Contacts of the strand formed by residues 34 - 40 (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 34 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33H  TYR*     1.3    73.1    -      -       -      +
     35H  TRP*     1.3    67.8    +      -       -      +
     36H  ASN*     3.6     8.7    +      -       -      +
     51H  TYR*     4.1    31.4    -      -       +      -
     52H  ILE      3.8     4.7    -      -       -      -
     53H  SER*     4.1     5.8    -      -       -      +
     98H  ARG*     3.6     3.6    -      -       -      +
     99H  GLY      3.0    32.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 35 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2H  VAL*     4.8     1.8    -      -       +      -
      4H  LEU*     4.4     9.2    -      -       +      -
     24H  VAL*     4.0    27.6    -      -       +      -
     27H  TYR*     3.8    32.1    -      +       +      -
     29H  ILE*     3.6    40.0    +      -       +      -
     32H  ASP      3.1    24.6    +      -       -      -
     33H  TYR*     3.2    11.5    +      -       +      -
     34H  ALA*     1.3    75.3    -      -       -      +
     36H  ASN*     1.3    60.6    +      -       -      +
     50H  ALA      4.1     0.2    -      -       -      +
     51H  TYR*     3.0     4.6    -      -       -      -
     52H  ILE*     2.8    51.1    +      -       +      +
     53H  SER      4.6     0.4    -      -       -      -
     54H  TYR      4.5     0.9    -      -       -      -
     70H  ILE*     4.2     1.0    -      -       -      +
     79H  PHE*     3.6    41.3    -      +       +      -
     97H  ALA      3.6     3.6    -      -       -      -
     98H  ARG*     3.7    38.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 36 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34H  ALA*     3.6    11.9    +      -       -      +
     35H  TRP*     1.3    73.6    -      -       -      +
     37H  TRP*     1.4    62.9    +      -       -      +
     38H  ILE*     4.4     7.4    -      -       +      -
     48H  TRP*     2.8    27.5    +      -       +      +
     50H  ALA      3.2     4.7    -      -       -      +
     51H  TYR*     2.8    20.8    -      -       -      +
     79H  PHE*     3.6     3.1    -      -       -      -
     96H  CYS*     3.0     9.9    -      -       -      +
     97H  ALA      2.7    38.9    +      -       -      +
     99H  GLY*     3.6    20.6    -      -       -      +
    103H  PHE*     3.3    33.4    -      -       +      -
     96L  LEU*     5.4     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 37 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6H  GLN*     4.1    12.3    -      -       +      -
     20H  LEU*     3.2    45.1    -      -       +      -
     21H  THR      3.9     6.3    -      -       -      -
     22H  CYS*     3.4    29.4    -      -       +      -
     36H  ASN*     1.4    71.1    -      -       -      +
     38H  ILE*     1.3    64.0    +      -       -      +
     48H  TRP*     3.9     0.5    -      -       -      -
     49H  MET*     2.9    42.7    +      -       +      +
     50H  ALA      2.8    12.3    +      -       -      +
     70H  ILE*     3.7    20.4    -      -       +      -
     79H  PHE*     3.1    32.7    -      +       -      -
     80H  PHE      3.8     0.6    -      -       -      -
     81H  LEU*     3.5    41.3    -      -       +      +
     94H  TYR*     4.5    12.8    -      -       +      -
     95H  TYR      3.2    32.5    -      -       -      -
     96H  CYS*     4.0     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 38 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36H  ASN*     4.4     3.4    -      -       +      -
     37H  TRP*     1.3    80.7    -      -       -      +
     39H  ARG*     1.3    62.2    +      -       -      +
     46H  LEU*     4.5     6.7    -      -       +      -
     47H  GLU      3.2    27.1    -      -       -      +
     48H  TRP*     3.9    15.0    -      -       +      +
     49H  MET*     4.4     3.3    -      -       -      +
     94H  TYR*     3.6     0.9    -      -       -      +
     95H  TYR*     2.6    44.3    +      -       +      +
     97H  ALA*     4.3    11.2    -      -       +      -
    103H  PHE*     3.7    45.8    -      -       +      -
    106H  TRP*     3.9    28.5    -      -       +      -
     98L  PHE*     4.4     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 39 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38H  ILE*     1.3    76.6    -      -       -      +
     40H  GLN*     1.3    60.5    +      -       -      +
     41H  PHE*     3.2    27.5    -      -       +      -
     45H  LYS      3.8     0.9    -      -       -      +
     46H  LEU*     3.6     3.1    -      -       -      +
     47H  GLU*     2.8    67.9    +      -       -      +
     49H  MET*     3.7    20.1    -      -       -      -
     64H  LEU*     3.5    22.9    -      -       -      +
     67H  ARG*     5.2     2.8    -      -       -      +
     83H  LEU*     5.4     3.2    -      -       -      +
     89H  GLU      5.3     0.2    +      -       -      -
     90H  ASP*     3.2    35.0    +      -       -      +
     92H  ALA*     4.8     3.4    -      -       +      -
     93H  ILE      3.2    10.5    -      -       -      +
     94H  TYR*     3.3    41.1    +      -       +      -
     95H  TYR*     5.0     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 40 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39H  ARG*     1.3    76.0    -      -       -      +
     41H  PHE*     1.3    63.6    +      -       -      +
     44H  ASN*     3.0    34.2    +      -       -      +
     45H  LYS      3.3    11.9    -      -       -      +
     46H  LEU*     3.3    20.7    -      -       +      +
     92H  ALA*     2.9    20.7    -      -       -      +
     93H  ILE*     2.7    35.6    +      -       +      +
     95H  TYR*     3.6    22.6    +      -       +      -
     38L  GLN*     2.9    43.1    -      -       -      +
----------------------------------------------------------
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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