Contacts of the strand formed by residues 108 - 115 (chain A) in PDB entry 6AL5


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 GLN 108 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  LEU*     3.4     7.5    -      -       -      -
     97A  CYS*     2.7    61.3    +      -       +      +
     98A  GLN*     4.5     0.7    -      -       -      -
     99A  PRO*     4.3    20.7    -      -       -      +
    106A  ALA      3.9     7.0    +      -       -      +
    107A  TRP*     1.3    78.5    -      -       -      +
    109A  PRO*     1.3    79.6    -      -       +      +
    110A  GLY      3.1     0.5    +      -       -      -
    200A  CYS*     4.8     8.9    -      -       -      +
    201A  GLY*     5.6     1.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  LEU*     4.4     3.1    -      -       +      -
     97A  CYS*     4.9     1.4    -      -       -      +
    108A  GLN*     1.3    89.0    -      -       +      +
    110A  GLY*     1.3    63.1    +      -       -      +
    124A  TRP*     3.6    46.0    -      -       +      -
    159A  TRP*     5.2     7.4    -      -       +      +
    186A  GLN*     3.7    18.5    +      -       -      +
    902A  NAG      5.5     4.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  TYR      3.0    15.1    +      -       -      -
     96A  LEU*     4.2     0.2    -      -       -      +
     97A  CYS*     4.7     5.6    -      -       -      -
    108A  GLN      3.1     5.3    +      -       -      -
    109A  PRO*     1.3    70.9    -      -       -      +
    111A  TRP*     1.3    76.0    +      -       -      -
    124A  TRP*     4.0     2.1    +      -       -      -
    186A  GLN*     2.8    34.6    +      -       -      +
    199A  SER      5.1     1.3    -      -       -      -
    201A  GLY      6.0     2.5    -      -       -      -
    214A  TRP*     4.3    12.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81A  TRP*     6.2     1.3    -      +       -      -
     95A  TYR*     2.7    38.9    +      -       +      +
    110A  GLY*     1.3    86.2    -      -       -      +
    112A  THR*     1.3    61.0    +      -       -      +
    113A  VAL*     5.5     0.9    -      -       +      -
    124A  TRP*     3.6     7.0    -      -       -      +
    185A  SER      3.6    20.9    -      -       -      -
    186A  GLN*     3.4    40.4    -      -       +      +
    188A  LEU*     3.9    35.2    -      -       +      -
    197A  TRP      5.8     0.4    -      -       -      -
    198A  LEU*     3.4    37.5    -      -       +      +
    199A  SER*     3.5    35.6    +      -       -      +
    201A  GLY      5.0     5.1    -      -       -      +
    202A  VAL*     4.8    14.4    -      -       +      -
    214A  TRP*     4.0     4.0    -      +       -      -
----------------------------------------------------------
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Residues in contact with THR 112 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  GLY      3.2     7.9    -      -       -      -
     94A  PHE*     3.5    28.3    -      -       +      -
    111A  TRP*     1.3    75.8    -      -       -      +
    113A  VAL*     1.3    62.5    +      -       -      +
    114A  ASN*     3.3     2.9    +      -       -      -
    122A  PHE*     3.2    21.3    +      -       -      +
    124A  TRP*     3.3    24.5    -      -       +      +
    186A  GLN      3.1     4.8    +      -       -      -
    187A  ASP*     2.6    36.0    +      -       -      +
    188A  LEU*     3.1    30.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 113 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  VAL*     4.5     6.1    -      -       +      -
     91A  MET      4.4     2.9    -      -       -      +
     92A  GLY*     3.3    10.1    -      -       -      -
     93A  GLY      2.7    34.7    +      -       -      +
     95A  TYR*     3.4    34.8    -      -       +      +
    111A  TRP      5.1     0.7    -      -       -      +
    112A  THR*     1.3    78.2    -      -       -      +
    114A  ASN*     1.3    64.3    +      -       -      +
    115A  VAL*     4.1    18.4    -      -       +      -
    122A  PHE*     3.5     6.9    -      -       -      -
    188A  LEU*     4.0     5.4    -      -       +      -
    190A  MET*     3.8    23.6    -      -       +      -
    196A  LEU*     3.7    26.2    -      -       +      -
    198A  LEU*     5.4     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 114 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  THR*     3.3    20.2    +      -       -      -
    113A  VAL*     1.3    80.3    +      -       -      +
    115A  VAL*     1.3    60.9    +      -       -      +
    116A  GLU      4.3     0.2    -      -       -      -
    120A  GLU      5.2     3.4    -      -       -      +
    121A  LEU*     3.8    10.8    -      -       +      +
    122A  PHE*     2.9    40.0    +      -       -      +
    123A  ARG*     3.3    20.9    +      -       -      +
    187A  ASP      4.7     0.4    -      -       -      -
    188A  LEU      2.6    28.3    +      -       -      +
    189A  THR*     4.0    13.7    -      -       +      +
    190A  MET*     3.0    31.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 115 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  VAL*     4.3     9.0    -      -       +      -
     88A  SER      4.7     0.4    -      -       -      -
     89A  GLN*     3.8    43.7    -      -       +      +
     92A  GLY*     4.1    13.2    -      -       -      +
    113A  VAL*     4.1    17.7    -      -       +      -
    114A  ASN*     1.3    77.5    -      -       -      +
    116A  GLU*     1.3    71.9    +      -       -      +
    117A  GLY      3.8     0.2    -      -       -      -
    118A  SER*     3.0    29.4    +      -       -      +
    120A  GLU      5.3     0.4    +      -       -      -
    122A  PHE*     6.1     0.2    -      -       -      -
    189A  THR*     5.9     0.2    -      -       -      -
    190A  MET*     3.4     4.3    -      -       +      +
    191A  ALA      4.2     1.1    -      -       -      +
    192A  PRO*     3.8    33.2    -      -       +      -
----------------------------------------------------------
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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