Contacts of the helix formed by residues 316 - 321 (chain O) 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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226O ASP 3.3 12.3 - - - -
229O ALA* 3.2 13.2 - - - -
231O TYR 3.0 22.6 + - - -
232O ILE* 4.4 1.8 - - - +
314O ALA 3.5 1.0 + - - -
315O LEU* 1.3 72.8 - - - +
317O ALA* 1.3 67.8 + - - -
318O THR 3.0 4.0 - - - -
319O PHE 2.9 11.3 + - - -
320O ILE* 3.0 14.2 + - - +
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Residues in contact with ALA 317 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17O ASP 4.0 0.7 - - - +
18O THR 5.7 0.2 - - - -
20O TYR* 3.9 20.0 - - + -
162O TYR* 3.9 20.2 - - + -
226O ASP 4.4 0.8 + - - -
229O ALA 2.7 15.0 + - - +
230O SER* 3.2 18.8 + - - +
316O GLY* 1.3 68.9 - - - -
318O THR* 1.3 65.0 + - - +
320O ILE* 3.1 1.4 + - - +
321O ARG* 2.9 45.4 + - - +
1341O C61 5.1 1.6 - - - -
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Residues in contact with THR 318 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230O SER 3.1 13.1 + - - -
231O TYR* 3.2 1.8 - - - -
232O ILE* 3.3 30.7 - - + -
279O LEU* 4.3 13.6 - - + +
283O ASP 4.0 20.9 - - - +
284O TYR* 4.8 2.9 - - + -
299O ALA* 2.6 37.4 + - + +
316O GLY 3.0 0.2 - - - -
317O ALA* 1.3 81.6 - - - +
319O PHE* 1.3 61.1 + - - +
321O ARG* 3.8 21.4 + - - +
322O LYS* 4.0 2.9 + - - +
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Residues in contact with PHE 319 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225O VAL* 6.2 0.4 - - + -
232O ILE* 3.9 11.2 - - + +
270O PHE* 3.7 39.0 - + + -
272O LEU* 4.8 5.2 - - + -
277O TYR* 3.4 31.4 - + + -
279O LEU* 4.9 9.0 - - + -
315O LEU* 3.8 40.4 - - + -
316O GLY 2.9 7.9 + - - +
318O THR* 1.3 78.1 - - - +
320O ILE* 1.3 61.6 + - + +
322O LYS* 3.0 18.9 + - - +
323O PHE* 3.3 32.3 + + + -
336O PHE* 4.1 32.8 - + - -
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Residues in contact with ILE 320 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160O PHE* 4.3 20.6 - - + +
162O TYR* 3.8 35.6 + - + +
225O VAL* 4.9 8.5 - - + -
226O ASP 4.0 9.0 - - - +
227O THR* 3.3 42.2 - - + -
315O LEU 4.4 6.5 - - - +
316O GLY 3.0 13.5 + - - +
317O ALA 3.8 3.4 - - - +
319O PHE* 1.3 74.9 - - + +
321O ARG* 1.3 58.9 + - - +
322O LYS 3.0 5.4 - - - -
323O PHE 3.1 24.1 - - - +
324O TYR* 4.1 3.8 + - - -
325O THR* 4.3 14.1 - - - +
339O ALA* 4.6 1.2 - - - +
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Residues in contact with ARG 321 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17O ASP* 2.5 49.3 + - - +
20O TYR* 2.7 18.0 + - - +
161O TYR* 5.9 0.2 - - - -
162O TYR* 3.4 30.5 - - + +
163O ASN 3.5 14.1 - - - +
164O ARG* 3.7 40.8 + - + +
230O SER 3.8 6.5 + - - -
283O ASP 5.2 4.9 + - - -
286O PHE* 4.5 12.5 - - - -
299O ALA* 4.8 4.8 - - - +
317O ALA* 2.9 34.6 + - - +
318O THR* 3.8 19.9 + - - +
319O PHE 3.3 0.2 - - - -
320O ILE* 1.3 75.2 - - - +
322O LYS* 1.4 58.7 + - - +
339O ALA* 4.0 8.2 - - - +
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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