Contacts of the strand formed by residues 101 - 107 (chain Y) 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 ASN 101 (chain Y).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4Y  LEU*     3.9     1.2    -      -       -      +
     47Y  VAL*     3.0    44.1    +      -       +      +
     48Y  GLY*     4.9     0.4    -      -       -      -
     99Y  HIS      4.3     0.2    -      -       -      -
    100Y  VAL*     1.3    72.8    -      -       -      +
    102Y  LEU*     1.3    59.2    +      -       -      +
    117Y  TYR*     4.1    14.8    +      -       -      -
    118Y  MET      2.6    29.7    -      -       -      +
    119Y  ASP*     3.6    11.8    -      -       -      -
    120Y  TYR*     4.9     7.4    -      -       +      +
    132Y  HIS*     2.5    44.2    +      -       -      +
    133Y  GLY      4.1     5.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 102 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4Y  LEU*     4.7     0.2    -      -       -      -
     36Y  PHE*     4.9     0.2    -      -       +      -
     44Y  LEU*     2.9    54.3    -      -       +      -
     45Y  LEU      3.0    14.4    -      -       -      +
     46Y  CYS*     3.2    33.9    -      -       +      -
     56Y  PHE*     4.6     5.8    -      -       +      -
     57Y  ALA*     5.4     0.2    -      -       +      -
     84Y  THR*     5.8     0.2    -      -       -      +
     88Y  LEU*     6.2     1.3    -      -       +      -
    100Y  VAL*     3.9     6.0    -      -       +      -
    101Y  ASN*     1.3    76.3    +      -       -      +
    103Y  LEU*     1.3    89.2    +      -       -      +
    104Y  LEU*     3.5     4.9    -      -       -      +
    116Y  TYR      3.8     0.2    -      -       -      +
    118Y  MET*     3.0    51.9    +      -       +      +
    132Y  HIS*     3.1     7.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 103 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4Y  LEU*     4.9     0.4    -      -       +      -
      5Y  ILE      4.0     7.9    -      -       -      +
      6Y  GLY*     3.8    18.6    -      -       -      +
     15Y  VAL*     3.6    31.4    -      -       +      -
     43Y  LEU      3.3     5.7    -      -       -      +
     45Y  LEU*     3.1    40.3    +      -       +      +
    102Y  LEU*     1.3    79.6    -      -       -      +
    104Y  LEU*     1.4    58.3    +      -       -      +
    105Y  ALA*     3.4     2.0    +      -       +      +
    115Y  LEU*     4.2    15.3    -      -       +      -
    116Y  TYR      3.3    21.5    -      -       -      +
    130Y  ALA*     3.8    21.1    -      -       +      -
    132Y  HIS*     3.4    26.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 104 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42Y  ILE*     3.8    14.8    -      -       +      -
     43Y  LEU      3.7     3.1    -      -       -      +
     44Y  LEU*     3.5    26.7    -      -       +      +
     60Y  ILE*     6.0     0.9    -      -       +      -
     77Y  PRO*     3.1    32.1    -      -       +      +
     80Y  ALA*     3.8    15.9    -      -       +      +
     81Y  ALA*     3.7    24.5    -      -       +      +
     84Y  THR*     4.0     7.0    -      -       +      -
    102Y  LEU*     3.5     5.4    -      -       +      +
    103Y  LEU*     1.4    67.1    -      -       -      +
    105Y  ALA*     1.3    67.5    +      -       -      +
    106Y  GLY      4.0     0.3    +      -       -      -
    115Y  LEU*     3.7     2.0    -      -       -      -
    116Y  TYR*     3.0    31.7    +      -       +      +
    118Y  MET*     3.3    20.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 105 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13Y  VAL*     4.1     5.4    -      -       +      -
     15Y  VAL*     3.6    31.6    -      -       +      -
     42Y  ILE*     3.6     2.6    -      -       -      -
     43Y  LEU*     2.9    41.8    +      -       +      +
     45Y  LEU*     6.0     0.2    -      -       +      -
    103Y  LEU*     3.4     3.9    +      -       +      +
    104Y  LEU*     1.3    79.2    -      -       -      +
    106Y  GLY*     1.3    57.9    +      -       -      +
    114Y  ALA      4.0     4.0    -      -       -      -
    115Y  LEU*     4.3     5.4    -      -       +      +
    183Y  ILE*     3.8    17.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 106 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13Y  VAL*     3.4    11.7    -      -       -      +
     41Y  LYS      3.2    15.9    -      -       -      -
     42Y  ILE*     4.5     0.2    -      -       -      -
     77Y  PRO*     3.4    18.8    -      -       -      -
    105Y  ALA*     1.3    78.9    -      -       -      +
    107Y  TYR*     1.3    60.0    +      -       -      -
    114Y  ALA      2.7    28.2    +      -       -      +
    183Y  ILE*     4.5     6.0    -      -       -      +
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Residues in contact with TYR 107 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10Y  PRO      5.3     0.2    +      -       -      -
     11Y  ASP*     3.6    21.9    +      -       -      -
     12Y  TYR*     4.4     3.6    -      -       -      -
     13Y  VAL*     4.6     1.3    -      -       +      -
     41Y  LYS*     3.3    34.8    +      -       +      +
     77Y  PRO*     3.3     4.7    -      -       -      +
    106Y  GLY*     1.3    73.7    -      -       -      +
    108Y  ASP*     1.3    84.6    +      -       -      +
    109Y  GLU*     3.1    32.1    +      -       -      -
    112Y  GLY*     5.3     0.2    -      -       -      -
    113Y  PRO*     3.5    45.0    -      -       +      +
    183Y  ILE*     3.7    19.1    -      -       +      -
    184Y  ASP*     4.1    13.7    -      -       -      -
    185Y  LYS*     3.0    44.3    +      -       +      +
----------------------------------------------------------
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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