Contacts of the strand formed by residues 303 - 316 (chain D) in PDB entry 1SID


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 PRO 303 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53D  LEU      3.3     7.6    -      -       -      +
     54D  ASN*     3.4     9.6    -      -       -      +
     55D  PRO*     3.2    25.8    -      -       +      -
    129D  VAL*     3.3     5.4    -      -       -      +
    130D  VAL*     3.1    56.7    +      -       +      +
    302D  LEU*     1.3    92.9    -      -       +      +
    304D  ARG*     1.3    61.1    +      -       -      +
    177E  LEU*     3.9     3.6    -      -       +      -
    207E  VAL*     3.3    23.3    -      -       -      +
    208E  LEU*     4.0     9.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 304 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52D  PHE*     2.9    30.7    -      -       -      +
     53D  LEU      3.0    14.5    +      -       -      +
    127D  THR*     2.7    43.9    +      -       -      +
    128D  GLU*     3.2     6.2    -      -       -      +
    129D  VAL*     3.4    19.2    -      -       +      +
    130D  VAL*     5.5     1.6    -      -       -      -
    163D  HIS*     4.7     6.9    -      -       -      +
    164D  VAL      4.2    10.7    +      -       -      -
    165D  PHE*     4.1    19.5    -      -       -      +
    282D  CYS*     3.9    14.6    -      -       -      +
    284D  ASP*     2.6    43.3    +      -       -      +
    303D  PRO*     1.3    76.7    -      -       -      +
    305D  TYR*     1.3    59.2    +      -       -      +
    306D  PHE*     3.3    30.7    -      -       +      -
    208E  LEU*     6.1     0.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 305 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50D  GLU*     2.9    49.8    +      -       +      +
     51D  ALA*     3.3    12.1    -      -       -      -
     52D  PHE*     4.1     4.9    -      +       +      -
    126D  LYS*     4.4    13.0    -      -       +      -
    127D  THR*     2.5    36.7    +      -       -      -
    128D  GLU*     2.8    22.0    +      -       +      +
    130D  VAL*     5.3     3.6    -      -       +      +
    304D  ARG*     1.3    68.9    -      -       -      +
    306D  PHE*     1.3    80.0    +      -       -      +
    307D  LYS*     3.9    20.2    -      -       +      +
    231E  PRO*     3.2    51.6    -      -       +      -
    232E  ALA      3.5     6.2    +      -       -      -
    233E  LYS*     3.3     9.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 306 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49D  ILE      3.4     0.2    -      -       -      +
     50D  GLU*     3.0     7.1    -      -       -      +
     51D  ALA      2.7    41.0    +      -       -      +
     52D  PHE*     3.8     4.7    -      -       -      -
     53D  LEU*     3.8    32.8    -      -       +      -
    125D  VAL*     4.5     9.4    -      -       +      -
    126D  LYS      3.3     5.8    -      -       -      -
    127D  THR*     4.2     4.3    -      -       -      -
    165D  PHE*     4.4    15.0    -      +       -      -
    166D  ALA      4.9     0.4    -      -       -      -
    167D  VAL*     5.0     0.2    -      -       +      -
    280D  LEU*     3.5    36.6    -      -       +      -
    281D  SER      4.6     3.4    -      -       -      -
    282D  CYS*     4.2     4.5    -      -       +      -
    304D  ARG*     3.3    48.0    -      -       +      -
    305D  TYR*     1.3    92.4    -      -       -      +
    307D  LYS*     1.3    61.1    +      -       -      +
    308D  ILE*     3.3    18.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 307 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48D  GLU*     3.3    41.6    +      -       +      -
     49D  ILE      3.3     5.6    -      -       -      +
     50D  GLU*     3.9    24.9    +      -       +      +
    125D  VAL*     3.0    23.5    -      -       -      -
    126D  LYS*     2.8    42.0    +      -       +      +
    305D  TYR*     3.9    18.4    -      -       +      +
    306D  PHE*     1.3    75.3    -      -       -      +
    308D  ILE*     1.3    63.4    +      -       -      +
    309D  THR*     3.6     8.4    +      -       -      +
    233E  LYS      4.7     4.6    +      -       -      -
    266E  GLU*     4.6    15.6    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 308 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47D  THR      3.6     1.4    -      -       -      +
     48D  GLU*     3.4     4.7    -      -       -      +
     49D  ILE*     2.8    42.6    +      -       +      +
     51D  ALA*     5.6     1.1    -      -       +      +
    103D  LEU*     6.3     0.2    -      -       +      -
    122D  ALA*     4.2    13.0    -      -       +      -
    124D  SER      3.9     7.4    -      -       -      +
    125D  VAL*     3.7    12.8    -      -       +      -
    167D  VAL*     4.6     4.9    -      -       +      -
    263D  LEU*     4.8     1.6    -      -       +      -
    278D  LEU*     3.9    19.1    -      -       +      -
    280D  LEU*     3.8    23.8    -      -       +      -
    306D  PHE*     3.3    32.5    -      -       +      -
    307D  LYS*     1.3    74.2    -      -       -      +
    309D  THR*     1.3    67.8    +      -       -      +
    310D  LEU*     3.6    28.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 309 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46D  VAL*     4.2    16.6    -      -       +      -
     47D  THR      3.5     1.8    -      -       -      -
     48D  GLU*     3.8    28.0    -      -       +      +
    122D  ALA*     3.9     0.7    -      -       -      -
    123D  VAL*     2.8    32.3    +      -       +      +
    124D  SER*     2.9    30.4    +      -       -      +
