Contacts of the strand formed by residues 201 - 207 (chain M) in PDB entry 4R2G


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 SER 201 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114M  PRO*     5.4     1.6    -      -       -      +
    196M  VAL      4.4     0.3    -      -       -      +
    198M  HIS*     3.1    25.9    +      -       -      +
    199M  GLU*     2.8    11.1    +      -       -      -
    200M  GLY*     1.3    75.1    -      -       -      +
    202M  THR*     1.3    62.5    +      -       -      +
    203M  VAL*     4.1     5.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 202 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213E  ILE*     3.2    14.3    -      -       +      +
    214E  PRO*     5.0     5.9    -      -       +      +
    195M  GLN*     3.9    21.3    -      -       -      +
    196M  VAL      3.4     5.8    -      -       -      +
    197M  THR*     3.0    30.6    +      -       -      +
    200M  GLY      3.5     3.2    +      -       -      -
    201M  SER*     1.3    73.4    -      -       -      +
    203M  VAL*     1.3    77.7    +      -       -      +
    204M  GLU*     4.4     2.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 203 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113M  ALA*     5.9     2.2    -      -       +      -
    114M  PRO*     4.0    31.4    -      -       +      +
    116M  VAL*     3.6    30.7    -      -       +      +
    195M  GLN*     3.8     0.3    -      -       -      -
    196M  VAL*     2.8    36.0    +      -       -      +
    201M  SER      4.6     4.3    -      -       -      +
    202M  THR*     1.3    79.6    -      -       -      +
    204M  GLU*     1.3    67.3    +      -       -      +
    205M  LYS*     5.1     7.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 204 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150M  LYS*     5.6     0.5    -      -       -      +
    193M  SER*     3.8    10.2    +      -       -      -
    194M  CYS      3.7     3.4    -      -       -      -
    195M  GLN*     3.6    39.3    +      -       +      +
    202M  THR*     4.7     2.2    -      -       +      -
    203M  VAL*     1.3    77.1    -      -       -      +
    205M  LYS*     1.3    83.1    +      -       -      +
    206M  THR*     3.6    14.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 205 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116M  VAL*     3.3    42.1    +      -       +      +
    117M  THR*     5.0     2.0    -      -       -      +
    118M  LEU*     3.5    25.7    -      -       +      +
    193M  SER*     3.2     2.4    -      -       -      -
    194M  CYS      2.8    37.7    +      -       -      +
    203M  VAL*     5.1     8.5    -      -       +      -
    204M  GLU*     1.3    84.4    -      -       -      +
    206M  THR*     1.3    66.2    +      -       -      +
    207M  VAL*     6.0     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 206 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118M  LEU*     4.2     0.2    -      -       -      -
    191M  SER*     3.6    28.5    -      -       -      +
    192M  TYR      3.3    13.0    -      -       -      +
    193M  SER*     2.8    20.2    +      -       -      +
    204M  GLU*     3.6    10.6    +      -       -      -
    205M  LYS*     1.3    77.5    +      -       -      +
    207M  VAL*     1.3    70.7    +      -       -      +
    208M  ALA*     5.5     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 207 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118M  LEU*     3.7    45.7    -      -       +      +
    119M  PHE      4.5     0.2    -      -       -      -
    120M  PRO*     3.8    39.7    -      -       +      -
    133M  LEU*     4.5    10.1    -      -       +      -
    186M  TRP*     4.1     8.0    -      -       +      -
    191M  SER*     3.7     0.3    -      -       -      -
    192M  TYR*     3.0    30.4    +      -       -      +
    205M  LYS*     6.0     0.2    -      -       +      -
    206M  THR*     1.3    80.2    -      -       -      +
    208M  ALA*     1.3    63.5    +      -       -      +
----------------------------------------------------------
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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