Contacts of the strand formed by residues 30 - 39 (chain B) in PDB entry 3DGR


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 THR 30 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  TYR*     4.6     4.3    -      -       +      -
     27B  PRO*     2.7    31.7    +      -       -      +
     28B  PRO      3.4     0.4    -      -       -      -
     29B  ASN*     1.3    75.8    -      -       -      +
     31B  SER*     1.3    59.5    +      -       -      +
     32B  LYS      3.6     8.7    -      -       -      +
     33B  VAL*     4.0    12.6    -      -       +      -
    139B  PRO      3.9     1.6    -      -       -      +
    142B  TYR*     3.5    36.8    -      -       +      +
    404B  VAL*     3.5    28.7    -      -       +      -
    405B  VAL      3.3     6.1    -      -       -      +
    406B  THR*     3.1    14.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 31 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  ASN      3.7     4.7    +      -       -      -
     30B  THR*     1.3    72.6    -      -       -      +
     32B  LYS*     1.3    63.5    +      -       -      +
    136B  ASN*     2.9    18.4    -      -       -      +
    138B  ASP      4.6     0.2    -      -       -      -
    139B  PRO*     3.4    34.8    -      -       -      +
    142B  TYR*     4.1     3.8    -      -       -      -
    405B  VAL*     2.9    30.5    +      -       -      +
    408B  GLY*     5.0     3.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 32 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30B  THR*     3.5     1.8    -      -       -      +
     31B  SER*     1.3    84.3    +      -       -      +
     33B  VAL*     1.3    65.6    +      -       -      +
     34B  TYR*     4.6     2.0    -      -       +      -
    135B  GLU*     2.9    37.2    +      -       +      +
    136B  ASN*     3.1    35.7    +      -       -      +
    137B  THR*     4.8     4.6    -      -       -      +
    142B  TYR*     4.7     0.2    -      -       -      -
    403B  TYR*     4.6    14.8    -      -       +      -
    404B  VAL*     3.0    27.5    -      -       -      +
    405B  VAL*     3.1    35.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 33 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  TYR*     4.2    26.2    -      -       +      +
     30B  THR*     4.0    17.0    -      -       +      -
     32B  LYS*     1.3    79.3    -      -       -      +
     34B  TYR*     1.3    63.6    +      -       -      +
     35B  SER*     4.1     0.7    -      -       -      +
    135B  GLU*     3.5     5.2    -      -       -      +
    136B  ASN*     3.0    11.5    +      -       -      +
    142B  TYR*     3.2    26.5    -      -       +      +
    145B  THR*     2.7    31.7    +      -       +      +
    146B  ASN*     3.8    22.4    -      -       -      +
    401B  CYS*     3.8    18.8    -      -       -      -
    403B  TYR      3.8     3.6    -      -       -      -
    404B  VAL*     4.1     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 34 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32B  LYS*     4.6     3.1    -      -       +      -
     33B  VAL*     1.3    75.2    -      -       -      +
     35B  SER*     1.3    66.4    +      -       -      +
    117B  LYS*     6.5     0.4    -      -       +      -
    133B  THR*     3.4    33.4    +      -       +      +
    134B  VAL      3.4     6.5    -      -       -      -
    135B  GLU*     3.9    38.6    -      -       +      -
    401B  CYS*     3.5     1.9    -      -       -      -
    402B  SER*     3.1    43.8    +      -       -      -
    403B  TYR*     2.9    43.4    +      +       +      +
    428B  GLY      3.8     9.4    -      -       -      -
    429B  ARG*     3.9    13.5    -      -       +      +
    430B  LEU*     3.1    34.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with SER 35 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  VAL*     4.1     0.7    -      -       -      +
     34B  TYR*     1.3    74.1    -      -       -      +
     36B  TYR*     1.3    61.5    +      -       -      +
    133B  THR*     3.3     5.5    -      -       -      -
    134B  VAL      2.8    33.8    +      -       -      +
    145B  THR*     3.9     6.5    -      -       -      +
    146B  ASN*     2.9    21.1    +      -       -      -
    399B  PHE*     3.5    30.5    -      -       -      -
    400B  LYS      3.2    10.5    -      -       -      -
    401B  CYS*     3.1    19.2    +      -       -      +
    402B  SER      4.4     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 36 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34B  TYR*     5.2     0.7    -      -       +      -
     35B  SER*     1.3    75.9    -      -       -      +
     37B  PHE*     1.3    69.4    +      -       -      +
     38B  GLU*     2.6    46.5    +      -       +      -
    130B  VAL*     4.0     9.4    -      -       +      -
    132B  PHE*     3.3    11.4    -      -       -      +
    133B  THR*     4.1     4.5    -      -       +      -
    398B  SER      3.6     1.5    -      -       -      +
    399B  PHE*     3.2     9.1    -      -       -      -
    400B  LYS*     2.9    64.6    +      -       +      +
    402B  SER*     4.0    10.3    -      -       -      +
    425B  SER*     3.7     6.3    -      -       -      -
    426B  LYS*     2.9    52.3    +      -       +      +
    430B  LEU*     3.4    27.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 37 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36B  TYR*     1.3    75.4    -      -       -      +
     38B  GLU*     1.3    70.5    +      -       -      +
     39B  CYS*     4.2     5.6    -      -       -      -
    130B  VAL*     3.7     3.1    -      -       -      -
    131B  LEU*     2.8    46.0    +      -       +      +
    132B  PHE*     2.8    52.2    +      +       +      -
    153B  VAL*     4.1    22.0    -      -       +      -
    155B  SER*     4.0    15.9    -      -       -      -
    156B  TRP      4.3     3.8    -      -       -      -
    159B  ILE*     3.7    24.0    -      -       +      -
    397B  CYS*     3.5    29.2    -      -       +      -
    398B  SER      3.2    17.3    -      -       -      -
    399B  PHE*     4.4     9.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 38 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36B  TYR*     2.6    38.7    +      -       +      -
     37B  PHE*     1.3    79.3    -      -       -      +
     39B  CYS*     1.3    62.0    +      -       -      +
     40B  ARG*     3.5    32.5    -      -       +      +
    128B  GLY*     3.3    28.1    -      -       -      -
    129B  ASN      3.4    20.9    -      -       -      +
    131B  LEU*     4.4     1.8    -      -       -      -
    396B  ASN      3.5     1.0    -      -       -      +
    397B  CYS*     3.5     1.6    -      -       -      -
    398B  SER*     2.9    38.0    +      -       -      +
    424B  ARG      4.6     5.5    -      -       -      +
    425B  SER*     4.7     0.5    -      -       -      -
    426B  LYS*     3.6     9.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 39 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  PHE*     4.2     2.9    -      -       -      -
     38B  GLU*     1.3    72.4    -      -       -      +
     40B  ARG*     1.3    69.2    +      -       -      +
     57B  THR*     3.9    19.5    -      -       +      +
    127B  ARG*     3.0    20.8    -      -       +      +
    128B  GLY      2.9    20.6    +      -       -      +
    129B  ASN      4.5     2.0    +      -       -      -
    131B  LEU*     3.8    24.1    -      -       +      +
    159B  ILE*     4.2    10.1    -      -       -      -
    395B  LEU*     3.1    19.5    -      -       +      +
    396B  ASN      3.6     1.6    -      -       -      -
    397B  CYS*     3.9    23.8    -      -       -      -
----------------------------------------------------------
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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