Contacts of the helix formed by residues 382 - 389 (chain J) in PDB entry 3FKS
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.
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 VAL 382 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147J PRO* 4.4 20.0 - - + -
149J GLN* 4.3 16.6 - - + +
380J ALA 4.0 0.2 + - - -
381J GLN* 1.3 75.7 - - - +
383J LYS* 1.3 68.3 + - - +
384J ALA* 3.8 12.1 - - + +
385J LEU* 2.9 19.4 + - + +
386J LYS* 2.9 22.0 + - - +
440J THR* 4.0 31.4 - - + +
485J ILE* 6.2 0.4 - - + -
489J GLY* 3.9 16.2 - - - +
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Residues in contact with LYS 383 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381J GLN 3.3 5.6 + - - -
382J VAL* 1.3 73.5 - - - +
384J ALA* 1.3 61.4 + - - +
386J LYS* 3.5 12.1 + - + +
387J GLN* 3.0 40.0 + - + +
489J GLY 3.5 9.8 + - - +
490J GLU* 3.1 41.2 + - + +
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Residues in contact with ALA 384 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382J VAL* 3.1 5.3 - - + -
383J LYS* 1.3 73.1 - - - +
385J LEU* 1.3 65.7 + - - +
387J GLN* 3.1 22.8 + - - +
388J VAL* 3.2 13.5 + - - +
444J VAL* 3.9 13.5 - - + -
485J ILE* 4.4 10.1 - - + -
489J GLY* 2.8 31.1 + - - +
490J GLU* 3.7 11.0 - - - +
491J LEU* 3.6 11.2 - - + +
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Residues in contact with LEU 385 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156J ASP* 3.1 44.0 - - + +
157J ALA* 4.1 2.2 - - + -
381J GLN* 3.6 15.3 + - + +
382J VAL* 2.9 22.8 + - + +
384J ALA* 1.3 79.1 - - - +
386J LYS* 1.3 60.9 + - - +
388J VAL* 3.1 18.5 - - - +
389J ALA* 3.3 12.0 + - - +
440J THR* 4.1 13.9 - - + +
443J GLN* 4.0 16.2 - - + +
444J VAL* 3.8 16.5 - - + +
447J ILE* 3.5 31.6 - - + -
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Residues in contact with LYS 386 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378J SER* 4.2 37.0 + - - +
381J GLN* 4.1 21.5 - - + +
382J VAL 2.9 15.4 + - - +
383J LYS* 3.8 12.6 - - + +
384J ALA 3.2 0.2 - - - -
385J LEU* 1.3 76.9 - - - +
387J GLN* 1.3 58.1 + - + +
389J ALA* 3.4 3.6 - - - +
390J GLY* 3.1 28.2 + - - -
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Residues in contact with GLN 387 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383J LYS* 3.0 35.0 - - + +
384J ALA* 3.1 11.0 + - - +
386J LYS* 1.3 77.9 - - + +
388J VAL* 1.3 59.2 + - - +
389J ALA 3.2 5.2 + - - -
390J GLY* 3.8 6.5 + - - -
448J TYR* 6.0 0.2 - - - -
490J GLU* 3.8 2.2 + - - +
491J LEU* 3.0 58.6 + - + +
496J LEU* 5.8 7.3 - - + +
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Residues in contact with VAL 388 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384J ALA 3.2 6.5 + - - +
385J LEU* 3.1 22.9 - - - +
387J GLN* 1.3 76.7 - - - +
389J ALA* 1.3 56.1 + - - +
390J GLY 3.8 0.4 - - - -
444J VAL* 3.5 42.2 - - + +
447J ILE* 3.2 30.1 - - + +
448J TYR* 4.3 24.3 + - + +
451J VAL* 3.5 16.8 - - - +
452J ASN* 5.4 1.3 + - - +
491J LEU* 3.5 26.0 - - + -
499J LEU* 5.1 2.9 - - + -
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Residues in contact with ALA 389 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157J ALA* 4.9 14.3 - - + +
381J GLN* 5.4 1.1 - - - +
385J LEU 3.3 13.7 + - - +
386J LYS* 3.4 7.3 - - - +
387J GLN 3.2 0.4 - - - -
388J VAL* 1.3 81.1 - - + +
390J GLY* 1.3 63.2 + - - +
391J SER 3.2 3.1 + - - -
392J LEU* 3.6 33.4 + - + +
393J LYS* 5.0 0.9 + - - +
447J ILE* 3.8 16.2 - - + -
451J VAL* 4.8 2.2 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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