Contacts of the strand formed by residues 97 - 103 (chain I) in PDB entry 5A0Q


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 ALA 97 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45I  GLY*     3.5     2.6    -      -       -      -
     46I  ALA      2.9    32.4    +      -       -      +
     47I  GLY*     4.8     0.4    -      -       -      -
     52I  THR*     4.1     0.2    +      -       -      -
     87I  LEU*     5.3     1.1    -      -       -      -
     95I  GLY      4.2     0.8    +      -       -      +
     96I  ALA*     1.3    74.9    -      -       -      +
     98I  LEU*     1.3    63.0    +      -       -      +
    113I  ILE      3.4    13.0    -      -       -      +
    114I  TYR*     4.2     1.6    -      -       +      -
    115I  PRO*     3.8    24.9    -      -       +      -
    127I  MET*     3.2    26.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 98 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43I  CYS*     3.1    27.8    -      -       -      -
     44I  CYS      3.3     9.4    -      -       -      +
     45I  GLY*     3.8     1.1    -      -       -      -
     52I  THR*     3.3    27.1    -      -       -      +
     55I  THR*     4.2    17.0    -      -       +      -
     56I  THR*     3.4    17.0    -      -       -      +
     83I  LEU*     3.5    30.5    -      -       +      -
     87I  LEU*     4.4    12.1    -      -       +      +
     96I  ALA      4.9     2.2    -      -       -      +
     97I  ALA*     1.3    75.3    -      -       -      +
     99I  VAL*     1.3    62.1    +      -       -      +
    100I  LEU      4.0     0.7    -      -       -      -
    113I  ILE*     2.9    46.7    +      -       +      +
    127I  MET*     3.3     3.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 99 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3I  ILE*     3.6    30.3    -      -       +      -
      4I  ALA      4.6     6.1    -      -       -      +
     14I  LEU*     4.1    11.9    -      -       +      +
     42I  TYR      4.1     0.3    -      -       -      +
     43I  CYS*     3.4     2.8    -      -       -      -
     44I  CYS*     3.0    36.4    +      -       +      +
     98I  LEU*     1.3    75.7    -      -       -      +
    100I  LEU*     1.4    57.9    +      -       -      +
    101I  GLY      4.0     0.5    +      -       -      -
    110I  LEU*     3.4    30.5    -      -       +      -
    111I  TYR      3.7     4.9    -      -       -      +
    112I  SER*     4.6     0.9    -      -       -      +
    125I  VAL*     3.4    24.2    -      -       +      -
    126I  THR      5.1     0.2    -      -       -      -
    127I  MET*     3.9    18.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 100 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37I  ILE*     3.6    23.8    -      -       +      -
     41I  ILE*     3.5    18.8    -      -       +      -
     42I  TYR      3.7     4.0    -      -       -      +
     43I  CYS*     4.2     4.7    -      -       +      -
     76I  VAL*     3.4    33.9    -      -       +      -
     79I  ALA*     3.6    24.0    -      -       +      -
     80I  ASN*     3.8    20.2    -      -       -      +
     83I  LEU*     3.4    26.0    -      -       +      -
     98I  LEU      4.0     1.4    -      -       -      -
     99I  VAL*     1.4    72.5    -      -       -      +
    101I  GLY*     1.3    60.0    +      -       -      +
    109I  HIS      4.1     0.2    -      -       -      +
    110I  LEU*     3.3     5.1    -      -       -      +
    111I  TYR      2.9    34.2    +      -       -      +
    113I  ILE*     4.3     7.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 101 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12I  ILE*     4.5    10.5    -      -       -      -
     14I  LEU*     4.5     5.7    -      -       -      +
     41I  ILE*     3.2     5.9    -      -       -      +
     42I  TYR*     3.0    33.8    +      -       -      +
     99I  VAL      4.0     1.0    +      -       -      -
    100I  LEU*     1.3    76.3    -      -       -      +
    102I  GLY*     1.3    59.2    +      -       -      -
    109I  HIS      3.4     8.7    -      -       -      -
    110I  LEU*     4.2     9.9    -      -       -      -
    178I  ILE*     4.6     6.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 102 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12I  ILE*     3.1     7.6    -      -       -      +
     40I  ASN      3.9     6.5    -      -       -      -
     41I  ILE*     3.5    19.1    -      -       -      -
     76I  VAL*     3.4    12.3    -      -       -      +
    101I  GLY*     1.3    73.5    -      -       -      -
    103I  VAL*     1.3    62.3    +      -       -      -
    109I  HIS      3.0    30.4    +      -       -      +
    178I  ILE*     4.0     4.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 103 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10I  ASP      4.6     2.5    -      -       -      +
     11I  GLY*     4.3     8.3    -      -       -      -
     12I  ILE*     3.7     9.9    -      -       +      -
     40I  ASN*     4.1    26.8    +      -       -      +
     41I  ILE*     4.4     0.4    -      -       -      +
     73I  LEU*     5.5     1.4    -      -       -      +
     76I  VAL*     3.7     3.3    -      -       -      +
    102I  GLY*     1.3    76.4    -      -       -      +
    104I  ASP*     1.3    73.0    +      -       -      +
    107I  GLY*     4.0    10.3    -      -       -      -
    108I  PRO*     3.7    15.0    -      -       +      -
    178I  ILE*     3.4    26.7    -      -       +      +
    179I  SER*     4.6     3.8    -      -       -      -
    180I  LYS*     4.3    36.8    -      -       +      +
----------------------------------------------------------
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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