Contacts of the strand formed by residues 1531 - 1535 (chain E) in PDB entry 6C3P


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 THR1531 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1341E  GLN      4.3     2.9    +      -       -      -
   1342E  GLY      4.5     6.3    -      -       -      +
   1344E  ILE*     5.6     2.9    -      -       +      -
   1368E  ILE*     4.8     9.4    -      -       +      -
   1369E  ALA      4.1     8.1    -      -       -      +
   1370E  PRO*     2.2    47.1    +      -       +      +
   1371E  GLY      4.1     5.8    -      -       -      +
   1372E  GLN      3.4     3.8    -      -       -      -
   1374E  ILE*     5.8     0.7    -      -       +      -
   1500E  SER      2.3    19.0    +      -       -      -
   1501E  ILE*     3.0    46.0    -      -       +      +
   1502E  PHE      3.1     4.9    +      -       -      +
   1529E  ASP      3.6     3.1    +      -       -      -
   1530E  ARG*     1.3    66.5    -      -       -      +
   1532E  VAL*     1.3    64.4    +      -       -      +
   1533E  VAL*     4.3     5.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL1532 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1371E  GLY      4.8     0.3    -      -       -      +
   1372E  GLN      3.1    11.1    +      -       -      +
   1373E  LYS*     3.7     5.9    -      -       +      -
   1374E  ILE*     3.4    26.2    +      -       -      +
   1502E  PHE*     3.3    51.4    -      -       +      +
   1504E  MET*     4.2    12.3    -      -       +      -
   1523E  VAL*     5.6     2.2    -      -       +      -
   1524E  MET*     6.2     2.5    -      -       +      -
   1527E  PHE*     4.4    13.9    -      -       +      +
   1530E  ARG*     4.4     7.6    -      -       +      -
   1531E  THR*     1.3    78.2    -      -       -      +
   1533E  VAL*     1.3    75.3    +      -       -      +
   1534E  THR*     4.1    13.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL1533 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1344E  ILE*     5.3     7.4    -      -       +      -
   1368E  ILE*     4.9     9.6    -      -       +      -
   1374E  ILE*     3.7    24.2    -      -       +      -
   1376E  ILE*     3.7    31.6    -      -       +      -
   1387E  PHE*     5.4     0.4    -      -       +      -
   1391E  PHE*     4.5    17.9    -      -       +      -
   1502E  PHE      2.9    12.5    +      -       -      +
   1503E  ILE*     3.2    25.9    -      -       +      +
   1504E  MET      3.0    26.3    +      -       -      -
   1531E  THR*     5.4     7.4    -      -       +      +
   1532E  VAL*     1.3    77.9    -      -       -      +
   1534E  THR*     1.3    63.3    +      -       -      +
   1535E  ILE*     5.7     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR1534 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1373E  LYS*     5.4     0.9    -      -       +      -
   1374E  ILE      2.8    23.8    +      -       -      +
   1375E  GLY*     3.2     8.7    -      -       -      -
   1376E  ILE      2.8    28.0    +      -       -      +
   1504E  MET*     4.3    11.7    -      -       -      +
   1520E  GLN*     4.9    11.2    -      -       -      +
   1524E  MET*     4.6    19.3    -      -       +      -
   1532E  VAL*     4.1    19.5    -      -       +      +
   1533E  VAL*     1.3    77.4    -      -       -      +
   1535E  ILE*     1.3    66.6    -      -       -      +
   1536E  ALA*     3.9     3.5    +      -       -      +
   1541E  THR*     6.3     2.2    -      -       -      -
   1542E  ILE*     4.6     6.6    -      -       -      +
   1545E  ALA*     4.6     4.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE1535 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1376E  ILE*     3.4    33.0    -      -       +      +
   1384E  LYS*     3.6    52.9    -      -       +      +
   1387E  PHE*     6.2     0.4    -      -       +      -
   1388E  SER*     4.9     7.2    -      -       -      -
   1503E  ILE*     5.1     5.2    -      -       +      -
   1504E  MET*     2.9    27.4    +      -       -      +
   1505E  ASP*     3.5    18.6    -      -       +      +
   1506E  GLU*     3.1    38.6    +      -       +      +
   1507E  ALA      4.2     1.9    +      -       -      -
   1533E  VAL      4.0     0.4    +      -       -      -
   1534E  THR*     1.3    76.1    -      -       -      +
   1536E  ALA*     1.3    65.8    +      -       -      +
----------------------------------------------------------
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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