Contacts of the strand formed by residues 1073 - 1077 (chain A) in PDB entry 1M7N


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 LEU1073 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    993A  ARG*     4.0    24.9    -      -       +      +
    996A  ILE*     3.9    20.9    -      -       +      -
    998A  MET*     4.6    10.3    -      -       +      -
   1029A  ILE*     3.5    25.8    -      -       +      -
   1030A  LYS      3.5     2.9    -      -       -      -
   1031A  THR*     3.7    22.0    -      -       +      -
   1044A  PHE*     4.3     0.2    -      -       -      -
   1065A  VAL*     4.0     4.5    -      -       -      +
   1066A  VAL*     3.2    51.5    +      -       +      +
   1071A  PRO*     4.6    10.3    -      -       +      +
   1072A  THR*     1.3    80.0    -      -       -      +
   1074A  VAL*     1.3    75.0    +      -       -      +
   1075A  ILE*     5.1     1.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL1074 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1028A  ALA      3.5     0.9    -      -       -      +
   1029A  ILE*     3.4     3.4    -      -       -      -
   1030A  LYS*     2.9    54.0    +      -       -      +
   1044A  PHE*     3.3    33.0    -      -       +      -
   1045A  LEU*     4.6     5.8    -      -       +      -
   1048A  ALA*     3.9    25.6    -      -       +      -
   1062A  LEU*     4.1    10.8    -      -       +      -
   1064A  GLY      4.0     5.2    -      -       -      +
   1065A  VAL*     4.7     4.0    -      -       +      +
   1073A  LEU*     1.3    83.2    -      -       -      +
   1075A  ILE*     1.3    61.9    +      -       -      +
   1076A  MET*     3.7    17.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE1075 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    991A  VAL*     4.3    23.6    -      -       +      -
    996A  ILE*     3.1    41.5    -      -       +      -
   1015A  ALA*     4.2    10.5    -      -       +      -
   1018A  VAL*     4.5     2.9    -      -       +      -
   1027A  VAL*     3.6    37.2    -      -       +      -
   1028A  ALA      3.4     3.8    -      -       -      -
   1029A  ILE*     4.7    10.1    -      -       +      +
   1062A  LEU*     3.8     4.2    -      -       -      +
   1063A  LEU*     3.0    30.8    +      -       +      -
   1064A  GLY*     3.2    21.0    +      -       -      +
   1066A  VAL*     4.7     4.7    -      -       +      -
   1073A  LEU*     5.2     0.2    -      -       +      -
   1074A  VAL*     1.3    73.0    -      -       -      +
   1076A  MET*     1.3    60.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET1076 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1027A  VAL*     3.3    14.4    -      -       -      +
   1028A  ALA*     2.7    35.2    +      -       +      +
   1030A  LYS*     3.9    19.3    -      -       +      -
   1048A  ALA*     6.2     0.2    -      -       -      -
   1051A  MET*     3.6    16.6    -      -       +      +
   1060A  VAL*     3.4    14.4    -      -       +      -
   1061A  ARG      3.4    13.5    -      -       -      +
   1062A  LEU*     3.8    17.3    -      -       -      -
   1063A  LEU*     4.0     4.5    -      -       -      -
   1074A  VAL*     3.9    20.0    -      -       +      +
   1075A  ILE*     1.3    75.4    -      -       -      +
   1077A  GLU*     1.3    70.6    +      -       -      +
   1150A  ASP*     3.1    49.8    -      -       +      +
   1151A  PHE*     5.3     0.7    -      -       -      -
   1153A  MET*     6.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU1077 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1026A  ARG      5.3     0.2    -      -       -      -
   1028A  ALA*     4.0     3.6    -      -       -      +
   1059A  VAL      4.1     1.0    -      -       -      +
   1060A  VAL*     3.4    20.6    -      -       +      +
   1061A  ARG*     2.8    49.9    +      -       +      +
   1063A  LEU*     4.2    13.4    -      -       +      +
   1076A  MET*     1.3    79.3    -      -       -      +
   1078A  LEU*     1.3    71.7    +      -       -      +
   1079A  MET*     3.8     7.7    +      -       -      +
   1147A  LYS*     3.0    36.0    +      -       -      +
----------------------------------------------------------
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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