Contacts of the strand formed by residues 120 - 127 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116B  LEU*     4.1     2.9    -      -       -      -
    118B  GLY      3.9     1.6    +      -       -      -
    119B  SER*     1.3    76.8    -      -       -      +
    121B  TRP*     1.3    69.7    +      -       -      -
    138B  THR      3.1    13.2    -      -       -      -
    140B  ASN      3.6     7.6    -      -       -      -
    157B  VAL*     3.0    35.2    +      -       -      +
    158B  TRP*     3.4    14.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 121 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69B  GLN*     3.1    24.4    +      -       -      -
     72B  ASN*     3.4    43.4    -      -       +      +
     73B  HIS*     3.4    33.0    -      +       -      -
     76B  TYR*     4.0     9.9    -      -       +      -
    116B  LEU*     3.3     7.9    -      -       -      +
    120B  GLY*     1.3    74.6    -      -       -      -
    122B  ASN*     1.3    60.1    +      -       -      +
    123B  TRP*     3.4    26.9    -      +       +      +
    137B  GLN*     3.4     0.2    -      -       -      -
    138B  THR*     2.9    41.1    +      -       -      +
    140B  ASN      2.8    29.7    +      -       -      -
    142B  GLN      4.1     1.6    -      -       -      -
    154B  VAL*     3.8    16.2    -      -       +      -
    155B  VAL      3.6     5.2    -      -       -      -
    156B  ASP*     3.4    43.5    -      -       +      -
    157B  VAL*     4.4     0.2    -      -       -      -
    158B  TRP*     3.5     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 122 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109B  PHE*     3.0    59.2    +      -       -      -
    112B  SER*     2.7    30.7    +      -       -      +
    113B  ALA*     3.5    28.8    -      -       +      +
    116B  LEU*     4.6     2.4    -      -       +      +
    121B  TRP*     1.3    72.7    -      -       -      +
    123B  TRP*     1.3    61.1    -      -       -      +
    135B  ILE*     4.2     3.4    -      -       -      +
    136B  ILE      3.7     2.8    -      -       -      +
    137B  GLN*     3.7    10.0    -      -       -      +
    154B  VAL*     3.4     0.6    -      -       -      -
    155B  VAL*     3.0    35.0    +      -       +      -
    157B  VAL*     4.8     1.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 123 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71B  TYR*     4.1     6.1    -      +       -      -
     72B  ASN*     3.1    34.8    -      -       +      -
     75B  PHE*     4.2     8.1    -      +       -      -
    109B  PHE*     3.9     5.1    -      -       -      -
    121B  TRP*     3.4    16.3    -      -       +      +
    122B  ASN*     1.3    74.3    -      -       -      +
    124B  ALA*     1.3    65.4    +      -       -      +
    125B  ALA*     4.6     0.7    -      -       +      +
    135B  ILE*     3.2    11.8    -      -       -      +
    136B  ILE*     2.7    47.4    +      -       +      +
    138B  THR*     3.0    24.3    +      -       +      -
    142B  GLN      3.9     3.6    -      -       -      -
    143B  THR*     3.1    23.3    -      -       -      -
    144B  PRO*     3.2    29.3    -      -       +      +
    151B  PRO*     3.6    35.0    -      -       +      -
    153B  LEU      3.2     7.4    -      -       -      +
    154B  VAL*     3.3    32.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 124 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105B  PHE*     3.9    28.7    -      -       +      -
    109B  PHE*     4.3     2.7    -      -       +      -
    123B  TRP*     1.3    73.6    -      -       -      +
    125B  ALA*     1.3    52.9    +      -       -      +
    133B  ILE*     4.5     8.5    -      -       +      -
    134B  GLU      3.2     7.9    -      -       -      -
    135B  ILE*     4.4     0.9    -      -       -      +
    151B  PRO*     4.0     0.7    -      -       -      +
    152B  LEU*     2.7    38.3    +      -       +      +
    153B  LEU*     2.9    27.8    +      -       +      +
    186B  VAL*     6.3     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 125 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123B  TRP*     4.0     1.3    -      -       +      -
    124B  ALA*     1.3    75.0    -      -       -      +
    126B  TYR*     1.3    62.1    +      -       -      +
    127B  ASN      3.6     0.9    +      -       -      -
    133B  ILE*     3.5     0.6    -      -       -      -
    134B  GLU*     2.7    42.3    +      -       -      +
    136B  ILE*     3.9    24.0    -      -       +      -
    144B  PRO*     4.1    20.9    -      -       +      -
    149B  LYS*     4.1     6.5    -      -       +      -
    150B  VAL      3.3    14.8    -      -       -      +
    151B  PRO*     4.3     2.2    -      -       +      -
    152B  LEU*     4.3     4.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 126 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125B  ALA*     1.3    69.8    -      -       -      +
    127B  ASN*     1.3    67.9    +      -       -      +
    128B  LEU*     3.5    31.6    +      -       +      +
    131B  GLN*     3.2    52.6    +      -       +      +
    132B  LYS      3.8    11.4    -      -       -      -
    133B  ILE*     4.2     3.6    -      -       +      +
    149B  LYS*     3.7     5.7    -      -       -      -
    150B  VAL*     2.7    36.1    +      -       +      +
    152B  LEU*     3.9    12.6    -      -       +      +
    190B  TYR*     3.7    30.3    -      +       -      -
    193B  ALA*     4.0    26.2    -      -       +      -
    194B  LYS*     3.8    24.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 127 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125B  ALA      3.6     1.4    +      -       -      -
    126B  TYR*     1.3    75.2    -      -       -      +
    128B  LEU*     1.3    55.6    +      -       -      +
    129B  ASP*     2.8    21.1    +      -       -      +
    130B  THR*     2.7    43.8    +      -       -      -
    131B  GLN*     2.7    33.1    +      -       -      -
    132B  LYS      2.8    19.6    +      -       -      +
    134B  GLU*     3.2    33.8    +      -       +      +
    149B  LYS*     3.7    21.3    -      -       -      +
----------------------------------------------------------
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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