Contacts of the strand formed by residues 311 - 320 (chain B) in PDB entry 1DGB


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 ILE 311 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91B  ILE*     4.2    13.7    -      -       +      -
     94B  TYR*     4.1    21.5    -      -       +      +
    280B  TYR*     3.1     4.3    -      -       -      -
    281B  ILE*     2.7    52.3    +      -       +      +
    283B  VAL*     3.8    33.0    -      -       +      +
    309B  PRO*     4.0     9.6    -      -       +      +
    310B  LEU*     1.3    76.0    -      -       -      +
    312B  PRO*     1.3    79.1    -      -       +      +
    313B  VAL      3.6     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 312 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88B  THR*     5.1     0.4    -      -       -      +
     89B  HIS*     3.2    51.2    -      -       +      +
     91B  ILE*     4.3     1.4    -      -       -      +
    278B  THR*     5.3     4.9    -      -       +      -
    279B  PHE      3.8     1.1    -      -       -      +
    280B  TYR*     3.4    26.2    -      -       +      -
    310B  LEU      3.6     8.7    -      -       -      +
    311B  ILE*     1.3    94.0    -      -       +      +
    313B  VAL*     1.3    62.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 313 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85B  PHE*     4.1     8.5    -      -       +      -
     87B  VAL*     3.6     4.2    -      -       +      -
     88B  THR*     2.7    31.4    +      -       -      -
     89B  HIS*     2.8    15.8    +      -       -      +
     91B  ILE*     3.9    24.2    -      -       +      -
    100B  PHE*     3.8    33.2    -      -       +      -
    278B  THR*     5.8     0.2    -      -       -      +
    279B  PHE*     2.9    21.3    +      -       +      +
    280B  TYR      4.4     0.2    -      -       -      -
    281B  ILE*     3.8    28.0    -      -       +      +
    311B  ILE      3.6    11.2    -      -       -      +
    312B  PRO*     1.3    78.1    -      -       -      +
    314B  GLY*     1.3    51.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 314 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85B  PHE*     4.1     6.1    -      -       -      -
     86B  GLU      3.1    13.7    -      -       -      -
     87B  VAL*     4.3     0.2    -      -       -      -
     88B  THR*     3.3    11.2    +      -       -      -
    278B  THR*     3.6     9.0    -      -       -      +
    279B  PHE*     2.7    35.5    +      -       -      +
    313B  VAL*     1.3    84.4    -      -       -      +
    315B  LYS*     1.3    61.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 315 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84B  TYR      3.9     0.3    -      -       -      +
     85B  PHE*     3.1    10.7    -      -       -      -
     86B  GLU*     2.9    38.8    +      -       +      +
     88B  THR*     4.2    14.6    -      -       +      -
    239B  ASP*     2.9    20.5    +      -       -      +
    276B  SER*     5.0     4.9    +      -       -      -
    277B  TRP      3.3    15.0    -      -       -      +
    278B  THR*     2.7    32.6    +      -       -      +
    279B  PHE*     4.4     0.7    -      -       -      +
    314B  GLY*     1.3    76.8    -      -       -      +
    316B  LEU*     1.3    63.0    +      -       -      +
    317B  VAL*     4.2    12.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 316 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84B  TYR      3.7     0.7    -      -       -      -
     85B  PHE*     3.7    29.2    -      -       +      -
    109B  ILE*     4.0    17.3    -      -       +      -
    111B  VAL*     6.2     0.4    -      -       +      -
    132B  PHE*     5.0     4.0    -      -       +      -
    134B  VAL*     4.3    11.0    -      -       +      -
    136B  PHE*     4.2    15.3    -      -       +      -
    236B  TYR*     3.6    45.5    -      -       +      -
    275B  PRO      3.9     0.2    -      -       -      +
    276B  SER*     3.0    29.6    -      -       -      -
    277B  TRP*     2.8    26.3    +      -       +      +
    279B  PHE*     3.9    15.9    -      -       +      -
    315B  LYS*     1.3    72.6    -      -       -      +
    317B  VAL*     1.3    62.1    +      -       -      +
    318B  LEU*     6.4     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 317 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83B  GLY*     2.9     4.9    -      -       -      -
     84B  TYR*     2.8    82.2    +      -       +      +
    109B  ILE*     3.7     3.6    -      -       -      +
    274B  TYR*     4.4    13.0    -      -       +      -
    275B  PRO      3.8     6.3    -      -       -      +
    276B  SER*     4.3    11.7    -      -       -      -
    315B  LYS*     4.6     9.2    -      -       +      -
    316B  LEU*     1.3    84.1    -      -       -      +
    318B  LEU*     1.3    74.0    +      -       -      +
    319B  ASN*     4.4     4.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 318 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81B  ALA*     3.9    12.1    -      -       +      -
     82B  PHE*     3.3    25.1    -      -       -      +
    109B  ILE*     3.8     8.1    -      -       +      -
    111B  VAL*     3.7    31.0    -      -       +      -
    113B  PHE*     3.9    34.1    -      -       +      -
    132B  PHE*     5.9     0.2    -      -       +      -
    265B  LEU*     4.7     1.8    -      -       +      -
    269B  ILE*     4.0    11.8    -      -       +      +
    274B  TYR*     3.3    19.2    -      -       -      +
    275B  PRO*     3.3    26.5    +      -       +      +
    277B  TRP*     4.2    18.2    -      -       +      -
    316B  LEU*     5.8     0.4    -      -       +      -
    317B  VAL*     1.3    79.7    -      -       -      +
    319B  ASN*     1.3    59.4    +      -       -      +
    320B  ARG      3.6     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 319 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82B  PHE      2.8     9.9    +      -       -      +
     83B  GLY*     3.1    12.8    -      -       -      -
     84B  TYR*     3.8    25.5    -      -       -      -
    269B  ILE*     3.6    13.6    -      -       -      +
    274B  TYR*     3.6    40.0    +      -       +      -
    317B  VAL*     4.5     4.3    -      -       +      -
    318B  LEU*     1.3    74.1    -      -       -      +
    320B  ARG*     1.3    65.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 320 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81B  ALA*     3.5     5.9    -      -       -      +
     82B  PHE*     2.8    91.7    +      -       +      +
     83B  GLY*     4.6     6.3    +      -       -      +
    269B  ILE*     3.8     6.1    -      -       -      +
    318B  LEU      3.6     1.4    -      -       -      -
    319B  ASN*     1.3    87.5    +      -       -      +
    321B  ASN*     1.3    73.5    +      -       -      +
    323B  VAL*     5.9     4.7    -      -       +      +
    328B  GLU*     4.7     5.9    +      -       -      -
----------------------------------------------------------
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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