Contacts of the helix formed by residues 315 - 327 (chain F) in PDB entry 3EXF
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 GLN 315 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218F HIS* 5.1 2.9 - - - -
310F ASP* 3.1 41.4 + - - +
311F ASN* 4.9 5.6 + - - +
313F ILE* 3.4 3.9 + - - +
314F PRO* 1.3 76.3 - - - +
316F VAL* 1.3 67.2 + - - +
317F LYS* 3.3 35.3 + - + +
318F ASP* 3.2 21.0 + - - +
319F ILE* 3.3 23.1 + - - +
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Residues in contact with VAL 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218F HIS* 4.0 22.1 - - + +
221F GLU* 3.4 33.9 - - + +
222F ALA* 3.6 28.3 - - + +
225F VAL* 5.0 4.0 - - + -
315F GLN* 1.3 71.1 - - - +
317F LYS* 1.3 63.2 + - - +
319F ILE* 3.2 10.1 + - - +
320F ILE* 3.0 44.7 + - + +
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Residues in contact with LYS 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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311F ASN* 5.3 6.9 + - - -
315F GLN* 3.4 29.4 - - + +
316F VAL* 1.3 77.3 - - - +
318F ASP* 1.3 67.1 + - - +
320F ILE* 3.4 9.1 + - - +
321F PHE* 3.1 28.4 + - - +
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Residues in contact with ASP 318 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295F VAL* 4.2 11.3 - - + +
310F ASP 5.4 0.2 - - - +
311F ASN* 5.9 1.9 - - - -
313F ILE 4.4 1.0 - - - +
315F GLN* 3.2 36.0 + - - +
316F VAL 3.3 0.6 - - - -
317F LYS* 1.3 84.9 - - - +
319F ILE* 1.3 64.1 + - - +
321F PHE* 3.5 7.1 + - - +
322F ALA* 3.2 20.6 + - - +
351G ALA* 3.7 19.9 - - + +
352G ASN* 3.4 18.7 + - - +
355G ILE* 3.3 26.6 - - - +
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Residues in contact with ILE 319 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209F VAL* 5.0 2.0 - - + -
218F HIS* 3.7 39.0 - - + +
219F CYS* 4.0 17.9 - - + -
222F ALA* 3.6 21.1 - - + -
260F VAL* 5.3 2.4 - - + +
262F VAL* 3.9 30.1 - - + -
295F VAL* 4.3 14.8 - - + +
314F PRO* 4.9 4.3 - - + +
315F GLN 3.3 13.9 + - - +
316F VAL 3.2 6.4 + - - +
318F ASP* 1.3 74.2 - - - +
320F ILE* 1.3 65.5 + - - +
322F ALA* 3.3 2.9 + - - +
323F ILE* 3.0 35.1 + - + +
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Residues in contact with ILE 320 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222F ALA* 4.0 17.7 - - + -
225F VAL* 4.3 22.0 - - + -
226F LEU* 3.7 28.9 - - + -
316F VAL* 3.0 33.2 + - + +
317F LYS* 3.8 7.4 - - - +
319F ILE* 1.3 75.1 - - - +
321F PHE* 1.3 58.2 + - - +
323F ILE* 3.2 9.0 + - - +
324F LYS* 2.8 48.8 + - + +
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Residues in contact with PHE 321 (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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317F LYS 3.1 18.3 + - - +
318F ASP* 3.6 11.4 - - - +
319F ILE 3.2 0.2 - - - -
320F ILE* 1.3 77.6 - - - +
322F ALA* 1.3 64.2 + - - +
324F LYS* 3.5 9.3 + - - +
325F LYS* 3.0 53.3 + - + +
352G ASN* 3.8 13.9 - - - +
354G TRP* 4.1 28.0 - + + -
355G ILE* 6.5 0.7 - - + -
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Residues in contact with ALA 322 (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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260F VAL* 4.8 3.8 - - + -
293F VAL* 4.2 13.6 - - + +
294F ARG 5.5 0.2 - - - +
295F VAL* 3.9 20.9 - - + -
318F ASP 3.2 13.6 + - - +
319F ILE 3.3 2.2 + - - +
320F ILE 3.3 0.2 - - - -
321F PHE* 1.3 78.2 - - - +
323F ILE* 1.3 67.1 + - - +
325F LYS* 2.8 12.3 + - - +
326F THR* 2.9 17.8 + - - -
352G ASN* 4.4 2.5 - - + +
354G TRP* 3.9 27.1 - - + -
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Residues in contact with ILE 323 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207F ILE* 3.8 27.8 - - + -
209F VAL* 4.1 18.2 - - + -
222F ALA* 4.8 2.5 - - + -
226F LEU* 3.5 39.5 - - + -
231F VAL* 4.6 4.9 - - + -
233F CYS* 4.2 3.1 - - - -
260F VAL* 4.2 8.8 - - + +
319F ILE* 3.0 38.9 + - + +
320F ILE 3.4 6.7 - - - +
322F ALA* 1.3 74.7 - - - +
324F LYS* 1.3 60.7 + - + +
326F THR* 3.3 2.1 + - - -
327F LEU* 3.0 47.9 + - + +
329F ILE* 6.3 0.9 - - + -
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Residues in contact with LYS 324 (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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226F LEU* 4.7 10.3 - - + -
229F GLU* 4.5 18.2 + - - -
320F ILE* 2.8 43.8 + - + +
321F PHE* 3.7 7.9 - - - +
323F ILE* 1.3 75.2 - - + +
325F LYS* 1.3 64.6 + - + +
327F LEU* 4.0 2.2 - - - +
328F ASN* 3.4 13.9 + - - -
329F ILE* 3.5 38.8 + - + +
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Residues in contact with LYS 325 (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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321F PHE* 3.0 44.9 + - + +
322F ALA* 2.8 8.9 + - - +
324F LYS* 1.3 81.0 - - + +
326F THR* 1.3 64.1 + - - +
328F ASN* 3.5 17.0 + - - +
354G TRP* 3.9 49.6 - - + +
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Residues in contact with THR 326 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207F ILE* 4.4 9.2 - - + -
258F HIS* 3.7 33.2 + - + -
259F LEU 4.6 7.2 - - - +
260F VAL* 4.1 2.9 - - - +
290F ALA* 3.5 24.0 - - + +
291F PRO* 4.0 12.7 + - - +
293F VAL* 3.4 24.1 - - - +
322F ALA 2.9 13.3 + - - -
323F ILE 3.7 7.9 - - - -
325F LYS* 1.3 72.2 - - - +
327F LEU* 1.3 59.0 + - - +
328F ASN* 3.1 22.3 - - - +
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Residues in contact with LEU 327 (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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206F HIS* 3.9 17.0 - - + +
207F ILE* 4.2 20.9 - - + -
231F VAL* 3.8 29.8 - - + -
258F HIS* 3.5 39.7 - - + +
323F ILE* 3.0 21.7 + - + +
324F LYS 3.9 0.4 + - - +
326F THR* 1.3 75.5 - - - +
328F ASN* 1.3 60.2 + - - +
329F ILE* 2.5 47.7 + - + +
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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