Contacts of the strand formed by residues 207 - 216 (chain F) in PDB entry 3SDI


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 ASP 207 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53F  LEU*     3.8     2.8    -      -       -      +
     54F  ILE*     2.8    49.4    +      -       +      +
    202F  HIS*     4.5     1.1    -      -       -      -
    206F  LYS*     1.3    77.0    +      -       -      +
    208F  PHE*     1.3    87.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 208 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51F  GLU*     4.1    18.2    -      -       +      -
     52F  LYS      3.2    17.0    -      -       -      +
     53F  LEU*     4.5     1.8    -      -       -      -
     54F  ILE*     3.8    10.4    -      -       -      +
    197F  ILE*     3.8    24.5    -      -       +      -
    198F  TYR*     3.6    55.5    +      +       -      -
    202F  HIS*     3.4    42.0    -      +       +      +
    207F  ASP*     1.3    97.9    +      -       -      +
    209F  GLU*     1.3    71.2    +      -       -      +
    210F  LEU*     4.6     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 209 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51F  GLU*     3.9     0.5    -      -       -      -
     52F  LYS*     2.8    66.8    +      -       +      +
     54F  ILE*     3.9    18.7    -      -       +      +
     60F  VAL      4.6     1.4    -      -       -      +
     61F  PRO*     3.4    13.2    -      -       -      +
     62F  GLN*     2.8    58.5    +      -       -      +
    208F  PHE*     1.3    80.1    -      -       -      +
    210F  LEU*     1.3    68.2    +      -       -      +
    211F  GLU*     5.1     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 210 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49F  ALA*     4.7     0.7    -      -       +      -
     50F  VAL      3.9     5.8    -      -       -      +
     52F  LYS*     5.0     0.4    -      -       -      -
     62F  GLN*     5.1     3.5    +      -       -      +
    194F  ALA*     3.9    18.2    -      -       +      +
    197F  ILE*     3.8    36.3    -      -       +      -
    198F  TYR*     4.3    11.2    -      -       +      +
    208F  PHE*     4.6    10.3    -      -       +      -
    209F  GLU*     1.3    83.3    -      -       -      +
    211F  GLU*     1.3    66.4    +      -       -      +
    212F  ILE*     3.7    36.2    +      -       +      -
    229F  LEU*     4.5    18.7    -      -       +      +
    233F  ILE*     3.8    32.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 211 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49F  ALA*     3.2     5.0    -      -       -      +
     50F  VAL*     3.0    46.8    +      -       +      +
     52F  LYS*     3.3    35.4    +      -       +      -
     62F  GLN*     5.3     1.0    -      -       -      +
     65F  VAL*     3.4    22.1    -      -       -      +
     66F  LYS*     2.7    29.5    +      -       -      +
     67F  ILE*     3.0    25.7    +      -       +      +
    209F  GLU*     4.1     0.8    +      -       -      +
    210F  LEU*     1.3    74.2    -      -       -      +
    212F  ILE*     1.3    65.6    +      -       -      +
    223F  PHE*     4.5    10.1    -      -       +      -
    229F  LEU*     5.4     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 212 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47F  VAL*     3.8    21.3    -      -       +      -
     48F  PHE      3.2    12.1    -      -       -      +
     49F  ALA*     4.3     6.3    -      -       +      -
     67F  ILE*     3.9     3.1    -      -       -      -
    190F  VAL*     4.1    21.5    -      -       +      +
    193F  ALA*     4.9     1.1    -      -       +      -
    194F  ALA*     4.0    19.5    -      -       +      +
    210F  LEU*     3.7    32.7    -      -       +      -
    211F  GLU*     1.3    81.3    -      -       -      +
    213F  SER*     1.3    65.7    +      -       -      +
    223F  PHE*     4.0     6.9    -      -       -      -
    224F  VAL*     3.0    44.9    +      -       +      +
    229F  LEU*     4.0    15.8    -      -       +      +
    232F  ALA*     4.5     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 213 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47F  VAL*     3.6     4.0    -      -       -      +
     48F  PHE*     2.9    35.9    +      -       -      +
     67F  ILE*     3.2    24.0    -      -       -      +
    212F  ILE*     1.3    76.6    -      -       -      +
    214F  TRP*     1.3    64.5    +      -       -      +
    221F  HIS*     2.8    32.9    +      -       -      -
    222F  LYS      3.5    12.6    -      -       -      -
    223F  PHE*     4.0     8.3    -      -       -      -
    224F  VAL*     3.9     5.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 214 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46F  VAL      3.3    12.6    -      -       -      +
     47F  VAL*     4.4     8.1    -      -       +      -
     48F  PHE*     5.0     1.6    -      -       -      +
    186F  ALA*     4.0    25.8    -      -       +      -
    187F  ARG*     4.4     6.7    -      -       +      -
    190F  VAL*     3.6    21.5    -      -       +      -
    213F  SER*     1.3    77.3    +      -       -      +
    215F  CYS*     1.3    62.0    +      -       -      +
    216F  SER*     4.1     3.1    -      -       -      -
    218F  THR*     3.6    70.2    +      -       +      +
    220F  LEU      3.6     1.7    -      -       -      +
    221F  HIS*     3.6     5.6    -      -       -      -
    222F  LYS*     2.9    51.7    +      -       -      +
    223F  PHE      4.5     4.4    +      -       -      -
    224F  VAL*     3.7    18.3    -      -       +      +
    228F  LEU*     3.6    29.4    -      -       +      -
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Residues in contact with CYS 215 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45F  GLY*     3.1     5.2    -      -       -      -
     46F  VAL*     3.0    43.5    +      -       +      +
     73F  HIS      3.4    23.6    -      -       -      +
    139F  GLY      5.2     0.9    -      -       -      +
    140F  GLY*     4.3     2.5    -      -       -      -
    141F  VAL*     3.7    19.8    -      -       -      +
    214F  TRP*     1.3    75.3    -      -       -      +
    216F  SER*     1.3    59.4    +      -       -      +
    219F  GLY      3.6    24.9    -      -       -      -
    220F  LEU      3.5    15.9    -      -       -      +
    221F  HIS*     4.2    10.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 216 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42F  CYS*     5.2     0.2    -      -       -      -
     44F  ASP*     2.8    31.5    +      -       -      -
     45F  GLY*     4.0     2.5    -      -       -      -
     46F  VAL      5.4     0.2    -      -       -      -
    186F  ALA*     3.7    17.5    -      -       -      +
    214F  TRP*     4.1     6.4    -      -       -      -
    215F  CYS*     1.3    75.4    -      -       -      +
    217F  LEU*     1.3    63.0    +      -       -      +
    218F  THR*     2.8    61.0    +      -       -      +
    219F  GLY*     2.9    12.1    +      -       -      -
----------------------------------------------------------
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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