Contacts of the helix formed by residues 382 - 389 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147T PRO* 4.1 23.8 - - + -
149T GLN* 4.3 14.6 - - + +
381T GLN* 1.3 76.6 - - - +
383T LYS* 1.3 59.2 + - - +
384T ALA* 3.0 11.0 - - + +
385T LEU* 2.9 16.1 + - + +
386T LYS* 2.8 24.3 + - - +
440T THR* 4.0 27.4 - - + +
489T GLY* 3.3 29.8 - - - +
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Residues in contact with LYS 383 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378T SER 6.0 0.4 - - - +
381T GLN 3.4 4.9 + - - +
382T VAL* 1.3 76.0 - - - +
384T ALA* 1.3 57.6 + - - +
386T LYS* 3.7 30.5 - - + +
387T GLN* 3.1 38.9 + - + +
489T GLY 4.1 0.6 + - - -
490T GLU* 3.6 46.5 + - + +
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Residues in contact with ALA 384 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382T VAL* 3.0 7.6 - - + -
383T LYS* 1.3 78.1 - - - +
385T LEU* 1.3 61.0 + - - +
388T VAL* 3.2 17.0 + - - +
440T THR* 4.8 2.7 - - + -
444T VAL* 3.4 19.3 - - + +
485T ILE* 4.1 17.0 - - + -
489T GLY 3.1 24.8 + - - +
490T GLU* 4.5 1.1 - - - +
491T LEU* 3.4 29.1 - - + +
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Residues in contact with LEU 385 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156T ASP* 3.9 24.2 - - + +
157T ALA* 5.5 4.9 - - + -
381T GLN* 3.6 17.4 + - + +
382T VAL* 2.9 17.9 + - + +
384T ALA* 1.3 77.6 - - - +
386T LYS* 1.3 64.0 + - - +
387T GLN 3.2 0.7 - - - -
388T VAL* 3.3 6.4 - - + +
389T ALA* 3.1 30.9 + - + +
440T THR* 3.8 26.9 - - + +
443T GLN* 3.9 35.2 - - + +
444T VAL* 3.6 19.3 - - + +
447T ILE* 4.5 8.3 - - + -
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Residues in contact with LYS 386 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378T SER* 3.8 39.2 - - - +
381T GLN* 4.3 15.5 - - + +
382T VAL 2.8 15.3 + - - +
383T LYS* 3.7 33.2 - - + +
384T ALA 3.3 0.2 - - - -
385T LEU* 1.3 78.9 - - - +
387T GLN* 1.3 62.4 + - + +
389T ALA* 3.3 17.8 - - - +
390T GLY* 4.9 1.4 - - - -
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Residues in contact with GLN 387 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383T LYS* 3.1 21.1 + - + +
384T ALA 3.7 0.2 + - - -
385T LEU 3.2 0.4 - - - -
386T LYS* 1.3 82.9 - - + +
388T VAL* 1.3 65.9 + - - +
389T ALA 3.2 1.9 + - - -
390T GLY* 4.0 7.3 + - - -
490T GLU* 4.8 5.7 + - - +
491T LEU* 3.1 60.3 + - + +
496T LEU* 5.2 10.1 - - + +
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Residues in contact with VAL 388 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384T ALA 3.2 14.1 + - - +
385T LEU* 3.3 15.7 - - + +
387T GLN* 1.3 76.3 - - - +
389T ALA* 1.3 60.9 + - - +
390T GLY 3.4 4.9 + - - -
444T VAL* 3.2 33.4 - - + +
447T ILE* 3.7 18.8 - - + +
448T TYR* 4.0 28.3 - - + +
451T VAL* 3.5 27.4 - - - +
491T LEU* 3.6 23.1 - - + -
496T LEU* 6.2 0.7 - - + -
499T LEU* 5.0 4.7 - - + -
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Residues in contact with ALA 389 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157T ALA* 4.9 16.2 - - + +
381T GLN* 5.0 3.8 - - - +
385T LEU* 3.1 18.3 + - + +
386T LYS* 3.3 16.0 - - - +
387T GLN 4.1 0.2 - - - -
388T VAL* 1.3 75.3 - - + +
390T GLY* 1.3 60.4 + - - +
391T SER 3.2 7.8 + - - -
392T LEU* 4.5 17.4 + - + +
447T ILE* 3.6 18.8 - - + -
451T VAL* 4.7 3.1 - - - -
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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