Contacts of the strand formed by residues 98 - 103 (chain B) in PDB entry 1KLG


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 LYS 98 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  SER*     4.6    13.4    +      -       -      -
     96A  PRO*     4.4    24.2    -      -       +      -
     96B  GLU      3.9     1.2    +      -       -      -
     97B  PRO*     1.3    72.0    -      -       -      +
     99B  VAL*     1.3    62.6    +      -       -      +
    100B  THR*     4.8    11.4    -      -       +      -
    118B  SER      3.2     6.3    -      -       -      +
    119B  VAL*     3.4     1.0    -      -       -      -
    120B  SER*     2.8    45.8    +      -       -      +
    121B  GLY*     5.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 99 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97B  PRO*     3.6    13.6    +      -       +      +
     98B  LYS*     1.3    80.6    -      -       -      +
    100B  THR*     1.3    66.6    +      -       -      +
    117B  CYS*     3.8    26.2    -      -       -      -
    118B  SER      3.3     4.0    -      -       -      +
    119B  VAL*     4.3     9.4    -      -       +      -
    173B  CYS*     4.7     1.3    -      -       -      +
    175B  VAL*     4.2    21.1    -      -       +      -
    184B  LEU*     4.2    23.1    -      -       +      +
    185B  THR      5.9     0.2    -      -       -      -
    186B  VAL*     3.7    30.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 100 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  PRO*     4.2    15.3    -      -       +      -
     98A  GLU*     6.1     0.7    -      -       -      +
     98B  LYS*     4.8     9.4    -      -       +      -
     99B  VAL*     1.3    76.6    -      -       -      +
    101B  VAL*     1.3    70.2    +      -       -      +
    102B  TYR*     4.2    14.0    -      -       +      -
    116B  VAL      3.6     0.5    -      -       -      +
    117B  CYS*     3.6     2.6    -      -       -      -
    118B  SER*     2.8    53.2    +      -       -      +
    186B  VAL*     4.7     3.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 101 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100B  THR*     1.3    83.2    +      -       -      +
    102B  TYR*     1.3    71.5    +      -       -      +
    115B  LEU*     5.2     2.9    -      -       +      -
    116B  VAL      3.3     8.3    -      -       -      +
    117B  CYS*     3.9     6.7    -      -       -      -
    131B  TRP*     4.0    17.3    -      -       +      -
    173B  CYS*     3.8    22.7    -      -       +      -
    186B  VAL*     3.4    37.4    -      -       +      +
    187B  GLU      4.9     1.3    -      -       -      +
    188B  TRP*     4.1    34.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 102 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  PRO*     4.5    16.0    -      -       +      +
     98A  GLU*     6.0     1.8    -      -       -      -
    100B  THR*     4.2    15.7    -      -       +      +
    101B  VAL*     1.3    82.8    -      -       -      +
    103B  PRO*     1.3    84.1    -      -       +      +
    105B  LYS*     4.0    27.3    +      -       -      -
    115B  LEU*     4.7     4.7    -      -       -      -
    116B  VAL*     2.8    55.1    +      -       +      +
    118B  SER*     4.0    24.9    -      -       -      -
    158B  LEU*     4.5     8.3    -      -       -      +
    188B  TRP*     4.6     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 103 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102B  TYR*     1.3   101.1    -      -       +      +
    104B  SER*     1.3    66.7    +      -       -      +
    105B  LYS*     3.9     2.9    +      -       -      +
    107B  GLN*     4.8     1.3    -      -       -      +
    113B  ASN*     3.9    23.8    -      -       -      +
    114B  LEU      3.5     6.3    -      -       -      +
    115B  LEU*     4.2     9.2    -      -       +      -
    188B  TRP*     3.8    26.9    -      -       +      -
----------------------------------------------------------
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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