Contacts of the helix formed by residues 308 - 317 (chain F) in PDB entry 4LQL
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 ASP 308 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190F VAL 3.8 2.6 - - - +
191F THR* 3.1 39.7 - - - +
276F THR* 4.1 2.0 - - - -
304F GLY* 3.7 6.2 + - - -
305F PRO* 4.8 2.5 - - + -
306F GLU 3.3 3.2 + - - +
307F GLY* 1.3 73.9 - - - +
309F PHE* 1.3 55.5 + - - +
310F LYS* 3.1 15.1 + - - +
311F MET* 3.2 15.2 + - + +
312F ALA* 2.8 23.6 + - - +
446F HIS* 6.0 0.9 - - - -
447F HIS* 2.7 50.1 + - + +
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Residues in contact with PHE 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178F ILE* 5.3 9.2 - - + -
191F THR 4.3 7.0 + - - -
204F TRP* 5.4 6.8 - - - -
206F VAL* 6.1 6.3 - - - -
276F THR* 4.1 6.1 - - + -
307F GLY 2.8 13.0 + - - +
308F ASP* 1.3 68.7 + - - +
310F LYS* 1.3 62.6 + - - +
312F ALA* 3.4 15.9 - - + -
313F GLY* 3.4 16.6 + - - -
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Residues in contact with LYS 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F VAL 5.1 4.0 - - - +
191F THR 4.8 4.4 + - - +
192F GLU 5.7 2.5 - - - +
308F ASP* 3.1 14.0 + - - +
309F PHE* 1.3 80.5 - - - +
311F MET* 1.3 57.3 + - - +
314F LEU* 2.9 27.1 + - - +
393F LEU* 3.9 42.9 - - + +
400F TYR* 5.5 7.4 - - + +
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Residues in contact with MET 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303F PHE 3.9 6.0 - - - +
304F GLY* 5.5 1.6 - - - -
305F PRO* 6.2 0.7 - - + -
308F ASP* 3.2 22.5 + - + +
310F LYS* 1.3 80.0 - - - +
312F ALA* 1.3 67.6 + - - +
314F LEU* 3.6 8.0 - - + +
315F THR* 3.1 22.2 + - - -
329F LEU* 5.2 10.5 - - + +
391F ILE 5.3 0.2 - - - +
392F THR* 5.5 1.1 - - - +
393F LEU 6.0 0.7 - - - +
447F HIS* 4.1 18.2 - - + +
448F THR 3.4 29.6 - - - +
449F VAL* 3.9 16.6 - - + -
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Residues in contact with ALA 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178F ILE* 4.8 9.4 - - + -
274F ALA* 4.9 1.6 - - - -
275F PHE 4.3 3.6 - - - +
276F THR* 3.9 9.2 - - + -
302F GLY* 4.1 4.9 - - - +
303F PHE 3.5 8.1 + - - +
304F GLY* 3.5 29.2 - - - +
308F ASP 2.8 6.5 + - - -
309F PHE* 3.4 24.2 - - + -
310F LYS 3.5 0.2 - - - -
311F MET* 1.3 74.1 - - - +
313F GLY* 1.3 60.9 + - - +
315F THR* 2.6 25.5 + - - -
316F ARG 3.6 2.4 + - - -
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Residues in contact with GLY 313 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176F ILE* 4.8 11.1 - - - +
178F ILE* 5.4 4.9 - - - +
204F TRP* 5.4 9.4 - - - -
274F ALA* 5.0 4.2 - - - +
309F PHE 3.4 10.0 + - - -
312F ALA* 1.3 74.3 - - - +
314F LEU* 1.3 52.8 + - - +
315F THR 3.0 2.9 - - - -
316F ARG* 3.0 10.5 + - - +
317F LEU* 2.4 45.9 + - - +
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Residues in contact with LEU 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309F PHE 4.6 0.2 + - - -
310F LYS 2.9 25.5 + - - +
311F MET* 3.6 11.2 - - + +
312F ALA 3.2 1.0 - - - -
313F GLY* 1.3 76.3 - - - +
315F THR* 1.3 55.5 + - - +
317F LEU* 3.5 12.8 - - + +
318F LEU* 3.0 46.6 + - + +
391F ILE* 4.2 12.8 - - + +
392F THR* 4.3 3.1 - - - -
393F LEU* 4.1 40.2 - - + +
402F PHE* 6.5 0.4 - - + -
449F VAL* 3.7 26.2 - - + -
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Residues in contact with THR 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297F MET* 6.4 1.6 - - - -
302F GLY* 3.9 0.7 - - - -
303F PHE 3.6 21.2 + - - -
311F MET* 3.1 10.2 + - - -
312F ALA 2.6 22.5 + - - -
314F LEU* 1.3 75.8 - - - +
316F ARG* 1.3 52.8 + - - +
318F LEU* 3.0 5.5 - - - -
319F LYS* 2.4 58.9 + - - +
327F THR* 5.7 1.1 - - - -
328F ALA 5.4 0.9 - - - -
329F LEU* 5.0 12.6 - - - -
449F VAL* 4.4 12.8 - - - +
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Residues in contact with ARG 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176F ILE* 4.3 14.8 - - + -
273F ASP* 4.8 8.5 - - + +
274F ALA* 4.3 11.2 - - + -
300F GLY 5.0 2.7 - - - +
301F TYR* 5.9 0.2 - - - -
302F GLY* 4.2 21.6 - - - +
312F ALA 3.6 0.4 + - - -
313F GLY* 3.0 10.7 + - - +
315F THR* 1.3 78.8 + - - +
317F LEU* 1.3 62.8 + - - +
318F LEU 3.3 0.3 + - - -
319F LYS* 4.2 5.8 - - - +
320F ILE* 3.5 26.9 + - - +
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Residues in contact with LEU 317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169F ALA* 4.2 19.3 - - + +
173F SER* 4.0 26.2 - - - +
176F ILE* 5.2 5.6 - - + +
202F LEU* 5.6 5.6 - - + +
204F TRP* 5.2 13.7 - - + -
313F GLY* 2.4 41.5 + - - +
314F LEU* 3.5 19.1 - - + +
316F ARG* 1.3 67.9 - - - +
318F LEU* 1.3 61.1 + - + +
319F LYS 3.6 0.2 - - - -
320F ILE* 4.4 5.3 + - - +
321F ALA* 4.9 2.4 + - - +
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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
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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