    125D  VAL*     4.3     0.3    +      -       -      -
    126D  LYS*     6.1     0.2    -      -       -      +
    260D  THR*     5.1     2.3    -      -       -      +
    307D  LYS*     3.6    12.5    +      -       -      +
    308D  ILE*     1.3    76.4    -      -       -      +
    310D  LEU*     1.3    61.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 310 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46D  VAL*     3.7     5.3    -      -       -      +
     47D  THR*     2.9    82.5    +      -       +      +
     49D  ILE*     4.1    12.1    -      -       +      -
    105D  LEU*     3.8    19.7    -      -       +      -
    120D  TRP*     4.0    14.6    -      -       +      -
    121D  GLU      3.1    20.0    -      -       -      +
    122D  ALA*     3.9     5.2    -      -       +      +
    123D  VAL*     4.4     1.3    -      -       -      +
    278D  LEU*     3.3    35.2    -      -       +      -
    308D  ILE*     3.6     9.2    -      -       +      +
    309D  THR*     1.3    77.6    -      -       -      +
    311D  ARG*     1.3    59.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 311 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43D  PRO      5.6     0.4    -      -       -      +
     44D  ASP*     5.2     9.2    -      -       -      +
     45D  SER      4.6     4.0    -      -       -      -
     46D  VAL*     5.0     6.1    -      -       +      +
    119D  MET      3.8     0.3    -      -       -      +
    120D  TRP*     3.6    11.6    -      -       -      -
    121D  GLU*     2.7    82.8    +      -       +      +
    123D  VAL*     4.2    16.2    -      -       +      +
    264D  LEU*     4.4    11.7    -      -       -      +
    268D  GLY      3.3    10.5    +      -       -      -
    310D  LEU*     1.3    73.1    -      -       -      +
    312D  LYS*     1.3    70.8    +      -       -      +
    313D  ARG*     3.0    28.1    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 312 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40D  VAL*     4.0     8.9    -      -       -      +
     41D  THR*     2.9    28.6    +      -       -      -
     42D  GLY      2.5    37.3    +      -       -      +
     43D  PRO*     3.0    27.7    +      -       +      +
     44D  ASP      5.4     0.2    -      -       -      -
     45D  SER*     3.3    23.6    +      -       -      +
    108D  LEU*     3.6    35.0    -      -       +      +
    109D  ASN*     4.0    13.1    +      -       -      +
    118D  GLN*     4.1    12.9    -      -       -      +
    119D  MET      4.1     2.7    -      -       -      -
    120D  TRP*     4.0    18.4    -      -       +      -
    311D  ARG*     1.3    79.6    -      -       -      +
    313D  ARG*     1.3    60.4    +      -       -      +
    314D  TRP*     4.2     3.6    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 313 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22C  PRO*     5.6     0.2    -      -       -      +
     23C  ALA*     3.7    31.9    -      -       -      +
    118D  GLN*     3.2     5.2    -      -       -      -
    119D  MET*     2.5    49.4    +      -       -      +
    121D  GLU*     2.6    38.8    +      -       +      +
    267D  ASN      5.0     0.4    +      -       -      -
    268D  GLY      2.3    32.5    +      -       -      -
    269D  VAL*     3.2    16.6    -      -       -      +
    272D  LEU*     4.8     7.7    -      -       +      +
    311D  ARG*     3.0    16.7    +      -       -      +
    312D  LYS*     1.3    75.6    -      -       -      +
    314D  TRP*     1.3    87.4    +      -       +      +
    315D  VAL*     3.6    10.1    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 314 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20C  PRO*     3.8    32.0    -      -       +      +
     21C  ARG      5.3     2.0    -      -       -      -
     22C  PRO*     3.6    27.2    -      -       +      +
     23C  ALA      4.7     0.2    +      -       -      -
     43D  PRO*     5.5     6.0    -      -       +      +
    109D  ASN*     4.1     9.9    -      -       +      -
    110D  GLU*     4.2    15.3    -      -       -      -
    111D  ASP*     4.7     3.1    -      -       +      -
    116D  THR*     2.8    38.4    -      -       +      +
    117D  LEU      2.9    34.3    -      -       -      -
    118D  GLN*     3.4    35.1    +      -       +      -
    312D  LYS      4.2     3.3    +      -       -      -
    313D  ARG*     1.3    92.3    +      -       +      +
    315D  VAL*     1.3    62.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 315 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22C  PRO*     3.5    14.0    -      -       -      +
    116D  THR*     3.3    10.2    +      -       -      -
    117D  LEU*     2.7    42.4    +      -       +      +
    119D  MET*     3.4    51.1    -      -       +      -
    272D  LEU*     4.8     7.4    -      -       +      -
    313D  ARG*     3.6    11.9    -      -       -      +
    314D  TRP*     1.3    80.7    -      -       -      +
    316D  LYS*     1.3    73.3    +      -       -      +
    317D  ASN*     4.9     0.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 316 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22C  PRO*     3.9    15.0    -      -       +      +
    114D  CYS      3.5    14.8    +      -       -      -
    115D  ASP*     3.2    31.9    -      -       +      +
    116D  THR*     5.1     0.7    -      -       -      +
    315D  VAL*     1.3    84.2    -      -       -      +
    317D  ASN*     1.3    78.5    +      -       -      +
    318D  PRO*     2.8    17.8    -      -       +      +
----------------------------------------------------------
 Back to top of page


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