Contacts of the strand formed by residues 77 - 88 (chain A) in PDB entry 1CGP


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 77 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  GLY      3.1    12.3    +      -       -      +
     75A  LEU      5.4     0.2    -      -       -      -
     76A  PHE*     1.3    79.9    -      -       +      +
     78A  GLU*     1.3   109.0    +      -       -      +
     79A  GLY      3.2     1.9    +      -       -      -
     80A  GLN*     3.1    46.2    +      -       -      +
    103A  ARG*     6.0     0.7    -      -       -      -
    122B  ARG*     4.8     6.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 78 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  GLU*     5.8     0.3    -      -       -      +
     76A  PHE      4.2     0.4    +      -       -      -
     77A  GLU*     1.3   102.1    +      -       -      +
     79A  GLY*     1.3    62.5    +      -       -      +
     99A  TYR*     6.0     0.3    -      -       -      -
    100A  LYS*     5.3     2.3    -      -       -      +
    103A  ARG*     3.4    30.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 79 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  LYS*     6.1     2.7    -      -       -      -
     36A  ALA      5.6     3.9    +      -       -      -
     37A  GLU*     6.1     1.6    -      -       -      -
     77A  GLU*     3.2     1.8    +      -       -      -
     78A  GLU*     1.3    78.9    +      -       -      +
     80A  GLN*     1.3    63.2    +      -       -      +
     81A  GLU*     4.2     2.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 80 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  LYS*     3.7     3.7    -      -       -      +
     36A  ALA*     2.9    32.2    +      -       -      +
     73A  LEU      3.4    21.7    +      -       -      +
     74A  GLY*     4.1     9.1    -      -       -      -
     76A  PHE*     5.6     0.6    -      -       -      +
     77A  GLU*     3.1    53.6    +      -       -      +
     79A  GLY*     1.3    78.9    -      -       -      +
     81A  GLU*     1.3    69.6    +      -       -      +
    122B  ARG*     3.1    34.5    +      -       -      +
    125B  GLN*     4.4     3.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 81 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  GLY*     3.7    29.7    -      -       -      +
     34A  GLU      3.2     9.2    -      -       -      +
     35A  LYS*     5.3     2.0    -      -       +      -
     36A  ALA*     4.6     2.5    -      -       -      +
     74A  GLY*     5.9     0.7    -      -       -      -
     79A  GLY      5.4     1.8    -      -       -      +
     80A  GLN*     1.3    85.1    -      -       -      +
     82A  ARG*     1.3    67.1    +      -       -      +
     83A  SER*     3.4     3.8    +      -       -      -
    206A  CMP      4.2     2.9    +      -       -      -
    125B  GLN*     5.9     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 82 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  ILE*     3.4    34.9    -      -       +      +
     31A  HIS      3.7     6.5    -      -       -      +
     32A  GLN*     3.0     6.8    -      -       -      +
     33A  GLY*     2.9    22.6    +      -       -      +
     34A  GLU*     2.8    46.4    +      -       +      +
     35A  LYS      4.4     1.0    +      -       -      -
     36A  ALA*     3.7    12.8    -      -       -      +
     37A  GLU      3.9     4.9    -      -       -      +
     38A  THR*     3.0    35.7    +      -       -      +
     40A  TYR*     3.8    17.1    +      -       -      -
     71A  GLY*     3.1    12.6    +      -       -      -
     81A  GLU*     1.3    72.9    -      -       -      +
     83A  SER*     1.3    59.2    +      -       -      +
     84A  ALA      3.5     0.9    -      -       -      -
     99A  TYR*     2.9    22.4    +      -       -      -
    206A  CMP      2.8    37.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 83 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  GLN*     3.4    15.0    +      -       -      +
     51A  ILE*     4.1     6.9    -      -       -      +
     73A  LEU*     4.0     2.4    -      -       -      +
     81A  GLU      3.4     3.2    +      -       -      -
     82A  ARG*     1.3    71.9    -      -       -      +
     84A  ALA*     1.3    59.1    +      -       -      +
    206A  CMP      2.5    53.2    +      -       -      -
    125B  GLN*     4.4    27.6    -      -       -      -
    128B  SER*     5.9     5.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 84 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  ILE*     3.4    22.0    -      -       -      +
     32A  GLN*     3.5    17.3    -      -       -      +
     49A  VAL*     3.9    25.1    -      -       +      -
     50A  LEU      3.6    11.7    -      -       -      +
     51A  ILE*     3.8    13.2    -      -       +      -
     61A  LEU*     4.4     1.3    -      -       +      -
     82A  ARG*     3.5     0.6    -      -       -      +
     83A  SER*     1.3    81.5    +      -       -      +
     85A  TRP*     1.3    59.3    +      -       -      +
    206A  CMP      3.4    18.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 85 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  THR*     4.2    13.0    -      -       +      -
     30A  ILE      3.7     7.0    -      -       -      -
     31A  HIS*     3.6    27.1    -      -       +      +
     32A  GLN*     3.2    55.2    -      -       +      +
     48A  ALA      3.6     0.3    -      -       -      +
     49A  VAL*     3.3     3.8    -      -       -      -
     50A  LEU*     2.8    61.9    +      -       +      -
     51A  ILE*     4.3     2.2    -      -       -      -
     52A  LYS*     3.9    53.4    -      -       +      +
     84A  ALA*     1.3    73.8    -      -       -      +
     86A  VAL*     1.3    61.5    +      -       -      +
     87A  ARG*     4.0    10.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 86 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  THR*     4.1     1.0    -      -       -      +
     29A  LEU*     3.3    28.4    +      -       +      +
     30A  ILE*     3.4    38.9    +      -       +      +
     47A  VAL*     3.6    31.0    -      -       +      -
     48A  ALA      3.4     4.5    -      -       -      +
     49A  VAL*     4.3     7.2    -      -       +      -
     70A  ILE*     3.6    27.4    -      -       +      -
     85A  TRP*     1.3    79.6    -      -       -      +
     87A  ARG*     1.3    58.0    +      -       -      +
    206A  CMP      3.6    23.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 87 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  LYS*     4.4    22.2    -      -       -      +
     27A  SER      3.5     9.2    -      -       -      +
     28A  THR*     3.4    24.3    +      -       -      +
     47A  VAL*     3.5     3.4    -      -       -      -
     48A  ALA*     3.0    39.5    +      -       +      +
     50A  LEU*     3.6    28.6    -      -       +      +
     52A  LYS*     5.3     4.2    -      -       -      +
     58A  GLU*     3.3    28.3    +      -       -      -
     85A  TRP*     4.0     8.7    -      -       -      +
     86A  VAL*     1.3    75.1    -      -       -      +
     88A  ALA*     1.3    68.1    +      -       -      +
     89A  LYS*     3.3     2.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 88 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  TYR*     4.4     3.1    -      -       +      -
     24A  PRO      3.6    13.9    -      -       -      +
     26A  LYS*     2.8    30.8    +      -       -      +
     27A  SER*     2.8    23.3    +      -       -      +
     29A  LEU*     4.0    11.0    -      -       +      +
     46A  SER      4.0     0.4    -      -       -      -
     47A  VAL*     3.6    11.3    -      -       -      +
     87A  ARG*     1.3    70.9    -      -       -      +
     89A  LYS*     1.3    60.8    +      -       -      +
     90A  THR      3.3    16.6    -      -       -      +
     92A  CYS*     4.1     9.4    -      -       -      -
----------------------------------------------------------
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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