Contacts of the strand formed by residues 109 - 121 (chain E) in PDB entry 1GMO


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 LYS 109 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50E  LEU*     3.4     3.2    -      -       -      -
     51E  ILE*     2.5    53.9    +      -       +      +
     53E  ILE*     5.6     5.8    -      -       +      +
    108E  VAL*     1.3    79.1    -      -       -      +
    110E  LYS*     1.3    64.4    +      -       -      +
    111E  GLU*     4.0     0.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 110 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48E  THR*     4.6    11.4    -      -       +      -
     49E  THR      3.5     7.9    -      -       -      +
     50E  LEU*     4.8     0.7    -      -       -      +
    103E  SER*     5.6    13.6    +      -       -      +
    109E  LYS*     1.3    75.9    -      -       -      +
    111E  GLU*     1.3    62.1    +      -       -      +
    118E  LEU*     6.3     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 111 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48E  THR*     3.7     5.1    -      -       -      +
     49E  THR*     3.1    42.0    +      -       +      +
     51E  ILE*     5.4     8.1    -      -       +      -
    109E  LYS      5.0     2.5    -      -       -      +
    110E  LYS*     1.3    76.6    -      -       -      +
    112E  PHE*     1.3    70.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 112 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47E  LYS*     3.2    43.1    -      -       +      -
     48E  THR*     4.6     1.1    -      -       -      +
     49E  THR*     4.7     0.3    -      -       -      +
    111E  GLU*     1.3    80.9    -      -       -      +
    113E  GLY*     1.3    69.3    +      -       -      +
    114E  HIS*     3.6    44.9    -      +       -      -
    116E  PHE*     4.5     5.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 113 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47E  LYS*     2.7    40.1    +      -       -      -
    112E  PHE*     1.3    89.2    -      -       -      +
    114E  HIS*     1.3    61.0    +      -       -      -
    115E  GLU*     3.4    12.1    -      -       -      -
    116E  PHE*     3.7    13.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 114 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47E  LYS*     4.5     5.2    -      -       +      +
     91E  LYS*     2.8    23.7    +      -       -      -
    112E  PHE*     3.6    33.8    -      +       -      -
    113E  GLY*     1.3    73.8    -      -       -      +
    115E  GLU*     1.3    61.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 115 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90E  ASP*     3.0    31.2    -      -       -      +
     91E  LYS*     2.8    39.3    +      -       -      +
     92E  ALA*     3.6    20.4    -      -       +      +
    113E  GLY*     3.6     5.5    -      -       -      -
    114E  HIS*     1.3    85.9    +      -       -      +
    116E  PHE*     1.3    83.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 116 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47E  LYS*     3.1    18.4    +      -       -      -
     48E  THR      2.8    24.9    -      -       -      +
     49E  THR*     3.4    30.5    -      -       +      -
     88E  VAL*     4.0    16.2    -      -       +      -
     89E  PHE      3.6     1.8    -      -       -      -
     90E  ASP*     3.2    34.5    -      -       +      -
     91E  LYS*     3.5     3.6    +      -       -      -
     93E  ARG*     6.3     0.4    -      -       -      -
     97E  LEU*     5.5     7.9    -      -       +      -
    112E  PHE      4.5     2.2    -      -       -      -
    113E  GLY*     3.7    14.5    +      -       -      +
    114E  HIS      3.3     0.8    -      -       -      -
    115E  GLU*     1.3   110.2    +      -       +      +
    117E  ASP*     1.3    70.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 117 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44E  LYS*     6.5     0.2    -      -       +      -
     45E  SER      4.1     3.1    -      -       -      -
     46E  ALA*     3.4    10.5    -      -       -      +
     47E  LYS      3.3    13.0    +      -       -      -
     48E  THR      3.6     3.8    -      -       -      -
     88E  VAL*     3.2     6.5    -      -       -      +
     89E  PHE*     3.1    36.2    +      -       +      +
     91E  LYS*     3.5    27.4    +      -       +      +
    116E  PHE*     1.3    82.3    -      -       -      +
    118E  LEU*     1.3    61.7    +      -       -      +
    119E  TYR*     3.8    29.1    +      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 118 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43E  LYS      3.4     0.5    -      -       -      +
     44E  LYS*     3.2     5.2    -      -       -      -
     45E  SER*     2.7    54.3    +      -       -      +
     48E  THR*     3.6    27.7    +      -       +      +
     49E  THR      5.0     7.2    -      -       -      +
     50E  LEU*     5.3     5.2    -      -       +      +
     86E  ALA*     4.5     7.6    -      -       +      -
     87E  PHE      3.7     6.1    -      -       -      +
     88E  VAL*     3.7    20.2    -      -       +      -
     99E  PHE*     5.1     3.1    -      -       +      -
    102E  ASN*     6.2     0.2    -      -       -      -
    103E  SER*     4.4    15.3    -      -       -      +
    110E  LYS*     6.3     1.1    -      -       +      -
    117E  ASP*     1.3    72.9    -      -       -      +
    119E  TYR*     1.3    70.5    +      -       -      +
    120E  GLU*     4.0    33.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 119 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39E  ILE*     4.0    23.7    -      -       +      +
     42E  PHE*     3.8    24.2    -      +       +      -
     43E  LYS      3.6     3.6    -      -       -      -
     44E  LYS*     4.1    24.9    -      -       +      +
     67E  ALA*     4.7    17.3    -      -       +      +
     86E  ALA*     3.5     1.2    -      -       -      -
     87E  PHE*     3.0    73.0    +      +       +      +
     89E  PHE*     5.0     1.1    -      -       +      -
    117E  ASP*     3.8    34.6    +      -       +      -
    118E  LEU*     1.3    78.4    -      -       -      +
    120E  GLU*     1.3    62.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 120 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42E  PHE*     3.2     6.7    -      -       -      -
     43E  LYS*     2.9    49.7    +      -       -      +
     45E  SER*     4.4     7.8    +      -       -      -
     85E  LYS      4.5     0.9    -      -       -      +
     86E  ALA*     3.9    16.4    -      -       +      -
    102E  ASN*     3.4     8.5    -      -       +      +
    103E  SER*     2.4    49.3    +      -       -      -
    104E  MET*     4.4     0.7    -      -       -      +
    118E  LEU*     4.0    19.2    -      -       +      +
    119E  TYR*     1.3    75.5    -      -       -      +
    121E  ASN*     1.3    62.9    +      -       -      +
    122E  LYS      3.4     0.5    +      -       -      -
    125E  ILE*     3.6    27.0    -      -       +      +
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Residues in contact with ASN 121 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41E  GLU      5.1     0.7    -      -       -      -
     42E  PHE*     3.6    26.8    -      -       +      -
     74E  CYS*     4.8     3.2    +      -       -      -
     75E  THR*     5.1    10.1    +      -       -      +
     84E  CYS      3.9    11.1    +      -       -      +
     85E  LYS      2.8    27.3    +      -       -      +
    102E  ASN*     5.3     0.2    +      -       -      -
    120E  GLU*     1.3    70.3    -      -       -      +
    122E  LYS*     1.3    66.1    +      -       -      +
    123E  ASP*     2.9    39.1    +      -       -      +
    124E  TYR*     3.0    35.8    +      -       +      +
    125E  ILE*     3.8     7.4    +      -       -      +
----------------------------------------------------------
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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