Contacts of the strand formed by residues 92 - 99 (chain H) in PDB entry 1KCU


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 ALA 92 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39H  ARG*     4.8     3.4    -      -       +      -
     40H  GLN      2.9    22.9    -      -       -      +
     41H  PHE*     4.0    17.0    -      -       +      +
     42H  PRO*     5.1     2.5    -      -       -      -
     90H  ASP      3.0     9.2    +      -       -      +
     91H  THR*     1.3    77.2    -      -       -      +
     93H  ILE*     1.3    68.6    +      -       -      +
     94H  TYR*     3.5    13.2    -      -       +      -
    111H  THR*     3.7     3.1    -      -       -      +
    112H  LEU      3.0    30.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 93 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39H  ARG*     3.2     3.0    -      -       -      -
     40H  GLN*     2.7    49.6    +      -       +      +
     92H  ALA*     1.3    81.6    -      -       -      +
     94H  TYR*     1.3    64.0    +      -       -      +
     95H  TYR*     3.5    40.8    +      -       +      +
    108H  ALA      5.1     0.9    -      -       -      +
    109H  GLY*     4.5     2.2    -      -       -      -
    110H  THR      3.7    15.9    -      -       -      +
    111H  THR*     3.9    19.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 94 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6H  GLN*     3.8     2.3    -      -       -      +
     20H  LEU*     4.2    14.4    -      -       +      -
     37H  TRP*     4.5    11.0    -      -       +      -
     38H  ILE      3.8     2.0    -      -       -      -
     39H  ARG*     3.3    28.1    +      -       +      -
     49H  MET*     3.5    31.9    -      -       +      -
     81H  LEU*     4.3     0.7    -      -       +      -
     83H  LEU*     3.8    25.8    -      -       +      +
     90H  ASP*     2.5    38.0    +      -       -      +
     92H  ALA*     3.5    22.2    -      -       +      -
     93H  ILE*     1.3    73.4    -      -       -      +
     95H  TYR*     1.3    60.4    +      -       -      +
    109H  GLY*     3.2     2.9    -      -       -      -
    110H  THR*     2.8    55.6    +      -       +      +
    112H  LEU*     3.8    20.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 95 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6H  GLN*     3.8     2.9    -      -       -      -
     37H  TRP*     3.2    10.7    -      -       -      -
     38H  ILE*     2.6    47.3    +      -       +      +
     39H  ARG*     4.9     0.7    -      -       -      -
     40H  GLN*     3.6    35.3    +      -       +      -
     46H  LEU*     5.1     2.0    -      -       +      -
     93H  ILE*     3.5    34.7    -      -       +      +
     94H  TYR*     1.3    73.3    -      -       -      +
     96H  CYS*     1.3    59.2    +      -       -      +
    106H  TRP*     4.0    29.4    -      +       +      -
    107H  GLY      3.8     8.7    -      -       -      -
    108H  ALA      3.7     5.8    +      -       -      -
    109H  GLY*     3.4    25.1    -      -       -      -
     38L  GLN*     3.8     8.0    +      -       -      -
     42L  GLN      4.2     2.8    +      -       -      -
     43L  PRO*     3.5    29.6    -      -       +      +
     44L  PRO*     4.2     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 96 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4H  LEU*     3.4    20.7    -      -       -      +
      5H  GLN      4.3     1.6    -      -       -      -
      6H  GLN*     3.4    22.9    +      -       -      +
     22H  CYS*     2.1    55.2    -      -       +      -
     36H  ASN      3.0    11.4    -      -       -      +
     37H  TRP*     4.0    10.3    -      -       +      -
     79H  PHE*     3.8     2.0    -      -       +      -
     95H  TYR*     1.3    76.8    -      -       -      +
     97H  ALA*     1.3    64.2    +      -       -      +
    106H  TRP*     3.9     0.5    -      -       -      -
    107H  GLY      3.5    14.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 97 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4H  LEU*     3.3     9.7    -      -       -      +
     35H  TRP*     3.6     3.9    -      -       -      +
     36H  ASN*     2.7    43.6    +      -       +      +
     38H  ILE*     4.3    23.1    -      -       +      -
     79H  PHE*     4.6     0.5    -      -       -      -
     96H  CYS*     1.3    76.9    -      -       -      +
     98H  ARG*     1.3    63.6    +      -       -      +
    103H  PHE*     4.4     7.2    -      -       +      -
    105H  TYR      3.2    16.2    -      -       -      +
    106H  TRP*     4.3    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 98 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2H  VAL*     3.3    32.0    -      -       -      +
      4H  LEU*     3.7     2.5    -      -       +      +
     27H  TYR*     3.5    28.9    -      -       -      -
     33H  TYR*     3.1    58.1    +      -       +      -
     34H  ALA      3.6     4.3    -      -       -      +
     35H  TRP*     3.7    29.6    -      -       +      -
     36H  ASN*     4.2     0.9    -      -       -      -
     97H  ALA*     1.3    75.9    -      -       -      +
     99H  GLY*     1.3    63.2    +      -       -      +
    103H  PHE*     3.5     5.1    -      -       -      -
    104H  ASP*     2.5    69.0    +      -       -      -
    105H  TYR*     3.1    27.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 99 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33H  TYR*     3.3    24.5    -      -       -      -
     34H  ALA*     3.0    26.4    +      -       -      +
     36H  ASN*     3.6     7.9    -      -       -      +
     98H  ARG*     1.3    78.3    -      -       -      +
    100H  GLY*     1.4    56.0    +      -       -      -
    101H  THR      4.1     1.1    -      -       -      -
    102H  GLY      3.6     9.6    -      -       -      -
    103H  PHE*     3.8    15.9    -      -       -      -
    104H  ASP*     4.5     2.5    -      -       -      -
----------------------------------------------------------
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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