Contacts of the strand formed by residues 1342 - 1348 (chain C) in PDB entry 3B13


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 TYR1342 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1340C  PRO*     4.0    18.4    -      -       +      -
   1341C  ASP*     1.3    76.7    +      -       -      +
   1343C  PHE*     1.3    58.6    +      -       -      +
   1362C  ILE*     4.2     2.0    -      -       +      -
   1363C  TYR      3.3     3.6    -      -       -      +
   1364C  ARG*     3.4    50.5    +      -       +      -
   1410C  THR*     3.2     8.3    -      -       -      +
   1411C  VAL*     2.7    53.3    +      -       +      +
   1413C  PRO*     3.9    29.4    -      -       +      +
   1436C  SER      2.6    30.8    +      -       -      -
   1437C  ASN*     3.9     1.9    -      -       -      -
   1439C  VAL*     3.7    11.4    -      -       +      +
   1442C  PHE*     3.6    20.0    -      +       +      -
   1475C  LEU*     3.8    23.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with PHE1343 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1341C  ASP*     3.8    25.4    -      -       +      -
   1342C  TYR*     1.3    74.5    -      -       -      +
   1344C  ALA*     1.3    59.6    +      -       -      +
   1345C  VAL      4.0     0.3    +      -       -      -
   1361C  PHE      3.6     0.5    -      -       -      +
   1362C  ILE*     3.5     2.5    -      -       -      -
   1363C  TYR*     2.9    41.6    +      -       +      +
   1365C  GLY*     3.7    24.5    -      -       -      -
   1369C  GLU*     3.9     7.4    -      -       -      -
   1370C  ARG*     3.8     7.4    -      -       -      -
   1371C  ARG*     3.3    44.2    -      -       +      -
   1374C  PHE*     3.5    49.1    -      +       +      -
   1408C  CYS*     4.3     6.3    -      -       -      -
   1409C  PHE      3.5     5.4    -      -       -      +
   1410C  THR*     3.6    20.4    -      -       -      -
   1411C  VAL*     4.3     4.0    -      -       -      -
     26D  ASN*     4.5     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA1344 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1343C  PHE*     1.3    71.8    -      -       -      +
   1345C  VAL*     1.3    62.2    +      -       -      +
   1346C  GLY      4.2     0.4    -      -       -      -
   1360C  VAL*     4.3     9.0    -      -       +      -
   1361C  PHE      3.4     5.6    -      -       -      +
   1362C  ILE*     4.0    13.2    -      -       +      -
   1407C  GLN      3.6     0.8    -      -       -      +
   1408C  CYS*     3.1     7.6    -      -       -      +
   1409C  PHE*     2.8    65.8    +      -       +      +
   1411C  VAL*     3.9    13.2    -      -       +      +
   1469C  PHE*     4.9     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL1345 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1343C  PHE      4.8     0.4    -      -       -      +
   1344C  ALA*     1.3    78.3    -      -       -      +
   1346C  GLY*     1.3    67.0    +      -       -      +
   1347C  TYR*     3.5    37.4    +      -       +      +
   1359C  LYS      3.8     0.9    -      -       -      +
   1360C  VAL*     3.3     4.8    -      -       -      +
   1361C  PHE*     2.9    38.2    +      -       -      +
   1363C  TYR*     4.0    27.4    -      -       +      -
   1374C  PHE*     4.0    21.1    -      -       +      -
   1378C  LEU*     4.1    12.3    -      -       +      -
   1406C  ILE*     3.9    10.5    -      -       +      -
   1407C  GLN      3.3     2.9    -      -       -      -
   1408C  CYS*     4.1     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY1346 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1344C  ALA      4.2     0.4    -      -       -      -
   1345C  VAL*     1.3    73.0    -      -       -      +
   1347C  TYR*     1.3    61.7    +      -       -      -
   1348C  TYR*     3.5    25.1    -      -       -      -
   1359C  LYS      3.6     6.3    -      -       -      -
   1360C  VAL*     4.1     7.6    -      -       -      +
   1405C  TYR      3.7     0.5    -      -       -      +
   1406C  ILE*     3.3    12.1    -      -       -      +
   1407C  GLN*     2.8    38.2    +      -       -      +
   1409C  PHE*     5.8     1.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR1347 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1345C  VAL*     3.5    26.9    -      -       +      +
   1346C  GLY*     1.3    72.9    -      -       -      -
   1348C  TYR*     1.3    56.3    +      -       -      +
   1352C  PHE*     3.4    36.1    -      +       +      -
   1356C  LEU*     3.7    26.9    -      -       +      +
   1358C  ASN*     2.6    37.4    +      -       -      -
   1359C  LYS      3.1     6.6    +      -       -      +
   1361C  PHE*     3.7    37.0    -      +       -      -
   1363C  TYR*     3.0    26.1    +      -       -      -
   1378C  LEU*     3.9     6.2    -      -       +      +
   1382C  PHE*     3.7    33.5    -      +       -      -
   1405C  TYR      4.0     0.2    -      -       -      -
   1406C  ILE*     3.9    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR1348 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1346C  GLY*     3.5    25.6    -      -       -      -
   1347C  TYR*     1.3    76.3    -      -       -      +
   1349C  GLY*     1.3    62.1    +      -       -      +
   1352C  PHE*     3.0     9.4    -      -       -      -
   1358C  ASN*     3.0    36.1    -      -       -      +
   1360C  VAL*     3.5    20.0    -      -       +      +
   1388C  MET*     4.3     9.2    -      -       -      -
   1393C  ALA*     5.0     3.1    -      -       -      +
   1394C  PRO*     3.6    37.8    -      -       +      +
   1398C  VAL*     4.7    11.9    -      -       +      +
   1399C  LYS*     3.9    15.3    -      -       +      -
   1404C  GLN*     3.6     0.5    -      -       -      -
   1405C  TYR*     2.9    53.1    +      -       +      +
   1407C  GLN*     3.5    25.6    +      -       +      -
----------------------------------------------------------
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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