Contacts of the helix formed by residues 295 - 306 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203C LEU* 5.3 0.7 - - - -
293C GLY 3.6 2.5 + - - -
294C VAL* 1.3 77.7 - - - +
296C ARG* 1.3 81.4 + - - +
297C ALA* 3.5 8.6 + - - +
298C MET* 3.0 26.2 + - - +
299C LEU* 3.1 21.8 + - - +
301C ARG* 4.9 1.6 + - - -
318C TYR* 5.2 1.0 - - - -
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Residues in contact with ARG 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C LEU* 3.4 45.6 - - + +
201C ALA* 4.5 11.4 - - - +
203C LEU* 4.1 21.0 - - + +
294C VAL 3.9 2.4 + - - -
295C SER* 1.3 88.4 - - - +
297C ALA* 1.3 60.2 + - - +
299C LEU* 4.6 1.1 - - - -
300C LEU* 3.0 28.0 + - - +
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Residues in contact with ALA 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295C SER* 3.2 8.5 + - - +
296C ARG* 1.3 82.0 - - - +
298C MET* 1.3 56.2 + - - +
300C LEU* 3.4 11.9 - - - +
301C ARG* 3.1 41.6 + - - +
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Residues in contact with MET 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C VAL* 3.7 22.0 - - + -
295C SER* 3.0 19.8 + - - +
297C ALA* 1.3 73.4 - - - +
299C LEU* 1.3 65.3 + - - +
301C ARG* 3.0 51.0 + - - +
302C LEU* 3.0 17.4 + - + +
314C TYR* 4.6 19.7 - - + +
316C CYS* 4.2 28.9 - - + -
317C PRO* 5.7 2.7 - - + -
318C TYR* 5.8 1.1 - - + -
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Residues in contact with LEU 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C PHE* 4.5 9.6 - - + -
200C LEU* 3.8 17.9 - - + -
203C LEU* 4.0 33.9 - - + -
258C VAL* 4.4 24.2 - - + -
259C LEU* 4.9 2.0 - - + -
290C VAL* 4.6 15.3 - - + -
294C VAL* 4.1 13.8 - - + +
295C SER 3.1 12.0 + - - +
296C ARG 3.7 7.6 - - - +
298C MET* 1.3 75.0 - - - +
300C LEU* 1.3 56.5 + - - +
302C LEU* 3.4 14.6 + - + +
303C PHE* 3.0 29.6 + - - +
1001C UUL 4.1 22.6 - - + -
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Residues in contact with LEU 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C PHE* 4.2 21.3 - - + -
200C LEU* 4.1 16.3 - - + +
296C ARG 3.0 15.1 + - - +
297C ALA* 3.4 14.1 - - - +
298C MET 3.1 0.2 - - - -
299C LEU* 1.3 77.2 - - - +
301C ARG* 1.3 62.9 + - + +
303C PHE* 3.4 6.1 + - + +
304C LEU* 3.0 59.8 + - + +
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Residues in contact with ARG 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295C SER* 4.9 1.4 + - - -
297C ALA* 3.1 21.2 + - - +
298C MET* 3.0 65.3 + - - +
300C LEU* 1.3 76.8 - - + +
302C LEU* 1.3 58.2 + - - +
304C LEU* 3.5 7.9 + - + +
305C ALA* 2.9 30.5 + - - +
314C TYR* 4.1 31.0 + - + +
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Residues in contact with LEU 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C VAL* 5.3 4.9 - - + -
294C VAL* 5.4 1.8 - - + -
298C MET* 3.0 20.5 + - - +
299C LEU* 3.6 20.2 - - + +
301C ARG* 1.3 74.3 - - - +
303C PHE* 1.3 59.8 + - - +
305C ALA* 3.1 4.0 + - - +
306C MET* 2.9 28.5 + - - +
311C HIS* 3.3 41.4 - - + +
314C TYR* 4.1 20.2 - - + -
316C CYS* 4.3 25.4 - - + +
319C LEU* 4.2 24.5 - - + -
1001C UUL 4.8 13.9 - - + -
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Residues in contact with PHE 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C PHE* 4.2 9.2 - - + -
193C THR* 4.5 15.3 - - + -
196C THR* 3.7 28.5 - - + -
197C PHE* 4.5 9.6 - + - -
200C LEU* 5.4 0.2 - - + -
272C MET* 3.9 18.9 - - + +
299C LEU 3.0 16.8 + - - +
300C LEU* 3.7 6.7 - - + +
302C LEU* 1.3 74.4 - - - +
304C LEU* 1.3 78.7 + - + +
306C MET* 3.3 31.6 - - + +
307C GLU* 4.0 2.4 + - - +
1001C UUL 3.2 58.9 - + - -
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Residues in contact with LEU 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C PHE* 4.3 13.2 - - + -
300C LEU* 3.0 47.9 + - + +
301C ARG* 4.0 7.0 - - + +
303C PHE* 1.3 88.8 - - + +
305C ALA* 1.3 65.5 + - - +
307C GLU* 3.2 22.2 - - - +
308C LYS* 5.5 1.2 - - - +
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Residues in contact with ALA 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C ARG 2.9 20.1 + - - +
302C LEU* 3.1 5.6 + - - +
304C LEU* 1.3 71.9 - - - +
306C MET* 1.3 58.7 + - - +
307C GLU 2.9 11.7 + - - -
308C LYS* 3.2 14.3 + - - +
310C ARG* 3.3 26.5 + - + +
311C HIS* 3.7 22.7 - - + +
314C TYR* 4.7 14.6 - - + +
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Residues in contact with MET 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268C LEU* 4.1 4.0 - - + -
271C GLU 4.5 0.7 - - - -
272C MET* 3.8 17.3 - - + -
273C PHE* 2.7 48.5 + - - +
274C ALA* 3.6 25.8 - - - -
302C LEU 2.9 10.5 + - - +
303C PHE* 3.3 38.1 - - + +
304C LEU 3.2 0.2 - - - -
305C ALA* 1.3 74.1 - - - +
307C GLU* 1.3 56.0 + - - +
308C LYS 3.3 0.7 - - - -
309C GLY 3.3 5.9 + - - +
311C HIS* 3.6 17.9 - - + +
1001C UUL 3.6 46.0 - - + +
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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