Contacts of the strand formed by residues 23 - 32 (chain B) in PDB entry 4MD4


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 ARG 23 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  PHE*     3.7     0.2    -      -       -      -
     18B  PHE*     2.9    59.6    +      -       +      +
     19B  ASN*     5.6     2.2    -      -       +      -
     20B  GLY      4.5     0.3    -      -       -      +
     22B  GLU*     1.3    85.5    -      -       +      +
     24B  VAL*     1.3    67.0    +      -       -      +
     80B  ARG*     4.5     0.2    -      -       -      +
    500B  NAG      5.4    15.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 24 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B  HIS      3.3     9.4    -      -       -      +
     17B  PHE*     3.7    23.6    -      -       +      -
     18B  PHE*     4.9     0.9    -      -       -      -
     21B  THR*     3.7     9.9    -      -       -      +
     23B  ARG*     1.3    81.3    -      -       -      +
     25B  ARG*     1.3    64.9    +      -       -      +
     42B  SER*     4.4     1.4    +      -       -      -
     75B  VAL*     3.5    21.0    -      -       +      +
     79B  CYS*     3.6    32.8    -      -       +      -
     80B  ARG*     3.5    41.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 25 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  GLU      3.7     0.7    -      -       -      +
     15B  CYS*     3.6     1.9    -      -       -      -
     16B  HIS*     2.8    46.4    +      -       +      +
     18B  PHE*     4.2    22.1    -      -       +      -
     24B  VAL*     1.3    76.3    -      -       -      +
     26B  PHE*     1.3    62.2    +      -       -      +
     27B  LEU*     3.6    19.4    -      -       +      +
     39B  ARG*     4.9     6.5    -      -       -      +
     41B  ASP*     2.4    37.1    +      -       -      +
     42B  SER*     3.5    11.7    -      -       -      +
     43B  ASP*     3.0    31.7    +      -       -      +
     75B  VAL*     4.2     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 26 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  HIS*     4.2     5.2    -      -       +      -
     14B  GLU      3.2    16.2    -      -       -      -
     25B  ARG*     1.3    74.3    -      -       -      +
     27B  LEU*     1.3    74.5    +      -       -      +
     28B  ASP*     3.4    31.6    -      -       +      -
     40B  PHE*     3.8    22.7    -      +       -      -
     41B  ASP*     3.7     0.2    -      -       -      -
     42B  SER*     2.9    35.3    +      -       -      +
     71B  LYS*     3.8    17.0    -      -       +      -
     74B  ALA*     3.7    17.7    -      -       +      -
     75B  VAL*     3.7    20.6    -      -       +      +
     78B  TYR*     3.8    24.9    -      +       -      -
     79B  CYS*     3.8    18.8    -      -       -      -
      7C  CIR      3.5    16.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 27 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  LYS      3.5     1.6    -      -       -      +
     13B  HIS*     3.4     3.1    -      -       -      -
     14B  GLU*     2.8    58.5    +      -       +      +
     16B  HIS*     3.8    20.6    -      -       +      +
     25B  ARG*     3.6    17.7    -      -       +      +
     26B  PHE*     1.3    91.0    -      -       -      +
     28B  ASP*     1.3    58.8    +      -       -      +
     29B  ARG*     3.8    25.4    -      -       +      +
     39B  ARG*     5.0    16.6    -      -       -      +
     40B  PHE      3.2     5.2    -      -       -      +
     41B  ASP*     3.5    31.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 28 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  LYS      4.0     1.1    -      -       -      -
     13B  HIS*     2.7    30.6    +      -       -      -
     26B  PHE*     3.4    17.1    -      -       +      -
     27B  LEU*     1.3    70.5    -      -       -      +
     29B  ARG*     1.3    58.4    +      -       -      +
     30B  TYR*     2.7    30.2    +      -       +      -
     39B  ARG*     3.1     6.2    -      -       -      -
     40B  PHE*     2.9    47.1    +      -       +      -
     47B  TYR*     2.7    22.5    +      -       -      +
     71B  LYS*     3.3    15.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 29 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141A  GLU*     5.3     1.0    +      -       -      +
    143A  HIS*     3.5    31.1    +      -       -      -
     11B  VAL*     3.3     8.6    -      -       -      +
     12B  LYS      2.9    39.2    +      -       -      +
     14B  GLU*     2.8    49.3    +      -       -      -
     27B  LEU*     3.8    23.2    -      -       +      +
     28B  ASP*     1.3    75.5    -      -       -      +
     30B  TYR*     1.3    63.7    +      -       -      +
     31B  PHE*     3.5    20.0    -      -       +      -
     36B  GLU*     2.9    41.4    +      -       -      +
     38B  VAL      4.0     4.0    -      -       -      -
     39B  ARG*     3.6    15.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 30 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  ASN*     4.3     5.2    -      -       -      -
      9B  GLU*     4.3     3.1    -      -       -      -
     10B  GLN      3.7     2.2    -      -       -      +
     11B  VAL*     3.7    31.9    -      -       +      -
     13B  HIS*     4.3     0.7    -      -       -      -
     28B  ASP*     2.7    47.3    +      -       -      -
     29B  ARG*     1.3    75.2    -      -       -      +
     31B  PHE*     1.3    61.3    +      -       -      +
     36B  GLU*     3.3     5.9    -      -       -      +
     37B  TYR*     2.9    52.0    +      -       +      -
     38B  VAL*     3.1    21.9    +      -       +      +
     47B  TYR*     4.0    10.3    -      +       -      -
     61B  TRP*     4.0    16.4    -      +       -      -
      8C  VAL      4.2     0.2    +      -       -      -
      9C  ASN*     3.6     9.0    -      -       +      -
     10C  SER*     2.8    44.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 31 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143A  HIS*     3.2    50.7    -      +       +      -
      9B  GLU*     3.5    10.6    -      -       -      +
     10B  GLN*     2.8    61.9    +      -       +      +
     12B  LYS*     3.7    21.1    -      -       +      -
     29B  ARG*     3.5    43.7    -      -       +      -
     30B  TYR*     1.3    74.8    -      -       -      +
     32B  TYR*     1.3    59.8    +      -       -      +
     33B  HIS      4.2     9.9    -      -       -      +
     34B  GLN      4.4     1.6    -      -       -      -
     35B  GLU      3.3     7.2    -      -       -      +
     36B  GLU*     3.5    32.8    -      -       +      -
     37B  TYR*     3.5     6.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 32 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  LEU*     3.8    21.3    -      -       +      -
     73A  MET*     3.6    18.6    -      -       +      -
     74A  THR*     3.5    15.6    -      -       -      -
     77A  SER*     3.0    32.0    +      -       -      -
     80A  THR*     2.9    19.1    +      -       +      -
      7B  PHE*     3.3    16.0    -      -       +      -
      8B  LEU      3.7     9.6    -      -       -      -
      9B  GLU*     4.4     2.0    -      -       -      -
     31B  PHE*     1.3    72.5    -      -       -      +
     33B  HIS*     1.3    93.6    +      +       -      +
     35B  GLU*     2.9    35.8    +      -       -      +
     37B  TYR*     3.5    16.9    -      -       +      -
     53B  LEU*     4.0    23.1    -      -       +      -
----------------------------------------------------------
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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