Contacts of the strand formed by residues 36 - 45 (chain G) in PDB entry 4CDC


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 GLN 36 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18G  GLN*     2.9    40.3    +      -       +      +
     19G  VAL      3.5    13.2    -      -       -      +
     20G  GLY*     3.8     1.1    -      -       -      +
     33G  MET*     3.2    36.4    -      -       -      +
     34G  GLY      4.1     5.4    -      -       -      +
     35G  PRO*     1.3    80.2    -      -       +      +
     37G  GLU*     1.3    62.2    +      -       -      +
     38G  LYS      3.8     0.7    -      -       -      +
    114G  THR*     3.3    19.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 37 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19G  VAL      2.8    10.0    +      -       -      +
     20G  GLY*     3.7     3.6    -      -       -      -
     21G  SER*     3.7     6.6    +      -       -      -
     22G  SER*     3.0    36.4    +      -       -      +
     35G  PRO*     3.0    35.6    -      -       +      +
     36G  GLN*     1.3    74.4    -      -       -      +
     38G  LYS*     1.3    60.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 38 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18G  GLN*     3.6     4.6    -      -       -      +
     19G  VAL*     2.7    45.9    +      -       +      +
     36G  GLN*     3.8     1.0    -      -       -      +
     37G  GLU*     1.3    82.5    -      -       +      +
     39G  LYS*     1.3    74.4    +      -       -      +
     40G  VAL*     4.5    11.3    -      -       +      +
    255K  GLN*     5.7     9.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 39 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16G  VAL*     4.1    21.7    -      -       +      +
     17G  PHE      3.2     6.5    -      -       -      +
     18G  GLN*     3.7    18.6    -      -       -      +
     38G  LYS*     1.3    89.4    +      -       -      +
     40G  VAL*     1.3    68.2    -      -       -      +
     41G  VAL*     4.6    16.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 40 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15G  TRP      3.8     0.7    -      -       -      +
     16G  VAL*     3.6     1.3    -      -       -      -
     17G  PHE*     2.8    34.9    +      -       +      +
     19G  VAL*     4.6     7.6    -      -       +      -
     38G  LYS*     4.5    14.6    -      -       +      +
     39G  LYS*     1.3    79.5    -      -       -      +
     41G  VAL*     1.3    69.5    +      -       -      +
     42G  VAL*     4.0    20.5    +      -       +      -
     52G  ASP*     5.6     4.7    -      -       +      -
     72G  LEU*     6.1     1.1    -      -       +      -
     77G  TRP*     4.0    32.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 41 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14G  THR*     3.6    29.4    -      -       +      -
     15G  TRP      3.4     5.6    -      -       -      +
     16G  VAL*     4.6    13.9    -      -       +      -
     39G  LYS*     4.6    24.0    -      -       +      +
     40G  VAL*     1.3    75.4    -      -       -      +
     42G  VAL*     1.3    65.5    +      -       -      +
     43G  TYR*     3.7    19.5    -      -       +      +
     52G  ASP*     3.8    23.0    -      -       -      +
     53G  ASP*     3.8    21.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 42 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13G  GLY      3.8     0.7    -      -       -      +
     14G  THR      3.7     0.7    -      -       -      -
     15G  TRP*     2.8    41.1    +      -       +      +
     17G  PHE*     3.8    32.5    -      -       +      -
     40G  VAL*     4.0    13.5    -      -       +      -
     41G  VAL*     1.3    78.6    -      -       -      +
     43G  TYR*     1.3    65.0    +      -       -      +
     44G  LEU*     3.7    26.0    +      -       +      -
     50G  ALA*     4.7     1.1    -      -       +      -
     51G  TYR      3.5     8.3    -      -       -      +
     70G  ILE*     4.1    13.7    -      -       +      -
     72G  LEU*     4.2    23.3    -      -       +      -
     77G  TRP*     5.2     4.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 43 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13G  GLY      3.5     4.7    -      -       -      +
     14G  THR*     3.2    37.0    -      -       +      -
     41G  VAL*     3.7    18.2    -      -       +      +
     42G  VAL*     1.3    73.7    -      -       -      +
     44G  LEU*     1.3    63.7    +      -       -      +
     45G  GLN*     4.1     3.1    -      -       +      +
     49G  THR      3.8     0.2    -      -       -      +
     50G  ALA*     3.4     4.9    -      -       -      -
     51G  TYR*     2.7    89.1    +      +       +      +
     52G  ASP*     4.2    11.0    -      -       -      -
     53G  ASP*     2.6    31.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 44 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11G  LEU*     3.5    49.8    -      -       +      +
     12G  LEU*     3.8     7.4    -      -       -      +
     13G  GLY*     2.9    27.3    +      -       -      +
     15G  TRP*     3.9    16.2    -      -       +      -
     42G  VAL*     3.7    20.6    -      -       +      -
     43G  TYR*     1.3    80.6    -      -       -      +
     45G  GLN*     1.3    64.8    +      -       -      +
     49G  THR      3.5     1.6    -      -       -      -
     50G  ALA*     4.0     8.5    -      -       +      -
     60G  PHE*     3.9    32.3    -      -       +      -
     68G  PHE*     5.6     0.2    -      -       +      -
     70G  ILE*     3.8    21.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 45 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    332E  ASN*     3.4    21.0    -      -       +      +
    333E  GLU*     3.1    36.5    +      -       -      +
    334E  ALA*     3.1    27.2    +      -       -      +
    420F  GLY      5.1     5.7    +      -       -      -
     12G  LEU*     4.0     4.7    -      -       -      -
     43G  TYR*     5.0     2.5    -      -       +      +
     44G  LEU*     1.3    80.6    -      -       -      +
     46G  LYS*     1.3    62.4    +      -       -      +
     49G  THR*     2.9    37.2    +      -       -      +
     51G  TYR*     3.4    27.4    +      -       +      -
     60G  PHE*     3.3     3.3    -      -       -      -
----------------------------------------------------------
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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