Contacts of the strand formed by residues 119 - 127 (chain I) in PDB entry 6ALH


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 GLU 119 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71I  VAL*     4.2     9.1    -      -       +      +
     99I  LYS*     4.7    18.3    -      -       +      +
    100I  LEU      3.3    14.1    -      -       -      +
    101I  ARG*     2.8    41.4    +      -       +      +
    117I  ILE*     5.7     5.6    -      -       +      +
    118I  LYS*     1.3    79.3    -      -       -      +
    120I  GLN*     1.3    61.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 120 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99I  LYS*     3.3     7.3    -      -       -      +
    100I  LEU*     3.3    26.6    +      -       +      +
    118I  LYS*     6.3     0.2    -      -       +      -
    119I  GLU*     1.3    75.0    -      -       -      +
    121I  GLU*     1.3    60.5    +      -       -      +
    122I  VAL*     3.1    22.4    +      -       +      +
    488I  MET*     3.9    15.7    -      -       -      +
    489I  PRO*     3.2    35.5    +      -       +      +
    490I  GLN*     2.5    44.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 121 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74I  ARG*     2.4    39.0    +      -       -      -
     97I  ARG*     3.3    33.9    +      -       +      +
     98I  VAL      3.4     6.5    -      -       -      +
     99I  LYS*     4.1    31.1    +      -       +      +
    120I  GLN*     1.3    71.8    -      -       -      +
    122I  VAL*     1.3    61.3    +      -       -      +
    123I  TYR      3.9     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 122 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97I  ARG*     3.6     2.8    -      -       -      -
     98I  VAL*     2.5    50.6    +      -       +      +
    100I  LEU*     3.7    31.2    -      -       +      -
    120I  GLN*     3.1    22.3    +      -       +      +
    121I  GLU*     1.3    76.3    -      -       -      +
    123I  TYR*     1.3    62.2    +      -       -      +
    124I  MET*     4.6     0.2    -      -       +      -
    489I  PRO*     3.3    24.5    -      -       +      +
    490I  GLN*     4.0     9.2    -      -       +      -
    493I  ILE*     3.8    27.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 123 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95I  PRO*     3.9    19.3    -      -       +      -
     96I  LEU      3.8     7.9    -      -       -      -
     97I  ARG*     3.3    40.2    -      -       -      +
    121I  GLU      3.9     0.6    +      -       -      -
    122I  VAL*     1.3    79.7    -      -       -      +
    124I  MET*     1.3    63.6    +      -       -      +
    125I  GLY*     3.0    44.6    +      -       -      -
    126I  GLU*     3.3    16.8    +      -       -      +
    493I  ILE*     3.6    16.3    -      -       -      +
    494I  ASN      5.3     1.2    -      -       -      +
    495I  ALA*     5.3    11.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 124 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53I  PHE*     4.2    19.5    -      -       +      -
     57I  PHE*     5.3     7.6    -      -       +      -
     96I  LEU*     3.1    45.0    +      -       +      +
     98I  VAL*     3.7    37.9    -      -       +      -
    100I  LEU*     4.7     6.3    -      -       +      -
    122I  VAL*     4.6     3.4    -      -       +      -
    123I  TYR*     1.3    74.4    -      -       -      +
    125I  GLY*     1.3    66.6    +      -       -      +
    126I  GLU      3.9     0.2    +      -       -      -
    464I  PHE*     4.7     5.2    -      -       -      -
    468I  LEU*     5.1     8.3    -      -       +      -
    493I  ILE*     3.7    28.5    -      -       +      -
    494I  ASN      5.0     7.9    -      -       -      +
    495I  ALA*     5.5     1.3    -      -       -      +
    498I  ILE*     5.3    20.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 125 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96I  LEU      3.3     9.9    +      -       -      -
    123I  TYR*     3.0    45.2    +      -       -      -
    124I  MET*     1.3    76.7    -      -       -      +
    126I  GLU*     1.3    57.5    +      -       -      +
    495I  ALA*     4.9    12.6    +      -       -      +
    498I  ILE*     6.3     0.4    -      -       -      -
    499I  SER*     4.3    18.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 126 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79I  VAL*     4.6    13.5    +      -       -      +
     91I  THR*     4.5     3.1    +      -       -      -
     93I  SER*     2.3    35.0    +      -       -      +
     94I  ALA      3.3    17.5    -      -       -      +
     95I  PRO*     3.7    20.4    -      -       +      +
     96I  LEU*     4.8     2.7    -      -       -      -
    123I  TYR*     3.3    20.0    +      -       -      +
    124I  MET      3.9     0.2    +      -       -      -
    125I  GLY*     1.3    71.6    -      -       -      +
    127I  ILE*     1.3    68.6    +      -       -      +
    128I  PRO*     4.7     0.9    -      -       -      +
    499I  SER*     4.3    12.2    +      -       -      +
    502I  VAL*     3.8    16.5    -      -       -      +
    503I  LYS*     5.2     4.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 127 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35I  PHE*     5.5     2.0    -      -       +      -
     38I  PHE*     3.6    34.8    -      -       +      -
     39I  ILE*     4.8     7.4    -      -       +      -
     49I  LEU*     4.9     9.4    -      -       +      -
     75I  LEU*     3.7    29.8    -      -       +      -
     93I  SER*     3.4     3.2    -      -       -      -
     94I  ALA*     2.8    27.4    +      -       +      +
     96I  LEU*     4.8    10.5    -      -       +      +
    126I  GLU*     1.3    79.2    -      -       -      +
    128I  PRO*     1.3    77.7    -      -       +      +
    129I  LEU*     5.9     1.1    -      -       +      -
    464I  PHE*     4.7    21.1    -      -       +      -
    498I  ILE*     6.2     0.7    -      -       +      -
    502I  VAL*     4.6    17.9    -      -       +      -
    506I  PHE*     5.7     0.9    -      -       +      -
----------------------------------------------------------
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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