Contacts of the strand formed by residues 27 - 34 (chain D) in PDB entry 3FTN


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 ALA 27 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22D  PRO*     4.5     0.9    -      -       -      -
     26D  ASP*     1.3    75.6    -      -       -      +
     28D  ILE*     1.3    67.8    +      -       -      +
     29D  VAL*     4.4     5.2    -      -       +      -
     65D  VAL*     4.4     6.7    -      -       +      -
     67D  GLU      3.1    12.3    -      -       -      +
     68D  VAL*     3.9    12.3    -      -       +      -
     75D  PHE*     5.8     0.2    -      -       +      -
    125D  HIS*     3.8     0.2    -      -       -      -
    126D  VAL*     2.9    34.6    +      -       +      +
    129D  ALA*     3.7    21.2    -      -       +      +
    133D  LEU*     4.1    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 28 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19D  LYS*     4.6     5.2    -      -       -      -
     20D  PRO*     3.2    35.4    -      -       +      +
     21D  ALA      3.9    10.3    -      -       -      -
     22D  PRO*     3.4    21.8    -      -       +      -
     27D  ALA*     1.3    79.9    -      -       -      +
     29D  VAL*     1.3    59.4    +      -       -      +
     65D  VAL*     3.7     1.0    -      -       -      +
     66D  VAL*     2.7    44.9    +      -       +      -
     67D  GLU*     2.7    27.7    +      -       +      +
    123D  PHE*     4.0    22.7    -      -       +      -
    124D  PHE      3.5    10.8    -      -       -      +
    125D  HIS*     4.1    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 29 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27D  ALA*     4.2    12.6    -      -       +      +
     28D  ILE*     1.3    80.3    -      -       -      +
     30D  ARG*     1.3    63.5    -      -       -      +
     63D  GLY*     3.9     6.5    -      -       -      -
     64D  GLU      3.6    26.9    -      -       -      +
     65D  VAL*     4.6     5.6    -      -       -      -
     66D  VAL*     4.9     0.2    -      -       -      -
     81D  VAL*     4.2     9.2    -      -       +      -
     83D  VAL*     4.7     0.7    -      -       +      -
    123D  PHE*     3.4     6.1    -      -       -      -
    124D  PHE*     2.9    60.5    +      -       +      -
    126D  VAL*     3.7    26.5    -      -       +      -
    133D  LEU*     4.6    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 30 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19D  LYS*     5.7     0.2    -      -       -      +
     29D  VAL*     1.3    74.4    -      -       -      +
     31D  PRO*     1.3    69.8    -      -       -      +
     32D  LEU*     4.7     3.8    -      -       +      -
     63D  GLY*     3.1     2.0    -      -       -      -
     64D  GLU*     2.7    74.1    +      -       +      +
     66D  VAL*     3.8    17.7    -      -       +      +
    122D  GLU*     3.6    17.6    +      -       -      +
    123D  PHE*     3.3    44.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 31 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29D  VAL      4.1     2.9    -      -       -      +
     30D  ARG*     1.3    90.6    -      -       +      +
     32D  LEU*     1.3    65.2    +      -       -      +
     34D  VAL*     3.7    27.1    -      -       +      -
     61D  ALA*     4.6     0.2    -      -       +      -
     62D  VAL      3.6     7.6    -      -       -      +
     63D  GLY*     3.8     1.8    -      -       -      -
    119D  VAL      3.6    11.9    -      -       -      +
    121D  GLY      3.3    19.1    -      -       -      +
    122D  GLU*     3.3    18.8    -      -       -      +
    124D  PHE*     3.9    15.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 32 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30D  ARG*     4.7     4.3    -      -       +      -
     31D  PRO*     1.3    80.1    -      -       -      +
     33D  ALA*     1.3    63.2    +      -       -      +
     62D  VAL*     2.8    12.0    +      -       +      +
     63D  GLY*     4.0    25.6    -      -       -      +
     64D  GLU*     3.9    28.9    -      -       +      +
     80D  ARG*     3.6    45.1    -      -       +      +
    142D  LEU*     4.1    21.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 33 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31D  PRO      3.6     0.2    -      -       -      -
     32D  LEU*     1.3    81.8    -      -       -      +
     34D  VAL*     1.3    69.6    +      -       -      +
     61D  ALA*     3.3     0.3    -      -       -      -
     62D  VAL*     3.0    47.2    +      -       +      +
    142D  LEU*     4.0    23.8    -      -       +      +
    143D  GLU*     5.4     0.9    -      -       -      +
    146D  VAL*     3.7     9.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 34 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31D  PRO*     3.7    25.4    -      -       +      -
     33D  ALA*     1.3    83.3    -      -       -      +
     35D  ALA*     1.3    62.3    +      -       -      +
     60D  GLU      3.2    13.7    -      -       -      +
     61D  ALA*     4.0     6.5    -      -       +      -
    119D  VAL*     4.2    13.0    -      -       +      +
    120D  PHE*     3.6    26.2    -      -       +      -
    146D  VAL*     3.9     8.4    -      -       -      +
----------------------------------------------------------
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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