Contacts of the strand formed by residues 38 - 42 (chain D) in PDB entry 1QO0


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 SER 38 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11D  ARG      4.5     7.7    +      -       -      -
     12D  GLU      5.4     1.1    +      -       -      -
     13D  LEU      3.0    13.5    +      -       -      +
     14D  GLN*     3.6    27.6    +      -       -      -
     15D  VAL*     2.8    30.4    +      -       -      +
     36D  GLY      4.0     0.2    +      -       -      -
     37D  CYS*     1.3    71.6    -      -       -      +
     39D  VAL*     1.3    58.0    +      -       -      +
     40D  ARG*     5.9     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 39 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15D  VAL*     3.3     7.0    -      -       +      +
     17D  VAL*     4.2    10.8    -      -       +      -
     29D  VAL*     4.0    31.4    -      -       +      +
     32D  LEU*     3.5    34.1    -      -       +      -
     33D  ILE*     3.8    21.9    -      -       +      +
     37D  CYS*     3.4    19.0    +      -       +      +
     38D  SER*     1.3    75.3    -      -       -      +
     40D  ARG*     1.3    78.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 40 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14D  GLN*     6.2     4.7    -      -       +      -
     15D  VAL      2.8     8.8    +      -       -      +
     16D  LEU*     3.2    12.8    -      -       +      -
     17D  VAL*     2.6    33.8    +      -       -      +
     29D  VAL*     5.0     0.9    -      -       -      -
     38D  SER      5.9     0.4    -      -       -      -
     39D  VAL*     1.3    83.8    +      -       -      +
     41D  GLN*     1.3    59.3    +      -       -      +
     42D  CYS*     6.2     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 41 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17D  VAL*     3.4    13.0    -      -       +      +
     19D  ASN      4.6     4.9    -      -       -      +
     21D  PRO*     3.9    19.1    -      -       -      +
     25D  SER*     3.8    26.6    -      -       -      -
     26D  ASP*     4.7    11.4    +      -       -      +
     29D  VAL*     3.8    26.9    -      -       +      +
     40D  ARG*     1.3    81.5    -      -       -      +
     42D  CYS*     1.3    64.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 42 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16D  LEU*     4.1    26.0    -      -       +      -
     17D  VAL      3.0     7.3    +      -       -      +
     18D  LEU*     3.7     5.8    -      -       +      -
     19D  ASN      3.4    19.7    +      -       -      +
     40D  ARG*     6.2     0.4    -      -       +      -
     41D  GLN*     1.3    77.0    -      -       -      +
     43D  TRP*     1.3    69.2    +      -       -      +
     44D  PRO      4.0     4.7    -      -       -      -
     46D  PRO*     3.8    35.4    -      -       -      -
     49D  PHE*     6.0     0.2    -      -       -      -
----------------------------------------------------------
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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