Contacts of the strand formed by residues 116 - 129 (chain E) 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 THR 116 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19D  CYS*     3.8    16.8    -      -       +      -
     20D  PRO*     3.1    27.6    +      -       +      +
     22D  PRO*     5.2     2.5    -      -       -      -
    109E  ASN*     3.1     9.0    -      -       -      +
    111E  ASP      3.3    12.5    -      -       -      +
    112E  LEU*     2.6    53.5    -      -       +      +
    114E  CYS      2.6     6.9    +      -       -      -
    115E  ASP*     1.3    77.6    -      -       -      +
    117E  LEU*     1.3    59.0    +      -       -      +
    314E  TRP*     3.2    21.4    -      -       -      -
    315E  VAL      3.4     7.5    +      -       -      -
    316E  LYS*     4.8     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 117 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109E  ASN*     2.7    24.0    -      -       +      +
    110E  GLU      4.7     1.8    -      -       -      +
    111E  ASP*     4.1    10.3    -      -       -      +
    115E  ASP*     2.7    17.9    +      -       -      +
    116E  THR*     1.3    76.4    -      -       -      +
    118E  GLN*     1.3    80.7    +      -       -      +
    119E  MET*     4.9    13.5    -      -       +      -
    314E  TRP*     2.8     7.6    -      -       -      -
    315E  VAL*     2.5    50.5    +      -       +      +
    316E  LYS      4.7     0.2    -      -       -      -
    317E  ASN*     4.5    15.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 118 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42E  GLY      5.3     0.3    -      -       -      +
     43E  PRO*     4.2     8.1    -      -       -      +
    108E  LEU*     3.2    30.7    +      -       +      +
    109E  ASN*     2.4    37.2    +      -       -      +
    117E  LEU*     1.3    79.4    -      -       -      +
    119E  MET*     1.3    66.0    +      -       -      +
    276E  GLU*     5.5     0.2    -      -       -      +
    312E  LYS*     4.0    36.3    -      -       +      +
    313E  ARG      3.1     9.9    -      -       -      +
    314E  TRP*     3.1    41.3    +      -       +      -
----------------------------------------------------------
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Residues in contact with MET 119 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108E  LEU*     4.2     8.7    -      -       +      -
    117E  LEU*     4.9    13.9    -      -       +      -
    118E  GLN*     1.3    76.2    -      -       -      +
    120E  TRP*     1.3    66.7    +      -       -      +
    121E  GLU      3.5     0.2    +      -       -      -
    272E  LEU*     4.1    26.2    -      -       +      -
    273E  CYS      3.6    22.9    -      -       -      +
    274E  LYS*     5.0     4.5    -      -       -      -
    276E  GLU*     5.4     6.5    -      -       -      +
    311E  ARG      3.5     0.9    -      -       -      +
    312E  LYS*     3.8     3.2    -      -       -      -
    313E  ARG*     2.9    34.8    +      -       +      +
    315E  VAL*     3.7    36.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 120 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37E  LEU*     5.3     6.1    -      -       +      -
     41E  THR*     4.6    11.0    -      -       +      -
     45E  SER      5.4     1.1    -      -       -      -
     47E  THR*     3.9    24.0    -      -       +      -
    105E  LEU*     3.2    41.1    -      -       +      +
    106E  PRO*     2.9    44.5    +      -       +      +
    108E  LEU*     3.6    19.6    -      -       +      +
    119E  MET*     1.3    77.5    -      -       -      +
    121E  GLU*     1.3    59.2    +      -       -      +
    272E  LEU*     3.1     5.0    -      -       -      +
    273E  CYS*     2.7    46.0    +      -       +      +
    276E  GLU*     4.7     9.2    -      -       +      -
    310E  LEU*     3.6    18.2    -      -       +      -
    311E  ARG*     3.5    22.0    -      -       -      -
    312E  LYS*     3.8    36.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 121 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120E  TRP*     1.3    75.4    -      -       -      +
    122E  ALA*     1.3    90.8    +      -       -      +
    123E  VAL*     4.2     0.2    -      -       -      -
    264E  LEU*     3.5     2.3    -      -       -      +
    269E  VAL      2.6    23.6    -      -       -      +
    270E  GLY*     3.2     6.2    -      -       -      -
    271E  PRO      2.8    14.7    -      -       -      +
    272E  LEU*     3.8     6.7    -      -       +      -
    310E  LEU*     2.9     5.0    -      -       -      +
    311E  ARG*     2.6    89.5    +      -       +      +
    313E  ARG*     3.0    26.2    +      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 122 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120E  TRP      4.2     0.4    -      -       -      -
    121E  GLU*     1.3    81.2    -      -       -      +
    123E  VAL*     1.3    58.4    +      -       -      +
    167E  VAL*     4.7     7.4    -      -       +      -
    263E  LEU*     3.5    16.7    -      -       +      +
    270E  GLY*     3.8     0.2    -      -       -      -
