Contacts of the strand formed by residues 2257 - 2263 (chain D) in PDB entry 3CMT


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 GLN2257 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2046D  SER*     4.7     1.2    -      -       -      +
   2050D  ALA*     3.9     9.4    -      -       -      +
   2243D  ARG*     3.4    34.4    +      -       +      +
   2244D  VAL      3.3    14.4    -      -       -      +
   2245D  LYS*     3.5    37.7    -      -       +      +
   2255D  PHE      5.2     3.9    +      -       -      +
   2256D  LYS*     1.3    77.0    -      -       -      +
   2258D  ALA*     1.3    61.7    +      -       -      +
   2259D  GLU*     4.3     5.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA2258 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2046D  SER*     3.4    26.9    -      -       -      +
   2047D  LEU*     3.5    32.5    -      -       +      +
   2050D  ALA*     4.2     2.4    -      -       +      +
   2242D  THR      3.9     0.2    -      -       -      +
   2243D  ARG*     3.3     3.3    -      -       -      -
   2244D  VAL*     2.8    40.0    +      -       +      +
   2257D  GLN*     1.3    75.3    -      -       -      +
   2259D  GLU*     1.3    63.4    +      -       -      +
   2260D  PHE*     4.3     7.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU2259 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2235A  GLU*     3.2    32.0    -      -       -      +
   2046D  SER*     3.5    11.9    +      -       -      -
   2228D  ILE*     4.0    13.8    -      -       +      +
   2241D  GLU*     5.6     3.4    -      -       +      +
   2242D  THR      3.2     6.3    -      -       -      +
   2243D  ARG*     2.4    51.0    +      -       +      -
   2257D  GLN*     4.3     5.5    -      -       +      +
   2258D  ALA*     1.3    76.3    -      -       -      +
   2260D  PHE*     1.3    64.2    +      -       -      +
   2273D  GLU*     4.6     3.1    -      -       -      +
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Residues in contact with PHE2260 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2044D  SER*     3.3    25.1    -      -       -      -
   2046D  SER*     4.1     3.1    -      -       -      -
   2047D  LEU*     4.8     2.2    -      -       +      -
   2075D  LEU*     3.9    17.5    -      -       +      -
   2225D  ILE*     4.6     0.2    -      -       +      -
   2241D  GLU*     3.7     7.0    +      -       -      +
   2242D  THR*     2.7    63.3    +      -       +      +
   2244D  VAL*     3.7    26.0    -      -       +      -
   2258D  ALA*     4.3     8.3    -      -       +      -
   2259D  GLU*     1.3    77.7    -      -       -      +
   2261D  GLN*     1.3    72.8    +      -       -      +
   2262D  ILE*     3.8    17.0    -      -       +      -
   2268D  ILE*     3.9    21.1    -      -       +      -
   2269D  ASN      5.0     0.4    -      -       -      +
   2273D  GLU*     3.6    26.0    -      -       +      +
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Residues in contact with GLN2261 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2234A  GLY*     4.4    13.3    -      -       -      +
   2231D  VAL*     3.6    25.9    -      -       +      +
   2240D  SER      3.6     3.4    -      -       -      -
   2241D  GLU*     3.2    34.9    +      -       -      +
   2260D  PHE*     1.3    79.2    -      -       -      +
   2262D  ILE*     1.3    59.7    +      -       -      +
   2263D  LEU*     3.8    14.1    -      -       +      +
   2268D  ILE*     3.4     3.8    -      -       -      -
   2269D  ASN*     2.7    63.3    +      -       +      +
   2302D  LYS*     5.3    13.3    -      -       -      +
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Residues in contact with ILE2262 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2070D  SER      4.3     2.0    -      -       -      +
   2071D  GLY*     3.9    29.6    -      -       -      +
   2074D  THR*     3.9    28.3    -      -       +      +
   2075D  LEU*     5.4     1.3    -      -       +      +
   2103D  TYR*     4.9     2.9    -      -       -      +
   2225D  ILE*     4.8     1.3    -      -       +      -
   2239D  GLY*     3.1     2.5    -      -       -      -
   2240D  SER*     2.7    47.3    +      -       -      +
   2242D  THR*     3.6    21.1    -      -       +      +
   2260D  PHE*     3.8    21.1    -      -       +      -
   2261D  GLN*     1.3    70.9    -      -       -      +
   2263D  LEU*     1.3    68.7    +      -       -      +
   2264D  TYR*     3.6     4.8    +      -       +      -
   2267D  GLY*     3.5     8.7    -      -       -      +
   2268D  ILE*     4.5     7.2    -      -       +      -
   2502D  ADP      4.7    15.5    -      -       -      +
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Residues in contact with LEU2263 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2103D  TYR*     4.7     0.2    +      -       -      -
   2231D  VAL*     4.0    21.3    -      -       +      -
   2238D  VAL*     3.8    16.8    -      -       +      +
   2239D  GLY*     4.5     0.7    -      -       -      -
   2261D  GLN*     3.8    17.9    -      -       +      +
   2262D  ILE*     1.3    77.2    -      -       -      +
   2264D  TYR*     1.3    64.1    +      -       -      +
   2265D  GLY      3.4     0.2    +      -       -      -
   2266D  GLU*     3.0    34.6    +      -       +      +
   2267D  GLY*     2.8    41.9    +      -       -      +
   2269D  ASN*     4.0    33.0    -      -       +      +
----------------------------------------------------------
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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