Contacts of the strand formed by residues 999 - 1004 (chain C) in PDB entry 3DLS


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 TYR 999 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    995C  TYR*     2.9    58.1    +      +       +      +
    996C  SER*     3.5    16.3    +      -       -      +
    998C  LYS*     1.3    97.1    +      -       +      +
   1000C  SER*     1.3    60.4    +      -       -      +
   1016C  ALA*     4.3     3.6    -      -       +      -
   1017C  VAL      3.2     6.1    -      -       -      +
   1018C  ASP*     3.7    30.5    +      -       +      -
   1019C  LYS*     4.1     5.0    +      -       -      -
   1023C  LYS*     5.8     0.2    +      -       -      -
   1025C  VAL*     3.7    25.4    -      -       +      -
   1068C  LEU*     4.1     7.8    -      -       -      +
   1069C  ASP*     2.4    28.6    +      -       -      +
   1071C  PHE*     3.4    24.2    -      +       -      -
   1080C  VAL*     3.6    25.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER1000 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    999C  TYR*     1.3    73.7    -      -       -      +
   1001C  THR*     1.3    64.9    +      -       -      +
   1002C  MET*     3.7    15.3    +      -       -      +
   1016C  ALA*     3.3     3.2    -      -       -      -
   1017C  VAL*     2.8    37.0    +      -       -      -
   1019C  LYS*     4.4    17.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR1001 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    991C  CYS*     3.7    13.1    -      -       -      -
    995C  TYR*     2.5    36.3    +      -       -      +
   1000C  SER*     1.3    73.9    +      -       -      +
   1002C  MET*     1.3    68.0    +      -       -      +
   1014C  TRP*     3.5    43.5    -      -       +      -
   1015C  THR      4.0     3.6    -      -       -      +
   1016C  ALA*     4.2     0.7    -      -       -      -
   1027C  VAL*     4.2     4.5    -      -       +      -
   1029C  PHE*     3.8     6.4    -      -       +      -
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Residues in contact with MET1002 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1175A  MET*     3.6    17.7    -      -       -      +
   1000C  SER*     3.9    22.4    -      -       -      +
   1001C  THR*     1.3    80.6    -      -       -      +
   1003C  SER*     1.3    65.5    +      -       -      +
   1014C  TRP*     4.4     3.4    -      -       -      -
   1015C  THR*     2.8    22.2    +      -       +      +
   1016C  ALA      4.4     0.7    -      -       -      -
   1017C  VAL*     3.6    30.7    -      -       +      -
   1024C  GLU*     5.9     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER1003 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1175A  MET*     4.4     1.1    -      -       -      -
   1210A  VAL*     6.5     0.4    -      -       -      -
   1002C  MET*     1.3    82.6    -      -       -      +
   1004C  PRO*     1.4    73.6    +      -       -      +
   1014C  TRP*     3.2     9.3    -      -       -      -
   1015C  THR*     2.7    48.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO1004 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1175A  MET*     4.1     8.7    -      -       +      -
   1207A  GLU*     3.4    33.2    -      -       +      +
   1210A  VAL*     5.7     3.8    -      -       +      -
   1003C  SER*     1.4    93.2    +      -       -      +
   1005C  LEU*     1.3    63.9    +      -       -      +
   1010C  PHE*     3.6    37.9    -      -       +      +
   1013C  VAL      3.7     5.8    -      -       -      +
   1014C  TRP*     3.2    22.4    -      -       +      -
----------------------------------------------------------
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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