Contacts of the strand formed by residues 2234 - 2241 (chain A) in PDB entry 4YNM


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 VAL2234 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2077A  TYR*     3.7    21.8    -      -       +      +
   2082A  PRO*     3.6    21.3    -      -       +      +
   2083A  LEU*     4.5    13.9    -      -       +      -
   2084A  SER*     4.7     0.2    -      -       -      -
   2230A  SER*     4.4     1.6    -      -       -      -
   2231A  VAL*     2.8    46.8    +      -       -      +
   2232A  ASN*     4.0     8.1    -      -       +      +
   2233A  GLY*     1.3    79.3    -      -       -      +
   2235A  TYR*     1.3    76.9    +      -       -      +
   2236A  ARG*     3.4     8.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR2235 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2075A  ASN*     5.2     1.7    +      -       -      -
   2077A  TYR*     4.8     1.2    +      -       -      -
   2082A  PRO*     2.9    38.0    +      -       +      +
   2083A  LEU      4.1     4.9    -      -       -      -
   2084A  SER*     3.5    36.0    +      -       -      -
   2086A  TYR*     3.7    30.0    +      -       -      -
   2198A  LEU*     4.1    16.5    -      -       +      +
   2199A  ASP*     3.6    27.6    -      -       +      -
   2202A  MET*     5.9     0.7    -      -       +      -
   2228A  LYS*     3.5    41.1    +      -       +      -
   2229A  TRP      3.2    13.5    -      -       -      -
   2230A  SER*     4.3     3.8    -      -       -      -
   2234A  VAL*     1.3    78.0    -      -       -      +
   2236A  ARG*     1.3    64.1    +      -       -      +
   2070B  LYS*     4.4    14.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG2236 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2074A  SER*     5.2     7.4    -      -       -      -
   2075A  ASN*     4.6    12.7    -      -       -      +
   2077A  TYR*     4.6     8.0    +      -       -      +
   2133A  ILE*     3.5    24.0    +      -       +      +
   2134A  GLN*     4.4    10.5    +      -       -      +
   2136A  HIS*     4.3    13.9    -      -       -      -
   2168A  GLU*     2.6    50.9    +      -       -      +
   2198A  LEU*     4.7     2.0    -      -       -      -
   2204A  ILE*     5.7     0.2    -      -       -      -
   2228A  LYS*     3.7     1.8    -      -       -      -
   2229A  TRP*     2.8    33.3    +      -       -      +
   2231A  VAL*     4.0    33.7    +      -       +      +
   2234A  VAL*     3.9    17.2    -      -       +      +
   2235A  TYR*     1.3    80.3    -      -       -      +
   2237A  ILE*     1.3    66.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE2237 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2133A  ILE*     4.7     1.3    -      -       -      -
   2168A  GLU*     3.4    10.5    +      -       -      +
   2169A  TYR*     2.8    28.3    +      -       +      -
   2196A  LEU*     3.7    30.5    -      -       +      -
   2197A  ASN      3.3    26.2    -      -       -      +
   2198A  LEU*     3.8    22.0    -      -       +      +
   2204A  ILE*     4.1    18.1    -      -       +      +
   2226A  MET*     3.8    26.9    -      -       +      -
   2227A  GLN      3.5     9.0    -      -       -      +
   2228A  LYS*     4.4    10.5    -      -       +      -
   2236A  ARG*     1.3    79.5    -      -       -      +
   2238A  GLY*     1.3    61.3    +      -       -      +
   2258A  HIS*     6.5     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY2238 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2133A  ILE*     4.3     5.4    -      -       -      +
   2165A  PHE*     4.0     9.6    -      -       -      -
   2167A  ILE      3.5     8.5    -      -       -      -
   2168A  GLU*     4.2     1.3    -      -       -      -
   2226A  MET*     3.4     3.7    -      -       -      -
   2227A  GLN      2.8    33.7    +      -       -      -
   2236A  ARG      4.2     0.8    +      -       -      -
   2237A  ILE*     1.3    76.6    -      -       -      +
   2239A  LEU*     1.3    61.4    +      -       -      -
   2240A  TYR*     3.3    19.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU2239 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2165A  PHE*     3.8     0.9    -      -       -      -
   2166A  ILE*     2.8    61.9    +      -       +      +
   2167A  ILE*     2.8    22.2    +      -       +      +
   2169A  TYR      5.1     1.0    -      -       -      +
   2213A  ALA*     6.0     0.2    -      -       +      -
   2216A  ILE*     3.5    27.1    -      -       +      -
   2224A  CYS*     3.7    26.2    -      -       +      -
   2225A  GLU      3.4    15.9    -      -       -      +
   2226A  MET*     3.5    31.8    -      -       +      -
   2238A  GLY*     1.3    72.2    -      -       -      -
   2240A  TYR*     1.3    57.5    -      -       -      +
   2251A  LEU*     4.2     2.9    -      -       +      -
   2253A  TYR*     4.2    11.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR2240 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2116A  GLU*     5.0     1.6    +      -       -      -
   2132A  ARG*     5.3     6.8    -      -       +      +
   2133A  ILE*     3.5    23.0    -      -       -      +
   2163A  GLY      3.9    14.8    -      -       -      +
   2164A  GLN      3.3     5.8    -      -       -      +
   2165A  PHE*     3.5    37.0    -      +       +      -
   2166A  ILE*     3.9     4.5    -      -       -      -
   2224A  CYS*     3.3     2.6    -      -       -      +
   2225A  GLU*     2.8    33.9    +      -       +      +
   2227A  GLN*     3.2    47.3    -      -       +      +
   2229A  TRP*     3.2    27.7    +      +       -      -
   2238A  GLY*     3.3    27.4    -      -       -      -
   2239A  LEU*     1.3    72.8    -      -       -      +
   2241A  ALA*     1.3    67.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA2241 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2160A  LEU*     4.9     3.1    -      -       +      -
   2161A  LYS      3.4    26.2    -      -       -      +
   2163A  GLY*     2.9    22.7    +      -       -      -
   2164A  GLN*     2.9    13.4    +      -       +      +
   2166A  ILE*     3.5    12.8    -      -       +      +
   2223A  ASN      3.8     4.7    -      -       -      -
   2225A  GLU*     5.4     0.5    -      -       -      +
   2240A  TYR*     1.3    74.6    -      -       -      +
   2242A  LEU*     1.3    61.7    +      -       -      +
   2243A  LYS      3.8     6.5    -      -       -      +
   2245A  MET*     3.4    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