    271E  PRO*     2.6    50.4    +      -       +      +
    273E  CYS*     5.3     4.7    -      -       -      -
    278E  LEU*     5.1     5.8    -      -       +      -
    308E  ILE*     4.0    16.2    -      -       +      -
    310E  LEU*     3.4    13.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 123 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121E  GLU*     3.5    16.8    -      -       -      +
    122E  ALA*     1.3    78.2    -      -       -      +
    124E  SER*     1.3    63.6    +      -       -      +
    262E  VAL*     3.3    10.6    -      -       +      +
    263E  LEU*     2.5    34.5    +      -       -      -
    264E  LEU*     3.0    28.4    +      -       +      -
    309E  THR*     2.9    13.2    +      -       -      +
    310E  LEU*     4.5     2.2    -      -       -      -
    311E  ARG*     3.8    34.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 124 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123E  VAL*     1.3    82.8    -      -       -      +
    125E  VAL*     1.3    68.5    +      -       -      +
    260E  THR*     3.7    16.8    -      -       -      +
    261E  THR      2.9    13.2    -      -       -      -
    262E  VAL*     3.9    12.3    -      -       -      -
    263E  LEU*     3.0     9.5    -      -       -      +
    308E  ILE*     3.7     0.7    -      -       -      -
    309E  THR*     3.0    45.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 125 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124E  SER*     1.3    80.0    -      -       -      +
    126E  LYS*     1.3    76.9    +      -       -      +
    127E  THR*     4.0     9.6    +      -       +      +
    165E  PHE*     5.1     9.6    -      -       +      -
    167E  VAL*     4.6    13.2    -      -       +      -
    240E  PHE*     6.2     0.4    -      -       +      -
    260E  THR*     3.9     1.9    -      -       -      +
    261E  THR*     2.6    40.4    +      -       -      +
    263E  LEU*     3.3    32.5    -      -       +      -
    306E  PHE*     4.6     2.5    -      -       +      -
    307E  LYS      2.9    13.0    -      -       -      +
    308E  ILE*     3.8    21.3    -      -       +      -
    309E  THR*     4.5     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 126 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266A  GLU*     3.0    32.1    +      -       -      +
    125E  VAL*     1.3    80.8    -      -       -      +
    127E  THR*     1.3    62.8    +      -       -      +
    256E  THR      5.8     1.1    -      -       -      +
    257E  ASN*     3.5    29.0    +      -       -      +
    258E  THR*     3.5    23.6    +      -       -      +
    259E  LEU      3.4    21.1    -      -       -      +
    260E  THR*     3.5    26.2    -      -       +      -
    305E  TYR*     3.9     5.8    -      -       +      -
    307E  LYS*     2.7    63.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 127 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125E  VAL*     4.6     9.0    -      -       +      +
    126E  LYS*     1.3    78.0    -      -       -      +
    128E  GLU*     1.3    62.8    +      -       -      +
    165E  PHE*     4.1    22.2    -      -       +      -
    256E  THR      4.8     5.4    -      -       -      +
    259E  LEU      4.6     3.1    +      -       -      +
    261E  THR*     5.6     3.3    +      -       -      +
    304E  ARG*     2.7    43.3    +      -       -      +
    305E  TYR*     2.5    23.8    +      -       -      -
    306E  PHE*     4.0     7.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 128 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229A  PRO      4.2     3.1    -      -       -      +
    231A  PRO*     3.8     9.5    -      -       -      +
    239A  TYR*     2.6    40.5    +      -       -      -
    127E  THR*     1.3    82.3    +      -       -      +
    129E  VAL*     1.3    72.2    +      -       -      +
    130E  VAL*     3.3    18.3    +      -       +      +
    254E  GLN      4.0    17.0    -      -       -      +
    255E  PHE*     3.6    13.7    -      -       -      -
    256E  THR      3.4    23.9    +      -       -      +
    257E  ASN*     4.7     0.3    -      -       -      -
    304E  ARG*     3.5     3.3    -      -       -      +
    305E  TYR*     3.0    38.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 129 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128E  GLU*     1.3    78.4    -      -       -      +
    130E  VAL*     1.3    62.3    +      -       -      +
    132E  SER*     3.5    12.3    +      -       -      -
    163E  HIS*     4.6     5.2    -      -       +      +
    253E  LEU*     3.6    38.2    -      -       +      +
    254E  GLN      5.1     0.6    +      -       -      -
    255E  PHE*     4.3     3.6    -      -       -      -
    284E  ASP*     3.3    35.0    -      -       +      +
    286E  MET*     4.9     0.9    -      -       -      -
    302E  LEU*     3.5    29.2    -      -       +      -
    303E  PRO      3.4     7.6    -      -       -      +
    304E  ARG*     3.4    22.6    -      -       +      +
----------------------------------------------------------
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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