Contacts of the strand formed by residues 398 - 407 (chain H) in PDB entry 1FNS


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 TYR 398 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    304H  THR*     5.6     2.6    -      -       -      +
    333H  THR*     3.6    24.0    +      -       +      +
    367H  GLY      3.1     7.6    +      -       -      -
    368H  TYR*     2.7    67.8    +      -       +      +
    369H  PHE*     3.7    26.0    -      +       -      -
    370H  PRO*     4.4     1.1    -      -       +      -
    371H  GLU*     3.7    44.2    -      -       +      +
    391H  ALA*     4.1    13.5    -      -       +      -
    392H  VAL      3.4    10.1    -      -       -      -
    393H  LEU*     3.7    35.9    -      -       +      +
    397H  LEU*     1.3    73.9    -      -       -      +
    399H  THR*     1.3    62.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 399 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    364H  LEU*     3.8    25.4    -      -       +      -
    365H  VAL      3.3    12.8    -      -       -      +
    366H  LYS*     3.5    17.4    -      -       +      +
    367H  GLY*     3.6     1.7    +      -       -      -
    368H  TYR*     4.2     0.9    -      -       -      -
    390H  PRO      4.4     0.7    -      -       -      +
    391H  ALA*     3.3     3.6    -      -       -      -
    392H  VAL*     2.9    41.9    +      -       +      +
    394H  GLN*     2.8    33.3    +      -       -      +
    397H  LEU      4.9     0.2    +      -       -      -
    398H  TYR*     1.3    78.0    +      -       -      +
    400H  LEU*     1.3    66.8    +      -       -      +
    178L  THR*     5.9     4.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 400 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    364H  LEU*     3.9     2.1    -      -       -      +
    365H  VAL*     2.8    54.8    +      -       +      +
    368H  TYR*     3.5    21.1    -      -       -      +
    371H  GLU*     5.0     1.8    -      -       -      +
    373H  VAL*     3.5    19.1    -      -       +      +
    375H  VAL*     3.9    14.8    -      -       +      -
    388H  THR*     4.3     9.6    -      -       +      -
    389H  PHE*     3.5    23.8    -      -       -      +
    390H  PRO      4.3     2.0    -      -       -      +
    391H  ALA*     3.8    12.1    -      -       +      +
    399H  THR*     1.3    78.3    -      -       -      +
    401H  SER*     1.3    77.1    +      -       -      +
    402H  SER      4.6     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 401 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    347H  LEU*     4.2     0.5    -      -       -      +
    363H  CYS      3.3    10.9    +      -       -      -
    364H  LEU*     3.5    25.3    -      -       -      +
    389H  PHE*     2.9    33.7    +      -       -      +
    400H  LEU*     1.3    77.1    -      -       -      +
    402H  SER*     1.3    62.5    +      -       -      +
    133L  VAL*     4.1    12.3    -      -       -      +
    135L  PHE*     3.7    22.6    -      -       -      -
    176L  SER*     3.9    11.4    -      -       -      -
    178L  THR*     4.6     3.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 402 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    362H  GLY*     3.1     3.1    -      -       -      -
    363H  CYS*     2.9    34.2    +      -       -      -
    375H  VAL*     3.7    22.2    -      -       -      +
    377H  TRP*     2.8    28.8    +      -       -      -
    386H  VAL*     4.0     1.2    -      -       -      +
    387H  HIS      3.3     7.7    +      -       -      -
    388H  THR*     2.8    27.6    +      -       -      -
    389H  PHE*     4.7     0.2    -      -       -      -
    400H  LEU*     5.0     0.4    -      -       -      -
    401H  SER*     1.3    75.1    -      -       -      +
    403H  SER*     1.3    61.4    +      -       -      +
    135L  PHE*     3.8     4.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 403 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    360H  THR*     4.1     4.7    -      -       -      +
    361H  LEU      3.2     8.1    -      -       -      -
    377H  TRP*     4.4     2.0    -      -       -      -
    385H  GLY      3.7     0.7    +      -       -      +
    386H  VAL*     3.3     6.9    -      -       -      +
    387H  HIS*     2.8    44.9    +      -       -      +
    389H  PHE*     4.5     0.4    -      -       -      -
    402H  SER*     1.3    73.8    +      -       -      +
    404H  VAL*     1.3    62.7    +      -       -      +
    405H  THR*     5.1     0.3    +      -       -      -
    135L  PHE*     3.4    37.6    -      -       -      -
    137L  ASN*     3.1    23.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 404 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    359H  VAL      3.7     1.2    -      -       -      +
    360H  THR*     3.2     1.5    -      -       -      -
    361H  LEU*     2.8    45.9    +      -       +      +
    377H  TRP*     3.5    42.2    -      -       +      -
    382H  LEU*     4.3    14.4    -      -       +      -
    385H  GLY*     3.3     7.9    -      -       -      +
    386H  VAL*     3.7    20.2    -      -       +      -
    403H  SER*     1.3    76.0    -      -       -      +
    405H  THR*     1.3    67.3    +      -       -      +
    406H  VAL*     3.8    20.1    +      -       +      -
    416H  VAL*     4.2     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 405 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    358H  MET*     3.7    38.0    -      -       +      +
    359H  VAL      3.3     4.0    -      -       -      +
    360H  THR*     2.6    28.9    +      -       -      +
    382H  LEU*     5.6     0.7    -      -       -      +
    385H  GLY*     3.0    28.5    +      -       -      -
    387H  HIS*     5.7     1.6    -      -       -      -
    403H  SER*     5.1     0.3    +      -       -      -
    404H  VAL*     1.3    75.5    -      -       -      +
    406H  VAL*     1.3    67.5    +      -       -      +
    137L  ASN*     4.7     7.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 406 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    358H  MET*     3.4     7.8    -      -       -      -
    359H  VAL*     2.9    51.5    +      -       +      +
    361H  LEU*     4.5     7.2    -      -       +      -
    382H  LEU*     3.8    27.4    -      -       +      -
    404H  VAL*     3.8    24.2    -      -       +      -
    405H  THR*     1.3    80.8    -      -       -      +
    407H  PRO*     1.3    75.3    -      -       +      +
    410H  THR*     3.5    18.8    -      -       -      +
    411H  TRP*     4.2    10.8    -      -       +      -
    416H  VAL*     4.8     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 407 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    357H  SER      3.8     2.0    -      -       -      +
    358H  MET*     3.6    24.9    -      -       +      -
    359H  VAL*     4.4     0.2    -      -       -      +
    382H  LEU*     6.2     0.9    -      -       +      -
    406H  VAL*     1.3    92.2    -      -       +      +
    408H  SER*     1.3    60.1    +      -       -      +
    409H  SER*     4.0    15.9    -      -       -      +
    410H  THR*     2.7    42.0    +      -       +      +
    411H  TRP      3.6     2.8    +      -       -      -
----------------------------------------------------------
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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