Contacts of the strand formed by residues 38 - 44 (chain A) in PDB entry 6TD3


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 ARG 38 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  LYS*     3.5    32.5    -      -       +      +
     12A  PRO*     4.1    20.0    -      -       +      +
     34A  ALA*     3.5     0.5    -      -       -      -
     35A  LYS*     3.1    40.0    +      -       +      +
     37A  THR*     1.3    94.3    +      -       -      +
     39A  LEU*     1.3    60.5    +      -       -      +
     40A  GLU*     5.5     1.6    -      -       +      -
     54A  GLU*     2.8    41.2    +      -       -      +
     55A  VAL*     3.7     3.2    -      -       -      +
     56A  GLY*     3.5    31.6    -      -       -      +
     61A  ILE*     3.3    13.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 39 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  PHE*     5.8     0.7    -      -       +      -
     32A  LEU*     4.1    10.8    -      -       +      -
     33A  ILE      3.7     6.5    -      -       -      +
     34A  ALA*     4.5     1.6    -      -       +      +
     38A  ARG*     1.3    74.6    -      -       -      +
     40A  GLU*     1.3    74.3    +      -       -      +
     41A  ILE*     4.2    13.3    +      -       +      +
     53A  LYS      4.2     0.3    -      -       -      +
     54A  GLU*     3.4     4.7    +      -       -      -
     55A  VAL*     2.9    55.8    +      -       +      +
     57A  MET*     5.3     4.5    -      -       +      -
     61A  ILE*     4.3     9.2    -      -       +      -
     64A  MET*     3.9    27.1    -      -       -      -
     77A  LEU*     3.9    23.1    -      -       +      -
     79A  ILE*     4.0    13.7    -      -       +      -
     89A  LEU*     5.1     6.5    -      -       +      -
    100A  ILE*     6.0     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 40 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  LEU      3.9     0.7    -      -       -      +
     32A  LEU*     3.3     5.9    -      -       -      -
     33A  ILE*     2.9    43.6    +      -       +      +
     35A  LYS*     3.2    43.4    +      -       +      +
     38A  ARG*     5.5     1.3    -      -       +      -
     39A  LEU*     1.3    78.2    -      -       -      +
     41A  ILE*     1.3    60.4    +      -       -      +
     42A  TYR*     2.8    43.2    +      -       +      -
     53A  LYS      3.9     4.0    -      -       -      -
     54A  GLU*     3.8    26.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 41 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  PHE*     4.3    10.3    -      -       +      -
     24A  THR*     4.0    17.5    -      -       +      -
     30A  ASN*     4.5     0.9    -      -       -      +
     31A  LEU      4.0     1.8    -      -       -      -
     32A  LEU*     3.8    26.7    -      -       +      -
     39A  LEU*     4.5    16.2    -      -       +      +
     40A  GLU*     1.3    76.7    -      -       -      +
     42A  TYR*     1.3    70.0    +      -       -      +
     51A  PRO*     4.0     1.4    -      -       -      +
     52A  VAL*     3.1    38.8    +      -       +      -
     53A  LYS*     2.8    37.8    +      -       +      +
     55A  VAL*     5.2     2.9    -      -       +      -
     91A  TYR*     4.3     5.6    -      -       +      -
    100A  ILE*     4.0    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 42 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  ASN*     3.2    13.0    +      -       -      +
     31A  LEU*     3.1    41.9    +      -       +      +
     33A  ILE*     3.7    21.0    -      -       +      +
     35A  LYS*     5.0     1.2    +      -       -      -
     40A  GLU*     2.8    46.8    +      -       +      -
     41A  ILE*     1.3    75.9    -      -       -      +
     43A  VAL*     1.3    64.0    +      -       -      +
     49A  LEU*     3.9    38.1    -      -       +      -
     50A  ARG      3.5     5.2    -      -       -      +
     51A  PRO*     3.5    38.8    -      -       +      -
     52A  VAL*     4.3     1.3    -      -       -      -
    353A  PHE*     6.0     5.8    -      +       -      -
----------------------------------------------------------
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Residues in contact with VAL 43 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  THR*     4.1     6.1    -      -       +      +
     28A  ASP*     3.4    29.2    -      -       +      +
     29A  LEU      3.7     6.3    -      -       -      +
     30A  ASN*     3.4    20.9    -      -       -      +
     42A  TYR*     1.3    73.0    -      -       -      +
     44A  VAL*     1.3    72.8    +      -       -      +
     45A  THR*     3.6     1.3    +      -       +      -
     49A  LEU*     3.8     0.8    -      -       -      -
     50A  ARG*     2.9    62.0    +      -       -      +
     52A  VAL*     3.5    23.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 44 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  THR*     5.7     0.4    -      -       +      -
     29A  LEU*     2.9    53.1    +      -       +      +
     30A  ASN      4.3    11.4    -      -       -      +
     31A  LEU*     4.5     1.3    -      -       +      -
     43A  VAL*     1.3    77.9    -      -       -      +
     45A  THR*     1.3    70.5    +      -       -      +
     48A  GLY      4.0     4.3    -      -       -      +
     49A  LEU*     4.1     8.1    -      -       +      -
    317A  LEU*     3.9    43.5    -      -       +      -
    318A  ASP*     5.1     5.8    -      -       +      +
----------------------------------------------------------
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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