Contacts of the strand formed by residues 215 - 220 (chain H) in PDB entry 3Q3G


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 215 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129H  PRO*     3.6     6.5    -      -       +      +
    130H  PRO*     4.8     5.2    -      -       +      +
    208H  VAL      4.7     0.4    -      -       -      -
    209H  ALA*     3.5     2.6    -      -       -      -
    210H  HIS*     3.0    35.9    +      -       -      +
    211H  PRO*     5.4     0.2    -      -       -      +
    213H  SER*     2.7    26.4    +      -       -      -
    214H  SER*     1.4    74.9    -      -       -      +
    216H  LYS*     1.3    70.2    +      -       -      +
    217H  VAL*     3.7    24.5    -      -       +      -
    217K  VAL*     4.7     4.3    -      -       +      -
    218K  ASP      4.0     2.0    -      -       -      -
    219K  LYS*     2.9    21.7    +      -       -      +
    601K  EDO      4.1    21.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 216 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208H  VAL      3.4     5.6    -      -       -      +
    209H  ALA*     4.2    17.5    -      -       +      -
    214H  SER      5.9     0.4    -      -       -      -
    215H  THR*     1.3    76.8    -      -       -      +
    217H  VAL*     1.3    64.3    +      -       -      +
    218H  ASP*     5.2     3.8    -      -       -      +
    216K  LYS      4.8     0.2    -      -       -      -
    217K  VAL*     3.5     4.3    -      -       -      +
    218K  ASP*     3.1    51.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 217 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130H  PRO*     5.0     7.9    -      -       +      +
    132H  VAL*     3.9    39.0    -      -       +      +
    206H  CYS      3.8     0.9    -      -       -      +
    208H  VAL*     2.8    37.3    +      -       +      +
    215H  THR*     3.7    20.4    -      -       +      -
    216H  LYS*     1.3    78.6    -      -       -      +
    218H  ASP*     1.3    77.0    +      -       -      +
    219H  LYS*     4.2     3.1    -      -       +      -
    801H   NA      4.5     8.3    -      -       -      -
    215K  THR*     4.5     5.8    -      -       +      -
    216K  LYS      3.5    10.1    -      -       -      +
    217K  VAL*     4.5    15.7    -      -       +      -
    601K  EDO      5.1     4.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 218 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167H  SER*     5.2     1.0    +      -       -      -
    205H  THR*     4.2    10.5    -      -       +      +
    206H  CYS      3.4     3.6    -      -       -      -
    207H  ASN*     3.1    30.9    +      -       -      +
    216H  LYS*     5.2     3.5    -      -       -      +
    217H  VAL*     1.3    81.8    +      -       -      +
    219H  LYS*     1.3    60.5    +      -       -      +
    220H  LYS      4.2     0.4    -      -       -      -
    214K  SER      3.7     5.2    -      -       -      +
    215K  THR*     3.7     2.1    -      -       -      -
    216K  LYS*     2.9    50.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 219 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129F  GLU*     3.2    43.4    +      -       -      +
    132H  VAL*     3.5    32.3    +      -       +      +
    134H  PRO*     4.1    23.1    -      -       +      -
    205H  THR*     3.4     4.7    -      -       -      +
    206H  CYS*     2.9    49.1    +      -       -      -
    217H  VAL*     4.2     1.8    -      -       +      -
    218H  ASP*     1.3    74.3    -      -       -      +
    220H  LYS*     1.3    66.7    +      -       -      +
    221H  ILE*     3.6     6.2    +      -       +      +
    129K  PRO*     3.9     9.9    -      -       -      +
    213K  SER      3.3    14.8    +      -       -      -
    214K  SER      3.7     3.1    -      -       -      +
    215K  THR*     2.9    28.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 220 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78D  SER*     6.2     0.6    -      -       -      -
    134H  PRO*     4.4     4.9    -      -       -      +
    202H  GLU      5.6     1.1    -      -       -      -
    203H  THR*     3.6    32.3    +      -       +      +
    204H  VAL      4.1     4.0    -      -       -      +
    205H  THR*     3.6    21.6    -      -       +      +
    218H  ASP      4.2     0.8    -      -       -      -
    219H  LYS*     1.3    79.0    -      -       -      +
    221H  ILE*     1.3    67.1    +      -       -      +
    222H  VAL*     3.3    29.0    +      -       +      +
    214K  SER*     3.2    33.3    +      -       -      +
----------------------------------------------------------
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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