Contacts of the strand formed by residues 41 - 47 (chain D) in PDB entry 3IT8


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 HIS 41 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35D  TYR*     3.5    12.1    -      -       -      -
     36D  ASN*     2.9    23.6    +      -       -      +
     39D  THR*     3.1    32.3    +      -       +      +
     40D  ARG*     1.3    80.3    -      -       -      +
     42D  GLY*     1.3    73.1    +      -       -      +
     43D  ASN*     3.3    17.1    +      -       -      -
     67D  ASN*     3.6    22.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 42 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33D  ILE*     4.2     3.4    -      -       -      -
     34D  SER      3.3    10.3    -      -       -      -
     41D  HIS*     1.3    85.2    +      -       -      +
     43D  ASN*     1.3    67.2    +      -       -      +
     63D  ASP*     5.2     8.4    -      -       -      +
     66D  PHE*     3.7    23.8    -      -       -      -
     67D  ASN*     3.0    15.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 43 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33D  ILE*     3.3     7.2    -      -       -      +
     34D  SER*     3.0    29.3    +      -       -      +
     36D  ASN*     2.9    44.0    -      -       -      +
     39D  THR*     5.3     0.4    +      -       -      -
     41D  HIS*     3.3    14.9    +      -       -      -
     42D  GLY*     1.3    81.3    -      -       -      +
     44D  VAL*     1.3    66.2    +      -       -      +
     45D  ASN*     3.3    12.2    +      -       -      +
     63D  ASP*     6.3     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 44 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31D  THR*     4.5     5.6    -      -       +      -
     32D  LYS      3.5     5.8    -      -       -      +
     33D  ILE*     4.0    15.3    -      -       +      -
     43D  ASN*     1.3    73.8    -      -       -      +
     45D  ASN*     1.3    60.2    +      -       -      +
     46D  PHE      3.3    29.6    -      -       -      +
     47D  ARG*     4.5    23.1    -      -       +      +
     63D  ASP*     3.6    26.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 45 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32D  LYS*     2.8    38.9    +      -       +      +
     33D  ILE      3.7     0.2    -      -       -      -
     34D  SER*     2.5    44.1    +      -       -      +
     43D  ASN*     3.4    13.9    -      -       -      +
     44D  VAL*     1.3    75.7    -      -       -      +
     46D  PHE*     1.3    62.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 46 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29D  LEU*     3.6    48.5    -      -       +      -
     30D  VAL      4.1     3.1    -      -       -      -
     31D  THR*     3.3     5.2    -      -       -      -
     32D  LYS*     3.1    38.2    +      -       +      -
     44D  VAL*     3.3    12.0    -      -       -      +
     45D  ASN*     1.3    82.7    -      -       +      +
     47D  ARG*     1.3    76.3    +      -       -      +
     48D  ALA*     3.4    27.8    -      -       +      -
     49D  ASP*     5.6     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 47 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30D  VAL      3.3     6.5    -      -       -      -
     31D  THR*     2.3    52.3    +      -       -      +
     44D  VAL*     4.5    22.6    -      -       +      +
     46D  PHE*     1.3    84.8    -      -       -      +
     48D  ALA*     1.3    73.0    +      -       -      +
     49D  ASP*     3.3     3.3    +      -       -      -
     51D  PHE*     4.3    21.6    +      -       -      +
     53D  ILE*     3.3    37.4    -      -       -      +
     63D  ASP*     4.9     5.9    +      -       -      +
     64D  TYR*     3.5    13.3    +      -       -      -
----------------------------------------------------------
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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