Contacts of the strand formed by residues 1548 - 1552 (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 LEU1548 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1368H  LEU*     4.4    18.8    -      -       +      +
   1370H  SER*     5.1     7.9    -      -       -      +
   1373H  GLN*     3.3    36.6    -      -       -      +
   1374H  LYS      4.0     3.0    +      -       -      -
   1375H  ILE*     3.5    28.1    -      -       +      +
   1376H  GLY      2.9    24.3    +      -       -      +
   1547H  ASP*     1.3    80.8    -      -       +      +
   1549H  VAL*     1.3    60.3    +      -       -      +
   1550H  MET*     5.6     0.4    -      -       -      -
   1559H  GLU*     5.5    10.1    -      -       +      +
   1560H  PHE      3.7     3.8    -      -       -      +
   1561H  ASP*     3.2    37.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL1549 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1376H  GLY*     3.1    13.9    -      -       -      +
   1378H  CYS*     5.0     5.4    -      -       -      -
   1543H  ILE*     3.5    38.6    -      -       +      +
   1546H  ALA*     3.7    19.3    -      -       +      +
   1547H  ASP      4.3     2.7    -      -       -      +
   1548H  LEU*     1.3    76.8    -      -       -      +
   1550H  MET*     1.3    60.4    +      -       -      +
   1551H  VAL      4.3     0.6    +      -       -      -
   1558H  LEU      4.1     0.5    -      -       -      +
   1559H  GLU*     4.5     0.9    -      -       -      -
   1560H  PHE*     2.9    39.1    +      -       +      +
   1566H  LEU*     3.8    34.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET1550 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1367H  ALA*     4.0    13.0    -      -       +      -
   1369H  ILE*     4.4    12.8    -      -       +      -
   1375H  ILE*     3.8    22.9    -      -       +      -
   1376H  GLY      2.9     9.3    +      -       -      +
   1377H  ILE*     3.2    36.3    -      -       +      +
   1378H  CYS*     2.9    26.9    +      -       -      -
   1388H  PHE*     4.5    13.2    -      -       +      -
   1534H  VAL*     5.1     0.2    -      -       +      -
   1548H  LEU      5.3     0.7    -      -       -      +
   1549H  VAL*     1.3    73.8    -      -       -      +
   1551H  VAL*     1.3    59.4    +      -       -      +
   1557H  ILE*     3.8    22.9    -      -       +      -
   1558H  LEU      3.1    12.3    -      -       -      +
   1559H  GLU*     3.6    35.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL1551 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1378H  CYS*     3.6    22.2    -      -       -      +
   1379H  GLY*     5.0     2.5    -      -       -      -
   1549H  VAL      4.4     0.4    +      -       -      +
   1550H  MET*     1.3    71.0    -      -       -      +
   1552H  LEU*     1.3    75.0    +      -       -      +
   1553H  LYS*     3.7    10.4    +      -       +      +
   1557H  ILE*     3.2     4.0    -      -       -      -
   1558H  LEU*     2.9    44.7    +      -       +      +
   1560H  PHE*     4.8     4.0    -      -       +      -
   1570H  LYS*     4.0    27.6    -      -       -      +
   1574H  PHE*     5.2    14.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU1552 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1362H  LEU*     4.1    20.0    -      -       +      -
   1377H  ILE*     4.2    13.9    -      -       +      -
   1378H  CYS      2.9    14.1    +      -       -      +
   1379H  GLY*     4.0     6.9    -      -       -      -
   1380H  ARG      4.8     0.9    +      -       -      -
   1383H  SER*     3.2    25.8    +      -       -      +
   1384H  GLY*     3.5     9.4    -      -       -      +
   1385H  LYS*     3.4    40.4    -      -       +      +
   1388H  PHE*     5.0     6.3    -      -       +      -
   1550H  MET      3.9     0.6    +      -       -      -
   1551H  VAL*     1.3    83.7    -      -       -      +
   1553H  LYS*     1.3    60.6    +      -       -      +
   1555H  GLY      4.8     1.1    -      -       -      +
   1556H  ALA      3.2    14.8    -      -       -      +
   1557H  ILE*     3.6    30.0    -      -       +      +
----------------------------------------------------------
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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