Contacts of the strand formed by residues 120 - 126 (chain A) in PDB entry 3CEI


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 120 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116A  LEU*     4.0     4.9    -      -       -      -
    118A  GLY      3.8     2.4    +      -       -      -
    119A  SER*     1.3    76.0    -      -       -      +
    121A  TRP*     1.3    69.8    +      -       -      -
    138A  THR      3.1    13.2    -      -       -      -
    140A  ASN      3.6     7.2    -      -       -      -
    157A  VAL*     2.9    33.0    +      -       -      +
    158A  TRP*     3.4    13.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 121 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  GLN*     3.1    20.3    +      -       -      -
     72A  ASN*     3.3    50.1    -      -       +      +
     73A  HIS*     3.5    26.9    -      +       -      -
     76A  TYR*     3.9    10.1    -      -       +      -
    116A  LEU*     3.1     9.5    -      -       -      +
    120A  GLY*     1.3    75.4    -      -       -      -
    122A  ASN*     1.3    61.4    +      -       -      +
    123A  TRP*     3.4    24.6    -      +       +      +
    137A  GLN*     3.4     1.2    -      -       -      -
    138A  THR*     2.8    39.1    +      -       -      +
    140A  ASN      2.8    29.0    +      -       -      -
    142A  GLN      4.1     1.3    -      -       -      -
    154A  VAL*     3.8    16.8    -      -       +      -
    155A  VAL      3.6     4.9    -      -       -      -
    156A  ASP*     3.4    49.4    -      -       +      -
    157A  VAL*     4.3     0.2    -      -       -      -
    158A  TRP*     3.5     3.6    -      -       -      +
    500A   FE      4.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 122 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109A  PHE*     3.0    61.3    +      -       -      -
    112A  SER*     2.9    31.9    +      -       -      +
    113A  ALA*     3.5    16.8    -      -       +      +
    116A  LEU*     4.8     2.0    -      -       +      -
    121A  TRP*     1.3    71.9    -      -       -      +
    123A  TRP*     1.3    62.0    +      -       -      +
    135A  ILE*     4.2     3.2    -      -       -      +
    136A  ILE      3.7     2.9    -      -       -      +
    137A  GLN*     3.8     9.0    -      -       -      +
    154A  VAL*     3.3     1.6    -      -       -      -
    155A  VAL*     3.0    44.8    +      -       +      +
    157A  VAL*     4.8     1.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 123 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  TYR*     4.2     6.5    -      +       -      -
     72A  ASN*     3.1    35.9    -      -       +      -
     75A  PHE*     4.2     8.5    -      +       -      -
    109A  PHE*     3.9     4.9    -      -       -      -
    121A  TRP*     3.4    15.4    -      -       +      +
    122A  ASN*     1.3    74.4    -      -       -      +
    124A  ALA*     1.3    64.4    +      -       -      +
    125A  ALA*     4.8     0.7    -      -       +      -
    135A  ILE*     3.3    12.1    -      -       -      +
    136A  ILE*     2.7    47.6    +      -       +      +
    138A  THR*     3.0    25.0    +      -       +      -
    142A  GLN      3.9     2.2    -      -       -      -
    143A  THR*     3.2    23.3    -      -       -      -
    144A  PRO*     3.2    29.7    -      -       +      +
    151A  PRO*     3.6    35.2    -      -       +      -
    153A  LEU      3.2     7.9    -      -       -      -
    154A  VAL*     3.4    33.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 124 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105A  PHE*     3.9    28.5    -      -       +      -
    109A  PHE*     4.4     2.9    -      -       +      -
    123A  TRP*     1.3    73.3    -      -       -      +
    125A  ALA*     1.3    53.7    +      -       -      +
    133A  ILE*     4.5     7.2    -      -       +      -
    134A  GLU      3.2     8.5    -      -       -      -
    135A  ILE*     4.5     0.9    -      -       -      +
    151A  PRO*     3.7     0.9    -      -       -      +
    152A  LEU*     2.7    40.0    +      -       +      +
    153A  LEU*     2.9    26.4    +      -       +      +
    186A  VAL*     6.2     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 125 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123A  TRP*     4.0     0.4    -      -       +      -
    124A  ALA*     1.3    76.1    -      -       -      +
    126A  TYR*     1.3    62.6    +      -       -      +
    127A  ASN      3.6     1.0    +      -       -      -
    133A  ILE*     3.5     3.1    -      -       -      +
    134A  GLU*     2.8    42.6    +      -       -      +
    136A  ILE*     3.9    23.3    -      -       +      -
    144A  PRO*     4.0    18.6    -      -       +      -
    149A  LYS*     4.1     6.3    -      -       +      -
    150A  VAL      3.2    17.5    -      -       -      +
    151A  PRO*     4.2     3.1    -      -       +      -
    152A  LEU*     4.3     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 126 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125A  ALA*     1.3    70.5    -      -       -      +
    127A  ASN*     1.3    69.9    +      -       -      +
    128A  LEU*     3.6    29.5    +      -       +      +
    131A  GLN*     3.2    52.0    +      -       +      +
    132A  LYS      3.8     6.3    -      -       -      -
    133A  ILE*     4.2     7.0    -      -       +      +
    149A  LYS*     3.6     6.5    -      -       -      -
    150A  VAL*     2.8    34.4    +      -       +      +
    152A  LEU*     3.9    12.1    -      -       +      +
    190A  TYR*     3.8    29.6    -      +       -      -
    193A  ALA*     4.0    26.9    -      -       +      -
    194A  LYS*     3.8    24.3    -      -       +      +
----------------------------------------------------------
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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