Contacts of the strand formed by residues 225 - 230 (chain 1) in PDB entry 1K2I


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 PRO 225 (chain 1).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1631  LEU*     3.5    25.6    -      -       +      -
    1681  CYS*     4.0     8.3    -      -       -      -
    1711  TYR*     3.4    39.9    -      -       +      -
    1721  TRP*     3.1    35.1    +      -       -      +
    1821  CYS*     4.2     4.9    -      -       +      -
    1831  ALA      3.7     8.5    -      -       -      +
    1851  ALA*     3.9    11.4    -      -       +      +
    2161  GLY*     4.7     1.0    -      -       -      -
    2171  SER      5.0     0.5    +      -       -      -
    2241  THR*     1.3    95.6    -      -       +      +
    2261  GLY*     1.3    65.3    +      -       -      +
    2271  VAL*     4.1     0.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 226 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1821  CYS*     3.3     6.6    -      -       -      +
    1831  ALA      2.8    35.4    +      -       -      -
    1841  GLY*     4.7     0.4    -      -       -      -
    1891  SER*     5.7     4.0    +      -       -      -
    1901  SER*     6.0     3.6    -      -       -      -
    2151  TRP      4.0     5.6    -      -       -      -
    2161  GLY*     4.8     3.8    -      -       -      -
    2241  THR      3.7     2.0    +      -       -      -
    2251  PRO*     1.3    75.4    -      -       -      +
    2271  VAL*     1.3    60.4    +      -       -      -
    2281  TYR*     3.5    14.2    -      -       -      -
    4001  SN1      5.2     7.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 227 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1721  TRP*     3.9    22.4    -      -       +      +
    1761  ILE*     4.0     8.1    -      -       +      -
    1801  MET*     3.8    29.4    -      -       +      -
    1811  ILE      3.8     4.0    -      -       -      +
    1821  CYS*     4.4     4.0    -      -       -      +
    2131  VAL*     5.3     0.2    -      -       -      +
    2141  SER*     3.1     7.1    +      -       -      -
    2151  TRP*     2.7    91.9    +      -       +      +
    2251  PRO      4.4     0.4    -      -       -      +
    2261  GLY*     1.3    75.4    -      -       -      +
    2281  TYR*     1.3    68.7    -      -       -      +
    4001  SN1      5.1     0.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 228 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1381  THR*     4.1     4.9    -      -       -      +
    1601  LEU*     3.6    22.0    -      -       +      +
    1801  MET*     3.3     6.0    -      -       -      +
    1811  ILE*     2.8    49.4    +      -       +      +
    1831  ALA*     3.9    18.6    +      -       +      -
    1901  SER*     2.8    27.0    +      -       -      -
    1991  LEU*     3.7    31.6    -      -       +      -
    2111  GLY*     4.1     2.5    -      -       -      -
    2121  ILE      3.2    13.9    -      -       -      +
    2131  VAL*     3.6    41.1    -      -       +      -
    2141  SER*     4.1     2.9    -      -       -      -
    2261  GLY*     3.5    27.7    -      -       -      -
    2271  VAL*     1.3    76.8    -      -       -      +
    2291  ALA*     1.3    60.3    +      -       -      +
    4001  SN1      5.8     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 229 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1021  ASP*     3.7    35.4    -      -       +      +
    1791  ALA      3.7     7.2    -      -       -      +
    1801  MET*     4.6     2.2    -      -       -      +
    1811  ILE*     4.4     0.4    -      -       -      -
    2111  GLY*     3.1    24.8    -      -       -      -
    2121  ILE*     2.8    24.9    +      -       +      +
    2141  SER*     4.0     4.1    -      -       -      -
    2281  TYR*     1.3    69.8    -      -       -      +
    2301  ARG*     1.3    59.2    +      -       -      +
    2311  VAL*     3.2     4.5    +      -       -      +
    2341  LEU*     4.0    17.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 230 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1301  PHE      5.6     2.4    +      -       -      -
    1631  LEU      5.4     1.2    +      -       -      -
    1641  SER*     6.1     0.2    -      -       -      +
    1651  ASN*     2.7    36.4    +      -       -      +
    1781  ASP      3.3    16.5    +      -       -      -
    1791  ALA*     2.9    23.1    +      -       -      +
    1801  MET      3.0    21.7    +      -       -      +
    1811  ILE*     3.6    35.4    -      -       +      +
    2101  VAL*     3.9     6.1    -      -       +      +
    2281  TYR      3.3     1.8    +      -       -      -
    2291  ALA*     1.3    67.9    -      -       -      +
    2311  VAL*     1.3    63.7    +      -       -      +
    2321  THR*     3.4    23.1    +      -       -      +
    2331  ALA*     3.1    18.4    +      -       +      +
    2341  LEU*     3.5    15.4    -      -       -      +
----------------------------------------------------------
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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