Contacts of the strand formed by residues 575 - 580 (chain A) in PDB entry 1MMG


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 575 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    460A  ILE*     5.3     1.3    -      -       -      -
    571A  THR*     4.4     4.3    -      -       -      -
    572A  HIS*     3.0    36.5    +      -       -      +
    573A  TYR      3.1     2.4    +      -       -      -
    574A  ALA*     1.3    79.5    -      -       -      +
    576A  GLN*     1.3    65.2    +      -       -      -
    577A  VAL*     3.5     4.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 576 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    460A  ILE*     4.3    10.2    -      -       -      +
    559A  GLU*     3.2    41.7    +      -       -      +
    569A  GLY*     4.0    12.7    -      -       -      -
    570A  VAL      3.1    11.9    -      -       -      +
    571A  THR*     4.0    19.8    +      -       +      +
    575A  GLY*     1.3    73.0    -      -       -      -
    577A  VAL*     1.3    75.4    +      -       -      +
    578A  MET*     4.3    13.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 577 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    458A  PHE*     6.1     0.7    -      -       +      -
    460A  ILE*     3.8    33.9    -      -       +      -
    464A  ASN*     3.3    32.1    -      -       -      +
    472A  ASN*     4.0     9.4    -      -       -      +
    569A  GLY*     3.2     1.6    -      -       -      -
    570A  VAL      2.9    29.6    +      -       -      -
    572A  HIS*     3.5    21.8    -      -       +      -
    575A  GLY      4.0     2.5    -      -       -      +
    576A  GLN*     1.3    83.6    -      -       -      +
    578A  MET*     1.3    61.2    +      -       -      +
    579A  TYR*     3.5    35.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 578 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    460A  ILE*     5.7     0.2    -      -       -      +
    462A  LYS      5.3     1.2    -      -       -      +
    464A  ASN*     2.9    30.2    +      -       -      +
    559A  GLU*     4.7     7.9    -      -       -      +
    561A  PRO*     3.8    14.6    -      -       +      -
    567A  GLU*     3.2    29.2    -      -       +      +
    568A  PHE*     2.9    47.1    -      -       -      +
    569A  GLY*     3.4    19.7    -      -       -      -
    576A  GLN*     4.2    18.3    +      -       +      +
    577A  VAL*     1.3    75.3    -      -       -      +
    579A  TYR*     1.4    58.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 579 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    464A  ASN*     3.3    13.2    -      -       +      +
    465A  SER      3.7    16.8    -      -       -      -
    468A  GLN*     3.8     7.9    -      -       +      -
    469A  LEU*     3.4    37.5    -      -       +      -
    472A  ASN*     2.9    20.4    +      -       -      +
    567A  GLU*     2.9     7.9    -      -       -      +
    568A  PHE*     2.6    70.9    +      +       +      +
    570A  VAL*     3.8    12.6    -      -       +      -
    572A  HIS*     2.7    32.8    +      -       -      -
    577A  VAL*     3.5    32.1    -      -       +      -
    578A  MET*     1.4    72.6    -      -       -      +
    580A  GLU*     1.3    60.2    +      -       -      +
    584A  TRP*     4.1     6.1    -      +       +      -
----------------------------------------------------------
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Residues in contact with GLU 580 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    463A  VAL*     3.1    31.0    -      -       +      +
    464A  ASN      3.0    13.3    +      -       -      +
    465A  SER*     3.9    12.0    +      -       -      -
    566A  THR*     3.3     6.1    -      -       -      -
    567A  GLU*     3.8    18.9    -      -       +      +
    579A  TYR*     1.3    75.2    -      -       -      +
    581A  ILE*     1.3    57.9    +      -       -      +
    582A  GLN*     2.6    47.4    +      -       -      +
    584A  TRP*     2.9    25.7    +      -       -      -
----------------------------------------------------------
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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