Contacts of the helix formed by residues 382 - 389 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147K PRO* 4.2 19.7 - - + -
149K GLN* 4.6 14.4 - - + +
381K GLN* 1.3 74.8 - - - +
383K LYS* 1.3 57.9 + - - +
384K ALA* 3.9 2.5 - - + +
385K LEU* 2.8 39.0 + - + +
386K LYS* 3.2 8.8 + - - +
440K THR* 3.8 37.2 - - + +
489K GLY* 3.2 31.9 - - - +
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Residues in contact with LYS 383 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378K SER 5.8 2.0 - - - +
381K GLN 3.3 7.2 + - - +
382K VAL* 1.3 73.7 - - - +
384K ALA* 1.3 62.5 + - - +
386K LYS* 3.6 17.4 - - + +
387K GLN* 3.2 34.7 + - - +
489K GLY 4.2 0.4 + - - -
490K GLU* 3.6 46.4 + - + +
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Residues in contact with ALA 384 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382K VAL* 3.0 6.5 - - + -
383K LYS* 1.3 77.9 - - - +
385K LEU* 1.3 62.7 + - - +
387K GLN* 3.4 3.3 + - - +
388K VAL* 3.3 26.2 + - - +
440K THR* 5.0 1.6 - - + -
444K VAL* 3.6 17.9 - - + -
485K ILE* 4.4 11.0 - - + -
489K GLY 3.1 26.5 + - - +
490K GLU* 4.2 3.1 - - - +
491K LEU* 4.1 22.1 - - + +
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Residues in contact with LEU 385 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156K ASP* 3.1 30.7 - - + +
157K ALA* 5.2 6.1 - - + -
381K GLN* 4.0 20.4 - - + +
382K VAL* 2.8 29.6 + - + +
384K ALA* 1.3 73.2 - - - +
386K LYS* 1.3 65.5 + - - +
388K VAL* 3.0 25.3 - - + +
389K ALA* 3.1 14.1 + - + +
440K THR* 4.4 11.0 - - + +
443K GLN* 3.9 33.2 - - + +
444K VAL* 3.9 19.1 - - + +
447K ILE* 4.8 6.7 - - + -
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Residues in contact with LYS 386 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378K SER* 3.3 40.7 - - - +
381K GLN* 3.7 17.8 + - + +
382K VAL 3.2 5.9 + - - +
383K LYS* 3.6 22.7 - - + +
385K LEU* 1.3 79.8 - - - +
387K GLN* 1.3 65.2 + - + +
389K ALA* 3.7 16.2 + - - +
390K GLY* 4.3 2.8 + - - -
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Residues in contact with GLN 387 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383K LYS* 3.2 22.9 + - - +
384K ALA 3.8 5.8 - - - +
385K LEU 3.1 1.0 - - - -
386K LYS* 1.3 81.7 - - + +
388K VAL* 1.3 64.1 + - + +
389K ALA 3.5 0.5 + - - -
390K GLY* 4.2 6.2 + - - -
448K TYR* 6.0 0.2 - - - -
490K GLU* 5.0 3.8 + - - +
491K LEU* 3.2 48.2 + - + +
496K LEU* 5.0 9.9 - - + +
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Residues in contact with VAL 388 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384K ALA 3.3 15.3 - - - +
385K LEU* 3.0 22.2 - - + +
387K GLN* 1.3 76.8 - - + +
389K ALA* 1.3 58.4 + - + +
390K GLY 3.6 0.7 - - - -
444K VAL* 3.7 31.4 - - + +
447K ILE* 3.1 37.5 - - + +
448K TYR* 4.3 19.5 + - + +
451K VAL* 3.3 19.6 - - - +
491K LEU* 3.6 23.1 - - + -
499K LEU* 6.1 1.6 - - + -
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Residues in contact with ALA 389 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157K ALA* 5.1 14.6 - - + +
381K GLN* 5.9 1.8 - - - +
385K LEU* 3.1 15.0 + - + +
386K LYS* 3.8 9.9 - - - +
387K GLN 3.3 0.4 - - - -
388K VAL* 1.3 77.4 - - + +
390K GLY* 1.3 59.8 + - - +
391K SER* 2.8 10.9 + - - -
392K LEU* 3.4 24.4 + - + -
447K ILE* 3.7 16.8 - - + -
451K VAL* 4.1 3.8 - - - -
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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
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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