Contacts of the strand formed by residues 150 - 155 (chain 4) in PDB entry 1O19


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 GLY 150 (chain 4).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1424  LEU*     3.8    14.1    -      -       -      +
    1494  THR*     1.3    78.3    -      -       -      +
    1514  ILE*     1.3    62.1    +      -       -      +
    1634  VAL      4.2     0.2    -      -       -      +
    1644  PRO*     3.7     0.7    -      -       -      +
    1654  ILE*     2.9    29.1    +      -       -      +
    2934  LEU*     3.8    13.2    -      -       -      +
    2964  ASN*     3.2    20.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 151 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1424  LEU*     4.4     0.2    -      -       -      +
    1504  GLY*     1.3    74.2    -      -       -      +
    1524  VAL*     1.3    65.7    +      -       -      +
    1534  LEU      4.0     0.5    +      -       -      -
    1624  ASN*     4.5     6.5    -      -       +      +
    1634  VAL      3.7     8.3    -      -       -      +
    1644  PRO*     3.9    21.5    -      -       +      -
    2784  THR*     3.6    29.8    -      -       +      +
    2814  SER*     3.6    20.9    -      -       -      +
    2824  ILE*     3.7    12.1    -      -       +      -
    2934  LEU*     3.4    33.4    -      -       +      +
    2964  ASN      2.8     8.4    +      -       -      +
    2974  ASN*     3.4    20.4    -      -       -      +
    2984  VAL      2.9    23.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 152 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1384  ALA*     3.3    41.5    -      -       +      +
    1414  SER*     4.3     2.9    -      -       -      -
    1424  LEU*     3.8    30.7    -      -       +      +
    1514  ILE*     1.3    73.3    -      -       -      +
    1534  LEU*     1.3    68.4    +      -       -      +
    1544  ASP*     3.6     9.8    +      -       +      -
    1614  HIS      3.6     0.3    -      -       -      +
    1624  ASN*     3.2     6.5    -      -       -      -
    1634  VAL*     2.9    32.6    +      -       -      +
    1654  ILE*     4.5     1.6    -      -       +      -
    2974  ASN*     5.6     0.2    -      -       -      -
    2984  VAL*     3.1    14.8    -      -       +      +
    3004  SER*     3.6    24.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 153 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1514  ILE      4.0     1.2    +      -       -      -
    1524  VAL*     1.3    71.1    -      -       -      +
    1544  ASP*     1.3    60.0    +      -       -      +
    1554  SER*     5.1     2.5    -      -       -      -
    1604  THR*     4.4     8.5    -      -       +      -
    1614  HIS      3.4     8.3    -      -       -      +
    1624  ASN*     3.6    24.5    -      -       -      +
    2744  ILE*     3.6    41.3    -      -       +      +
    2774  THR*     5.9     0.2    -      -       +      -
    2784  THR*     3.9     9.9    -      -       -      +
    2974  ASN*     4.5    13.5    -      -       -      +
    2984  VAL      2.9     7.6    +      -       -      +
    2994  MET*     3.6    33.7    -      -       +      -
    3004  SER      3.1    24.1    +      -       -      +
    3044  THR*     4.0    13.5    -      -       +      -
    3094  ILE*     5.7     5.2    -      -       +      -
    3134  MET*     4.5     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 154 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1094  PRO*     5.9     1.9    -      -       -      +
    1374  GLN*     4.0    26.0    -      -       -      +
    1384  ALA*     4.1    11.2    +      -       +      -
    1524  VAL*     3.6    12.5    +      -       +      +
    1534  LEU*     1.3    73.8    -      -       -      +
    1554  SER*     1.4    64.5    +      -       -      +
    1564  GLY      5.1     0.2    +      -       -      -
    1594  VAL      4.0     1.6    -      -       -      +
    1604  THR*     3.2     3.7    -      -       -      +
    1614  HIS*     2.7    51.2    +      -       +      +
    1634  VAL*     5.8     0.2    -      -       +      -
    3004  SER*     3.0    30.0    +      -       -      +
    3014  GLY*     4.0     4.2    +      -       -      -
    3394  VAL*     4.2     9.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 155 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1534  LEU*     5.1     3.8    -      -       -      -
    1544  ASP*     1.4    75.9    +      -       -      +
    1564  GLY*     1.3    60.9    +      -       -      +
    1594  VAL      3.6     4.0    -      -       -      -
    1604  THR*     2.6    27.2    +      -       -      +
    1804  LEU      4.6     0.5    +      -       -      -
    1814  ALA*     4.5     2.4    -      -       -      +
    2614  LEU*     4.8     4.8    -      -       -      +
    2744  ILE*     6.1     0.9    -      -       -      -
    3004  SER      3.1     8.3    +      -       -      -
    3014  GLY*     3.2    13.9    -      -       -      -
    3034  THR*     3.1    38.9    +      -       -      +
    3044  THR*     3.6    19.5    -      -       -      -
----------------------------------------------------------
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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