Contacts of the strand formed by residues 116 - 124 (chain B) in PDB entry 1AXI


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 GLY 116 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112B  THR*     3.3     5.8    -      -       -      -
    113B  SER*     2.8    38.5    +      -       -      -
    114B  ASN      3.7     0.2    -      -       -      -
    115B  GLY*     1.3    80.0    -      -       -      +
    117B  THR*     1.3    64.0    +      -       -      -
    118B  VAL*     4.8     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 117 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110B  LYS*     4.1    31.9    +      -       +      +
    111B  LEU      3.5     7.9    -      -       -      +
    112B  THR*     4.1    11.0    -      -       -      +
    116B  GLY*     1.3    71.0    -      -       -      -
    118B  VAL*     1.3    63.0    -      -       -      +
    119B  ASP      3.7    22.9    -      -       -      +
    120B  GLU*     5.2     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 118 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32B  GLU      3.9    23.7    +      -       -      +
     33B  PRO*     3.6    26.2    -      -       +      +
     34B  LYS*     3.2    24.4    +      -       -      -
     64B  ILE*     5.4     1.6    -      -       +      -
    111B  LEU*     2.8    36.8    +      -       +      +
    112B  THR*     4.5     2.9    -      -       -      +
    113B  SER*     3.8    26.9    -      -       -      +
    116B  GLY      3.6     1.7    +      -       -      +
    117B  THR*     1.3    75.9    -      -       -      +
    119B  ASP*     1.3    57.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 119 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  TYR*     5.2     0.7    +      -       -      -
     33B  PRO      4.5     0.2    -      -       -      +
     34B  LYS*     3.5    31.6    +      -       +      +
     35B  PHE*     2.8    49.6    +      -       +      +
    110B  LYS*     3.4     3.8    -      -       -      -
    111B  LEU*     2.9    33.1    +      -       +      +
    117B  THR*     3.7     8.3    -      -       -      +
    118B  VAL*     1.3    77.0    -      -       -      +
    120B  GLU*     1.3    83.9    +      -       -      +
    121B  LYS*     5.4     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 120 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  TYR*     2.9    48.6    +      -       +      +
     46A  GLN*     2.4    36.7    +      -       -      +
     35B  PHE*     4.1     1.8    -      -       -      -
     80B  TRP*     4.6     0.7    -      -       -      -
    108B  CYS*     4.0     3.5    -      -       -      +
    109B  ILE      3.3    15.3    -      -       -      +
    110B  LYS*     3.4    24.8    +      -       +      -
    117B  THR*     5.2     2.2    -      -       +      -
    119B  ASP*     1.3    88.4    +      -       -      +
    121B  LYS*     1.3    74.3    +      -       -      +
    122B  CYS*     3.7    13.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 121 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  TYR*     4.0     5.4    -      -       -      -
     35B  PHE*     3.7    30.3    -      -       +      -
     36B  THR      5.1     1.8    -      -       -      -
     37B  LYS*     4.6     4.5    -      -       -      +
     38B  CYS*     3.7    28.0    -      -       -      +
    107B  TYR      4.2     0.2    -      -       -      +
    108B  CYS*     3.4     1.7    -      -       -      -
    109B  ILE*     2.9    59.9    +      -       +      +
    119B  ASP*     5.4     0.4    -      -       -      +
    120B  GLU*     1.3    78.1    -      -       -      +
    122B  CYS*     1.3    68.7    +      -       -      +
    123B  PHE*     3.8    24.2    -      -       +      +
    128B  ILE*     5.1     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 122 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  LYS*     3.7    19.7    +      -       -      -
     42A  TYR*     3.7    29.7    -      -       +      -
     45A  LEU*     3.5    24.7    -      -       +      -
    107B  TYR      3.2     4.9    -      -       -      +
    108B  CYS*     2.1    47.3    -      -       -      -
    120B  GLU*     3.7    12.8    -      -       -      -
    121B  LYS*     1.3    78.8    +      -       -      +
    123B  PHE*     1.3    65.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 123 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  LEU*     4.6     5.3    -      -       -      +
     38B  CYS*     3.9    22.2    -      -       -      -
     46B  PHE*     3.8    26.0    -      +       -      -
     48B  CYS*     4.2     1.6    -      -       -      -
    106B  PRO*     3.6     3.1    -      -       -      +
    107B  TYR*     2.8    56.1    +      +       +      +
    109B  ILE*     4.0    22.9    -      -       +      -
    121B  LYS*     3.8    20.2    -      -       -      +
    122B  CYS*     1.3    80.4    -      -       -      +
    124B  SER*     1.3    73.6    +      -       -      +
    125B  VAL*     5.1     1.1    -      -       +      -
    127B  GLU*     3.4    13.9    -      -       +      +
    128B  ILE*     3.8    39.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 124 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  LEU*     5.8     0.7    -      -       -      +
    164A  TYR*     3.8    19.9    +      -       -      -
    167A  ARG*     3.8    17.6    +      -       -      -
    104B  ALA*     4.9     9.6    -      -       -      -
    105B  ILE      3.8    14.0    +      -       -      -
    106B  PRO*     3.9     3.5    -      -       -      +
    107B  TYR*     5.0     0.2    -      -       -      -
    123B  PHE*     1.3    83.2    +      -       -      +
    125B  VAL*     1.3    68.0    +      -       -      +
    126B  ASP*     4.4     6.7    -      -       -      -
    127B  GLU*     3.0    29.7    +      -       -      +
    128B  ILE      3.6     5.4    +      -       -      -
----------------------------------------------------------
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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