Contacts of the strand formed by residues 1532 - 1536 (chain H) in PDB entry 5YWB


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 THR1532 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1343H  GLY*     3.7    17.1    +      -       -      +
   1345H  ILE*     5.2     1.6    -      -       +      -
   1369H  ILE*     3.8    22.9    -      -       +      -
   1370H  SER      4.0     0.9    +      -       -      -
   1372H  GLY*     3.1    23.0    +      -       -      -
   1373H  GLN      3.2    23.1    +      -       -      +
   1375H  ILE*     4.1     6.5    -      -       +      -
   1501H  SER      3.3     4.7    +      -       -      +
   1502H  ILE*     3.5    22.8    -      -       +      -
   1503H  PHE*     2.9    24.5    +      -       -      +
   1531H  ARG*     1.3    72.6    -      -       -      +
   1533H  VAL*     1.3    64.2    +      -       -      +
   1534H  VAL*     4.4     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL1533 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1373H  GLN      3.9     2.8    +      -       -      -
   1374H  LYS*     3.6    14.8    -      -       +      +
   1375H  ILE*     2.7    34.0    +      -       -      +
   1503H  PHE*     3.6    32.3    -      -       +      +
   1505H  MET*     4.4    15.5    -      -       +      -
   1524H  VAL      6.0     0.2    -      -       -      +
   1525H  MET*     5.3    10.3    -      -       +      -
   1528H  PHE*     4.5    19.7    -      -       +      +
   1531H  ARG      3.7    10.9    +      -       -      +
   1532H  THR*     1.3    81.6    -      -       -      +
   1534H  VAL*     1.3    61.2    +      -       -      +
   1535H  THR*     3.8    22.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL1534 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1345H  ILE*     5.1     5.4    -      -       +      -
   1369H  ILE*     4.0    15.9    -      -       +      -
   1375H  ILE*     3.2    24.9    -      -       +      +
   1377H  ILE*     3.6    33.7    -      -       +      -
   1388H  PHE*     4.8    10.1    -      -       +      -
   1392H  PHE*     6.1     1.8    -      -       +      -
   1502H  ILE*     5.3     2.5    -      -       +      -
   1503H  PHE      2.9    15.3    +      -       -      +
   1504H  ILE*     3.4    21.0    -      -       +      +
   1505H  MET*     2.9    24.9    +      -       -      +
   1532H  THR*     4.4     8.1    -      -       +      -
   1533H  VAL*     1.3    76.6    -      -       -      +
   1535H  THR*     1.3    62.3    +      -       -      +
   1536H  ILE*     5.0     2.4    -      -       +      +
   1550H  MET*     5.1     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR1535 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1374H  LYS*     6.6     0.2    -      -       +      -
   1375H  ILE      2.9    15.7    +      -       -      +
   1376H  GLY*     3.8     7.4    -      -       -      -
   1377H  ILE*     3.0    29.5    +      -       -      +
   1505H  MET*     3.6    28.5    -      -       +      -
   1521H  GLN*     5.3     1.6    -      -       -      +
   1525H  MET*     4.7    14.4    -      -       +      -
   1533H  VAL*     3.8    22.2    -      -       +      +
   1534H  VAL*     1.3    75.5    -      -       -      +
   1536H  ILE*     1.3    67.8    +      -       -      +
   1537H  ALA*     5.1     5.5    -      -       -      +
   1542H  THR*     5.4     6.9    +      -       -      -
   1543H  ILE*     4.9     7.2    -      -       -      +
   1546H  ALA*     5.7     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1536 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1377H  ILE*     3.5    43.3    -      -       +      +
   1378H  CYS*     4.8     1.1    -      -       -      +
   1385H  LYS*     3.5    54.1    -      -       +      +
   1388H  PHE*     6.1     1.8    -      -       +      -
   1389H  SER*     4.6     9.0    -      -       -      -
   1504H  ILE*     5.2     4.0    -      -       +      -
   1505H  MET      2.9    18.6    +      -       -      +
   1506H  ASP*     3.6    28.3    -      -       +      +
   1507H  GLU*     2.8    37.0    +      -       -      +
   1534H  VAL*     5.0     3.1    -      -       +      +
   1535H  THR*     1.3    73.3    -      -       -      +
   1537H  ALA*     1.3    56.1    +      -       -      +
----------------------------------------------------------
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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