Contacts of the helix formed by residues 295 - 306 (chain F) in PDB entry 3VZC
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 SER 295 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203F LEU* 4.8 0.2 - - - -
293F GLY 3.5 2.6 + - - -
294F VAL* 1.3 79.0 - - - +
296F ARG* 1.3 68.1 + - - +
297F ALA* 4.1 9.8 - - - +
298F MET* 3.1 23.9 + - - +
299F LEU* 2.9 20.4 + - - +
318F TYR* 5.3 0.8 - - - -
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Residues in contact with ARG 296 (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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200F LEU* 3.6 48.6 + - + +
201F ALA* 4.4 17.2 + - - +
203F LEU* 3.6 31.8 + - + +
294F VAL 3.7 4.4 + - - -
295F SER* 1.3 71.6 - - - +
297F ALA* 1.3 56.6 + - - +
299F LEU* 3.0 5.4 + - - +
300F LEU 2.9 26.3 + - - -
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Residues in contact with ALA 297 (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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200F LEU* 5.4 0.2 - - - -
295F SER* 3.1 8.2 - - - +
296F ARG* 1.3 79.8 - - - +
298F MET* 1.3 59.0 + - - +
300F LEU* 3.7 9.2 + - - +
301F ARG* 3.0 48.6 + - - +
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Residues in contact with MET 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294F VAL* 3.8 8.7 - - + -
295F SER* 3.1 24.7 + - - +
297F ALA* 1.3 73.6 - - - +
299F LEU* 1.3 61.2 + - - +
300F LEU 3.2 0.2 - - - -
301F ARG* 3.1 22.4 + - - +
302F LEU* 2.9 36.2 + - + +
314F TYR* 4.0 29.4 - - + -
316F CYS* 3.6 45.1 - - + -
317F PRO* 5.7 1.6 - - + -
318F TYR* 5.8 1.1 - - + -
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Residues in contact with LEU 299 (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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173F PHE* 5.1 9.9 - - + -
200F LEU* 5.6 2.2 - - + -
203F LEU* 3.9 26.2 - - + -
258F VAL* 3.8 30.7 - - + -
259F LEU* 4.7 4.9 - - + -
290F VAL* 5.1 2.0 - - + -
294F VAL* 3.9 26.6 - - + +
295F SER 2.9 9.6 + - - +
296F ARG* 3.0 10.3 + - - +
298F MET* 1.3 75.8 - - - +
300F LEU* 1.3 57.4 + - - +
302F LEU* 3.4 17.5 - - + +
303F PHE* 3.1 24.4 + - - +
1001F UUL 3.8 28.6 - - + -
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Residues in contact with LEU 300 (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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193F THR* 6.1 0.7 - - + +
196F THR* 5.0 10.1 - - + -
197F PHE* 5.4 17.0 - - + -
200F LEU* 3.6 31.3 - - + +
296F ARG 2.9 8.7 + - - +
297F ALA* 3.8 8.1 - - - +
299F LEU* 1.3 75.1 - - - +
301F ARG* 1.3 54.0 + - + +
303F PHE* 3.2 17.7 + - + +
304F LEU* 2.7 58.5 + - + +
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Residues in contact with ARG 301 (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 ALA* 3.0 45.8 + - - +
298F MET* 3.1 20.2 + - - +
300F LEU* 1.3 75.3 - - + +
302F LEU* 1.3 59.9 + - - +
304F LEU* 4.4 8.3 - - + +
305F ALA* 2.8 36.5 + - - +
314F TYR* 3.9 29.3 + - + +
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Residues in contact with LEU 302 (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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290F VAL* 5.1 10.5 - - + -
294F VAL* 4.6 4.0 - - + -
298F MET* 2.9 23.4 + - + +
299F LEU* 3.4 26.9 - - + +
301F ARG* 1.3 74.1 - - - +
303F PHE* 1.3 64.0 + - - +
305F ALA* 4.9 0.4 - - - -
306F MET* 3.1 20.1 + - - +
311F HIS* 3.3 33.5 - - + +
314F TYR* 4.5 8.3 - - + -
316F CYS* 4.1 35.9 - - + -
319F LEU* 4.2 22.4 - - + -
1001F UUL 4.3 17.2 - - + -
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Residues in contact with PHE 303 (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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192F PHE* 4.6 2.9 - - + -
193F THR* 3.3 44.0 - - + -
196F THR* 3.7 15.3 - - + -
272F MET* 4.3 17.0 - - + +
299F LEU 3.1 6.2 + - - +
300F LEU* 3.4 14.8 - - + +
302F LEU* 1.3 79.7 - - - +
304F LEU* 1.3 85.0 + - + +
306F MET* 3.2 25.9 + - + +
307F GLU* 3.9 2.6 + - - +
1001F UUL 3.2 64.1 - + - -
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Residues in contact with LEU 304 (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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193F THR* 5.7 4.9 - - + -
300F LEU* 2.7 44.8 + - + +
301F ARG* 4.0 7.0 - - + +
303F PHE* 1.3 91.0 - - + +
305F ALA* 1.3 61.4 + - - +
307F GLU* 3.2 24.2 + - - +
308F LYS 4.7 0.2 + - - -
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Residues in contact with ALA 305 (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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301F ARG 2.8 20.9 + - - +
302F LEU 4.0 0.2 - - - +
304F LEU* 1.3 68.9 - - - +
306F MET* 1.3 61.3 + - - +
307F GLU 3.0 6.4 + - - -
308F LYS* 3.3 5.9 + - - +
309F GLY 3.1 3.6 + - - -
310F ARG* 2.9 50.7 + - + +
311F HIS* 4.0 7.0 - - + +
314F TYR* 4.3 13.0 - - + +
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Residues in contact with MET 306 (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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268F LEU* 4.4 2.5 - - + -
272F MET* 3.8 35.2 - - + -
273F PHE* 2.8 30.3 + - - +
274F ALA* 3.5 40.6 - - - +
302F LEU 3.1 13.9 + - - +
303F PHE* 3.2 25.1 - - + +
304F LEU 3.1 0.4 - - - -
305F ALA* 1.3 76.1 - - - +
307F GLU* 1.3 59.6 + - - +
309F GLY 3.2 5.4 + - - -
311F HIS* 3.6 16.1 - - + +
1001F UUL 3.8 48.2 - - + +
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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