Contacts of the helix formed by residues 316 - 321 (chain C) in PDB entry 2V10
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 GLY 316 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C ASP 3.5 11.2 - - - -
229C ALA* 3.3 15.9 - - - +
231C TYR 3.4 21.0 + - - -
232C ILE* 4.2 2.4 - - - +
314C ALA 3.5 1.6 + - - -
315C LEU* 1.3 72.2 - - - +
317C ALA* 1.3 67.9 + - - -
318C THR 3.0 5.1 + - - -
319C PHE 3.1 9.5 + - - -
320C ILE* 3.2 16.7 + - - +
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Residues in contact with ALA 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ASP 4.6 1.8 - - - +
20C TYR* 4.0 17.3 - - + -
162C TYR* 3.7 32.4 - - + -
226C ASP 4.6 0.2 + - - -
227C THR 5.2 0.2 + - - -
229C ALA 2.7 19.6 + - - +
230C SER* 3.7 13.4 + - - +
316C GLY* 1.3 71.1 - - - -
318C THR* 1.3 61.6 + - - +
319C PHE 3.1 0.9 + - - -
320C ILE* 4.1 2.2 - - - +
321C ARG* 3.1 34.9 + - - +
1341C C61 5.5 0.9 - - - -
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Residues in contact with THR 318 (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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230C SER 3.5 4.2 + - - -
231C TYR* 3.4 5.7 - - - -
232C ILE* 3.4 19.7 + - + -
279C LEU* 4.3 20.1 - - + +
283C ASP* 3.1 32.3 - - - +
284C TYR* 4.3 4.5 - - + -
299C ALA* 2.8 42.8 + - + +
316C GLY 3.0 2.4 + - - -
317C ALA* 1.3 76.6 - - - +
319C PHE* 1.3 59.4 + - - +
321C ARG* 3.6 25.7 + - - +
322C LYS* 4.4 2.4 + - - +
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Residues in contact with PHE 319 (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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225C VAL* 5.6 0.2 - - + -
232C ILE* 4.1 21.5 - - + -
270C PHE* 4.0 19.5 - + + -
272C LEU* 4.2 10.3 - - + -
277C TYR* 3.6 38.6 - + + -
279C LEU* 4.6 6.3 - - + -
315C LEU* 4.0 27.8 - - + -
316C GLY 3.4 8.3 - - - +
318C THR* 1.3 78.5 - - - +
320C ILE* 1.3 63.6 + - + +
321C ARG 2.9 9.2 + - - -
322C LYS* 3.1 10.7 + - - +
323C PHE* 3.2 29.5 + + - -
336C PHE* 3.1 41.5 - + - -
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Residues in contact with ILE 320 (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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160C PHE* 4.0 25.8 - - + +
161C TYR* 6.0 0.2 - - - -
162C TYR* 3.9 34.6 + - + -
225C VAL* 4.4 14.8 - - + -
227C THR* 4.7 17.3 - - + -
315C LEU 4.6 2.9 - - - +
316C GLY 3.2 21.7 + - - +
317C ALA* 3.3 6.0 + - - +
319C PHE* 1.3 76.6 - - + +
321C ARG* 1.3 61.6 + - - +
322C LYS 3.1 0.9 - - - -
323C PHE 3.3 20.1 - - - +
324C TYR* 4.1 2.9 + - - -
325C THR* 3.4 29.6 - - + +
339C ALA* 5.1 1.0 - - - +
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Residues in contact with ARG 321 (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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17C ASP* 2.9 55.6 + - - +
20C TYR* 3.3 18.2 + - - -
162C TYR* 3.5 28.4 - - + +
163C ASN 4.3 2.0 - - - -
164C ARG* 4.1 37.5 + - + +
230C SER 5.2 1.6 + - - -
283C ASP 4.9 10.5 + - - -
286C PHE* 5.2 8.9 - - - -
317C ALA* 3.1 23.1 + - - +
318C THR* 3.6 18.0 + - - +
319C PHE 2.9 1.6 + - - -
320C ILE* 1.3 82.2 - - - +
322C LYS* 1.3 60.8 + - + +
339C ALA* 3.8 11.4 - - - +
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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