      -       +      -
    362A  PHE*     3.7    33.2    -      -       +      -
    384A  SER*     6.3     0.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 139 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  VAL*     4.2    13.5    -      -       -      +
    136A  SER*     2.9    28.7    +      -       -      -
    138A  PRO*     1.3    73.9    -      -       -      +
    140A  TRP*     1.3    70.7    +      -       -      +
    141A  PRO*     3.2    10.8    -      -       -      +
    143A  HIS*     3.2    18.4    +      -       -      -
    144A  LYS*     5.9     3.1    -      -       -      -
    187A  LEU*     5.2     0.2    -      -       -      +
    189A  HIS*     3.4    15.1    -      -       -      -
    194A  ASN      3.9     9.2    -      -       -      -
    195A  PRO*     4.3     6.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 140 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  ILE*     4.3     7.0    -      -       +      +
    109A  SER*     4.0     9.0    -      -       -      -
    112A  LEU*     4.0    16.4    -      -       +      -
    139A  SER*     1.3    78.4    +      -       -      +
    141A  PRO*     1.3    78.2    -      -       +      +
    142A  ASN*     3.7    30.5    -      -       +      +
    143A  HIS*     2.8    59.5    +      +       +      +
    144A  LYS*     4.6     1.6    +      -       -      -
    146A  VAL*     5.7     0.7    -      -       +      -
    194A  ASN*     3.5    30.3    +      -       -      +
    386A  ARG*     4.5     2.5    -      -       -      -
    410A  PLP      3.5    46.4    -      +       +      -
    411A  IOP      2.9    61.3    +      +       -      -
----------------------------------------------------------
 Back to top of page


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