Contacts of the strand formed by residues 214 - 219 (chain 1) in PDB entry 1KZB


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 LEU 214 (chain 1).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1141  SER*     4.3     6.3    -      -       -      +
    1151  SER*     3.6    15.3    -      -       -      +
    1161  VAL      3.5    29.2    -      -       -      +
    1171  ARG      3.5    16.4    -      -       -      +
    1181  ARG*     3.0    27.2    -      -       +      +
    1511  ALA      5.2     0.2    -      -       -      -
    1521  LYS*     4.3    11.9    -      -       +      +
    1531  ASP*     3.6    35.4    -      -       +      +
    1541  VAL      3.3    10.3    +      -       -      +
    1551  ALA*     3.8     9.0    -      -       +      -
    1561  PHE*     2.9    23.0    +      -       -      -
    2131  PHE*     1.3    80.9    -      -       -      +
    2151  VAL*     1.3    61.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 215 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1131  MET      3.9     0.5    -      -       -      +
    1141  SER*     3.4     2.9    +      -       -      -
    1151  SER*     2.8    53.0    +      -       -      +
    1191  MET*     4.4     4.9    -      -       +      -
    1241  ALA*     3.5    32.8    -      -       +      -
    1271  LEU*     3.8    18.8    -      -       +      -
    1281  CYS*     3.9    15.9    -      -       -      -
    1351  VAL*     3.9    13.0    -      -       +      -
    1551  ALA*     4.4     0.2    -      -       -      -
    1561  PHE*     4.3     5.8    -      -       +      +
    2131  PHE      5.0     0.7    -      -       -      +
    2141  LEU*     1.3    76.9    -      -       -      +
    2161  VAL*     1.3    75.0    +      -       -      +
    2171  CYS*     4.1     6.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 216 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1121  PHE*     4.1     7.2    -      -       +      -
    1131  MET      3.3    10.5    -      -       -      +
    1141  SER*     4.4     4.5    -      -       -      -
    1351  VAL*     3.7     8.8    -      -       -      +
    1361  ALA*     2.8    37.6    +      -       +      +
    1471  ILE*     3.7    28.9    -      -       +      -
    1501  VAL*     3.7    19.3    -      -       +      -
    1511  ALA*     3.9    16.2    -      -       +      -
    1551  ALA*     3.8    19.5    -      -       +      -
    1561  PHE      3.9     8.0    +      -       -      +
    1571  LEU*     5.9     0.2    -      -       +      -
    2151  VAL*     1.3    78.2    -      -       -      +
    2171  CYS*     1.3    67.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 217 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1111  TYR      3.7     0.5    -      -       -      +
    1121  PHE*     3.4     6.2    -      -       -      -
    1131  MET      2.7    32.5    +      -       -      +
    1271  LEU*     4.4     0.9    -      -       -      -
    1281  CYS*     2.0    55.6    -      -       +      -
    1341  THR      3.3     4.5    -      -       -      -
    1361  ALA*     4.2     1.3    -      -       -      -
    2151  VAL*     4.4     7.9    -      -       -      -
    2161  VAL*     1.3    77.2    -      -       -      +
    2181  GLU*     1.3    59.5    +      -       -      +
    2191  PHE*     3.7    21.9    -      -       +      -
    1312  LEU*     4.0    24.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 218 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1101  LYS*     3.5    44.6    +      -       +      -
    1111  TYR      3.4     3.6    -      -       -      -
    1121  PHE*     3.7     8.8    -      -       +      -
    1331  GLY*     3.4     5.7    -      -       -      -
    1341  THR*     2.6    51.4    +      -       +      +
    1351  VAL      4.3     0.5    -      -       -      +
    1361  ALA*     3.5     9.3    -      -       -      -
    1371  THR*     2.9    35.1    +      -       -      +
    1391  ARG*     5.4     4.9    +      -       -      -
    2171  CYS*     1.3    73.4    -      -       -      +
    2191  PHE*     1.3    66.2    +      -       -      +
    2201  SER*     6.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 219 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1101  LYS*     3.2     6.6    -      -       -      +
    1111  TYR*     2.7    49.3    +      -       +      +
    1131  MET*     3.4    31.2    -      -       +      -
    1281  CYS      4.1     2.9    -      -       -      -
    1311  LEU*     3.4    34.1    -      -       +      -
    1321  GLN      4.4     2.2    -      -       -      -
    1331  GLY*     3.5    26.0    -      -       -      -
    2171  CYS*     3.7    30.1    -      -       +      -
    2181  GLU*     1.3    73.4    -      -       -      +
    2201  SER*     1.3    61.1    +      -       -      +
    1132  MET*     3.4    36.8    -      -       +      -
    1312  LEU*     4.0    17.3    -      -       +      -
----------------------------------------------------------
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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