Contacts of the strand formed by residues 91 - 101 (chain M) in PDB entry 4G7Z


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 GLN 91 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76M  PRO*     3.2     7.1    -      -       -      +
     77M  PRO*     3.1    29.0    -      -       +      +
     88M  LEU*     6.2     0.2    -      -       -      +
     89M  THR*     3.3    36.5    +      -       +      +
     90M  TYR*     1.3    78.7    -      -       -      +
     92M  ALA*     1.3    60.8    +      -       -      +
    117M  HIS*     3.4    41.6    -      -       +      +
    118M  ILE      3.2    19.7    -      -       -      +
    119M  PRO*     3.7     6.5    -      -       +      +
    120M  LEU*     3.7     9.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 92 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73M  LEU*     4.7    10.5    -      -       +      +
     74M  GLY      3.7    18.6    -      -       -      +
     76M  PRO*     4.4     5.6    -      -       +      -
     91M  GLN*     1.3    73.9    -      -       -      +
     93M  PRO*     1.3    74.7    -      -       +      +
     94M  LEU      3.6     0.3    +      -       -      -
    117M  HIS*     3.5     4.9    -      -       -      -
    118M  ILE*     3.0    33.0    +      -       -      +
    120M  LEU*     3.6    25.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 93 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72M  ARG      3.8     0.3    -      -       -      +
     73M  LEU*     3.5     5.0    -      -       -      +
     74M  GLY*     2.8    43.4    +      -       -      -
     75M  GLU      3.1    24.0    -      -       -      +
     77M  PRO*     4.3     2.0    -      -       +      -
     92M  ALA*     1.3    86.1    -      -       +      +
     94M  LEU*     1.3    61.3    +      -       -      +
     95M  TYR*     3.7    25.7    +      -       +      +
    114M  PHE*     3.8    10.3    -      -       +      -
    116M  GLY      3.8     2.2    -      -       -      +
    117M  HIS*     3.3    29.6    -      -       +      +
    283P  GLY      5.1     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 94 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44M  ILE*     5.4     1.8    -      -       +      -
     48M  PHE*     4.2     2.5    -      -       +      -
     71M  TYR*     3.6    29.8    -      -       +      -
     72M  ARG      3.6    15.7    -      -       -      +
     73M  LEU*     3.7    16.4    -      -       +      -
     92M  ALA      3.6     0.8    +      -       -      -
     93M  PRO*     1.3    73.2    -      -       -      +
     95M  TYR*     1.3    66.3    +      -       -      +
    114M  PHE*     3.9     2.9    -      -       -      -
    115M  LEU*     2.9    58.3    +      -       +      +
    116M  GLY      3.1    14.5    +      -       -      +
    118M  ILE*     3.8    30.5    -      -       +      -
    344M  PHE*     4.0    18.2    -      -       +      -
    378M  LEU*     4.9     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 95 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71M  TYR*     3.3     4.9    -      -       -      +
     72M  ARG*     2.9    77.3    +      -       +      +
     74M  GLY*     4.7     0.9    -      -       -      -
     93M  PRO*     3.7    34.6    -      -       +      +
     94M  LEU*     1.3    76.1    -      -       -      +
     96M  ALA*     1.3    60.9    +      -       -      +
    112M  GLU*     3.7    30.1    -      -       +      -
    113M  VAL      3.4     6.3    -      -       -      +
    114M  PHE*     3.3    43.3    -      +       +      -
    282P  LEU      5.3     0.9    +      -       -      -
    283P  GLY*     4.6    10.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 96 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48M  PHE*     3.9    19.5    -      -       +      -
     68M  PHE*     4.6     5.6    -      -       +      -
     70M  GLU      3.6     7.0    -      -       -      +
     71M  TYR*     4.1     2.2    -      -       +      +
     95M  TYR*     1.3    74.5    -      -       -      +
     97M  ARG*     1.3    60.9    +      -       -      +
     98M  LEU*     4.0     7.6    -      -       +      +
    112M  GLU*     4.1     2.2    -      -       -      -
    113M  VAL*     2.8    45.0    +      -       +      +
    115M  LEU*     3.6    28.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 97 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68M  PHE*     4.2     0.2    -      -       -      -
     69M  LEU*     3.0    45.0    +      -       -      +
     70M  GLU*     2.7    58.1    +      -       +      +
     96M  ALA*     1.3    72.2    -      -       -      +
     98M  LEU*     1.3    65.3    +      -       -      +
    110M  GLU*     3.1    32.3    +      -       +      +
    111M  ASP*     3.6    13.0    -      -       -      +
    112M  GLU*     3.9    23.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 98 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52M  PHE*     4.1    20.6    -      -       +      -
     66M  LEU*     3.7    26.0    -      -       +      -
     67M  ASP      3.5     4.0    -      -       -      +
     68M  PHE*     3.6    33.9    -      -       +      -
     69M  LEU*     4.8     1.1    -      -       -      -
     96M  ALA*     4.0     8.7    -      -       +      +
     97M  ARG*     1.3    84.5    -      -       -      +
     99M  GLN*     1.3    60.0    +      -       -      +
    100M  LEU      4.1     0.2    -      -       -      -
    110M  GLU*     3.4     2.9    -      -       -      +
    111M  ASP      2.8    33.7    +      -       -      +
    113M  VAL*     3.7    24.7    -      -       +      -
    115M  LEU*     6.1     1.8    -      -       +      -
    369M  PRO*     3.5    10.3    -      -       +      +
    373M  VAL*     4.0    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 99 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66M  LEU*     3.8     2.9    -      -       -      -
     67M  ASP*     3.2    38.1    +      -       +      +
     69M  LEU*     3.8    30.3    -      -       +      +
     98M  LEU*     1.3    71.1    -      -       -      +
    100M  LEU*     1.3    63.3    +      -       -      +
    101M  ILE*     3.4    31.7    +      -       +      +
    108M  ILE*     4.5    14.9    -      -       +      +
    109M  LYS      3.7     4.3    -      -       -      +
    110M  GLU*     3.6    30.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 100 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64M  LEU*     3.7    28.5    -      -       +      -
     65M  VAL      4.0     4.7    -      -       -      +
     66M  LEU*     3.7    22.9    -      -       +      +
     98M  LEU      4.1     0.4    +      -       -      -
     99M  GLN*     1.3    71.0    -      -       -      +
    101M  ILE*     1.3    60.7    +      -       -      +
    102M  HIS      3.9     0.4    +      -       -      +
    107M  LEU      3.7     1.9    -      -       -      +
    108M  ILE*     3.2     6.2    -      -       -      -
    109M  LYS*     2.9    41.5    +      -       +      +
    359M  MET*     4.8     2.7    -      -       -      -
    367M  LEU*     3.2    44.4    -      -       +      +
    368M  THR      4.0     4.0    -      -       -      +
    369M  PRO*     4.2     4.7    -      -       +      +
    372M  LEU*     3.7    28.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 101 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64M  LEU*     3.6     2.9    -      -       -      -
     65M  VAL*     2.7    57.2    +      -       +      +
     67M  ASP*     5.0     8.5    -      -       +      +
     99M  GLN*     3.6    33.9    -      -       +      +
    100M  LEU*     1.3    74.9    -      -       -      +
    102M  HIS*     1.3    74.0    +      -       -      +
    103M  LYS*     3.6     0.4    +      -       -      -
    106M  GLY*     5.2     4.5    -      -       -      +
    107M  LEU      3.8     3.1    -      -       -      +
    108M  ILE*     3.7    23.8    -      -       +      -
----------------------------------------------------------
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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