Contacts of the strand formed by residues 1481 - 1492 (chain C) in PDB entry 3B13


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 TRP1481 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1198C  ASP*     4.1    44.0    -      -       +      -
   1201C  MET*     4.1    27.8    -      -       +      -
   1202C  SER*     4.2    15.1    +      -       -      -
   1361C  PHE*     4.3    19.9    -      +       +      -
   1362C  ILE      3.1    10.5    -      -       -      +
   1363C  TYR*     3.3    50.1    +      +       +      -
   1475C  LEU*     4.3     0.7    -      -       -      -
   1479C  LEU*     3.1    36.9    +      -       +      +
   1480C  ARG*     1.3    98.7    -      -       +      +
   1482C  PHE*     1.3    74.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE1482 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1361C  PHE*     3.3     6.8    -      -       -      -
   1362C  ILE      2.9    32.6    +      -       -      +
   1471C  THR*     3.9    12.9    -      -       +      +
   1472C  ALA*     4.6     3.1    -      -       +      +
   1473C  TYR*     3.4    50.5    -      +       +      +
   1474C  LYS      3.0    28.9    -      -       -      -
   1475C  LEU*     3.5    25.8    -      -       +      -
   1477C  GLY*     3.9     7.9    -      -       -      -
   1478C  ILE*     3.7    28.0    -      -       +      -
   1479C  LEU*     3.8    20.9    -      -       +      -
   1481C  TRP*     1.3    81.3    -      -       -      +
   1483C  GLU*     1.3    64.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU1483 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1355C  PHE      5.0     0.5    -      -       -      +
   1359C  LYS*     2.8    47.7    +      -       +      +
   1360C  VAL      4.0     5.4    -      -       -      +
   1361C  PHE*     3.4    27.3    -      -       +      -
   1471C  THR*     3.2     5.5    -      -       -      -
   1472C  ALA*     3.0    31.4    +      -       +      +
   1482C  PHE*     1.3    74.4    -      -       -      +
   1484C  VAL*     1.3    74.5    +      -       -      +
   1485C  VAL*     4.6    10.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL1484 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1359C  LYS*     5.8     0.2    -      -       -      +
   1360C  VAL*     2.7    41.4    +      -       +      +
   1362C  ILE*     3.6    36.1    -      -       +      -
   1469C  PHE*     4.0    12.6    -      -       +      -
   1470C  VAL      3.6     6.5    -      -       -      +
   1471C  THR*     4.6     0.9    -      -       +      -
   1483C  GLU*     1.3    85.2    -      -       -      +
   1485C  VAL*     1.3    63.6    +      -       -      +
   1486C  HIS      3.4    16.8    -      -       -      +
   1487C  MET*     3.4    30.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL1485 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1470C  VAL*     2.8    26.4    +      -       +      +
   1471C  THR      4.5     7.0    -      -       -      +
   1472C  ALA*     4.2    23.6    -      -       +      +
   1483C  GLU*     4.2    11.4    -      -       +      +
   1484C  VAL*     1.3    79.0    -      -       -      +
   1486C  HIS*     1.3    74.4    +      -       +      +
   1487C  MET*     3.9     1.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS1486 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1441C  ARG*     5.0     9.9    -      -       -      -
   1468C  SER*     5.5     1.8    -      -       -      -
   1470C  VAL*     2.9    48.9    +      -       +      -
   1484C  VAL*     3.4     5.4    -      -       -      +
   1485C  VAL*     1.3    85.4    -      -       +      +
   1487C  MET*     1.3    81.9    +      -       -      +
   1488C  SER*     3.7    20.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET1487 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1360C  VAL*     4.4    16.2    -      -       +      -
   1467C  THR*     3.8    16.2    -      -       +      -
   1468C  SER      3.0    13.2    -      -       -      +
   1469C  PHE*     3.4    24.2    -      -       +      -
   1484C  VAL*     3.4    27.6    -      -       +      -
   1485C  VAL      3.9     2.3    +      -       -      +
   1486C  HIS*     1.3    87.1    +      -       -      +
   1488C  SER*     1.3    64.3    +      -       -      +
   1489C  GLN*     5.5     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER1488 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1441C  ARG*     5.6     0.5    +      -       -      -
   1466C  ARG      4.8     0.2    -      -       -      -
   1467C  THR*     3.4    10.0    -      -       -      +
   1468C  SER*     2.9    44.2    +      -       -      -
   1486C  HIS*     3.7    20.9    +      -       -      -
   1487C  MET*     1.3    75.4    -      -       -      +
   1489C  GLN*     1.3    66.9    +      -       -      +
   1490C  THR*     4.6     4.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN1489 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1446C  ARG*     4.9     5.4    +      -       -      -
   1465C  GLU*     3.2    33.2    -      -       -      +
   1466C  ARG      3.6     2.7    +      -       -      -
   1467C  THR*     2.4    46.4    +      -       -      +
   1487C  MET*     5.5     2.2    -      -       -      +
   1488C  SER*     1.3    77.8    +      -       -      +
   1490C  THR*     1.3    66.2    +      -       -      +
   1491C  THR*     5.7     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR1490 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1464C  ILE      3.9     0.2    -      -       -      +
   1465C  GLU*     3.6     4.8    -      -       -      +
   1466C  ARG*     2.9    42.5    +      -       -      +
   1468C  SER*     5.6     1.7    +      -       -      -
   1488C  SER*     4.6     5.9    +      -       -      -
   1489C  GLN*     1.3    78.5    +      -       -      +
   1491C  THR*     1.3    70.0    +      -       -      +
   1492C  ILE*     4.2    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR1491 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1448C  VAL*     5.1     1.3    -      -       +      -
   1450C  ARG*     3.6    34.1    +      -       -      +
   1463C  TRP*     4.1    19.2    -      -       +      -
   1464C  ILE      3.5    12.8    -      -       -      +
   1465C  GLU*     3.6    21.6    +      -       +      +
   1489C  GLN*     5.7     0.5    -      -       -      +
   1490C  THR*     1.3    81.0    -      -       -      +
   1492C  ILE*     1.3    68.1    +      -       -      +
   1493C  SER      4.0     0.9    +      -       -      -
   1496C  GLU*     3.9     5.0    -      -       -      +
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Residues in contact with ILE1492 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1463C  TRP*     3.2     9.3    -      -       -      -
   1464C  ILE*     2.8    57.3    +      -       +      +
   1466C  ARG*     3.6    32.8    -      -       +      +
   1490C  THR*     4.2    17.5    -      -       +      -
   1491C  THR*     1.3    79.0    -      -       -      +
   1493C  SER*     1.3    69.1    +      -       -      +
   1496C  GLU*     3.3    30.7    -      -       +      +
   1497C  ASN*     3.7    17.5    -      -       +      +
   1500C  GLU*     4.2    11.7    -      -       -      +
----------------------------------------------------------
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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