Contacts of the strand formed by residues 1270 - 1274 (chain U) in PDB entry 6FF7


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 TYR1270 (chain U).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1223U  LYS      3.1    11.4    +      -       -      +
   1224U  ILE*     3.4    11.9    -      -       +      -
   1225U  SER*     2.9    26.5    +      -       -      +
   1268U  ASN*     4.1     5.4    -      -       -      +
   1269U  ASP*     1.3    80.2    -      -       +      +
   1271U  ILE*     1.3    59.9    +      -       -      +
   1300U  GLY*     3.3    11.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1271 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1225U  SER*     3.3     8.7    -      -       -      +
   1227U  LEU*     5.7     7.4    -      -       +      -
   1268U  ASN*     6.1     1.3    -      -       +      -
   1270U  TYR*     1.3    75.7    -      -       -      +
   1272U  LEU*     1.3    61.2    +      -       -      +
   1273U  LEU*     4.0     4.3    +      -       +      +
   1293U  ALA      6.1     0.4    -      -       -      +
   1296U  ARG*     4.8    11.4    -      -       +      +
   1297U  ALA*     3.9    24.0    -      -       +      +
   1300U  GLY      2.8     8.8    +      -       -      +
   1301U  LEU*     3.6     3.8    -      -       +      -
   1302U  TYR*     3.0    27.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU1272 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1207U  VAL*     5.0    22.4    -      -       +      +
   1210U  LEU*     6.1     3.6    -      -       +      -
   1211U  PHE*     6.1     4.3    -      -       +      +
   1225U  SER      3.0    11.4    +      -       -      +
   1226U  ILE*     3.4    11.9    -      -       +      +
   1227U  LEU*     2.7    33.4    +      -       -      +
   1270U  TYR      4.2     0.2    -      -       -      -
   1271U  ILE*     1.3    72.3    -      -       -      +
   1273U  LEU*     1.3    56.2    +      -       -      +
   1302U  TYR*     3.5     9.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU1273 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1207U  VAL*     6.1     2.0    -      -       -      -
   1227U  LEU*     3.3    13.0    -      -       +      +
   1271U  ILE*     4.0     5.1    +      -       +      +
   1272U  LEU*     1.3    73.4    -      -       -      +
   1274U  SER*     1.3    55.8    +      -       -      +
   1275U  LEU      4.2     0.2    -      -       -      -
   1293U  ALA*     5.6     7.6    -      -       +      +
   1302U  TYR      2.8    15.9    +      -       -      +
   1303U  ILE*     3.3    12.4    -      -       +      +
   1304U  PHE*     2.7    34.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER1274 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1203U  GLU*     4.6    21.8    -      -       -      -
   1204U  ALA*     5.5     2.0    -      -       -      -
   1207U  VAL*     5.3     8.5    -      -       -      -
   1227U  LEU      3.0     8.2    +      -       -      -
   1228U  THR*     3.3    34.0    -      -       -      +
   1229U  THR      3.5     4.9    +      -       -      -
   1233U  GLN*     5.6     5.2    -      -       -      -
   1273U  LEU*     1.3    74.1    -      -       -      +
   1275U  LEU*     1.3    63.0    +      -       -      +
   1276U  VAL*     3.4     4.8    +      -       -      +
   1304U  PHE*     3.6     8.7    -      -       -      +
----------------------------------------------------------
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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