Contacts of the helix formed by residues 308 - 319 (chain V) in PDB entry 1O1F
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 308 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219V VAL* 3.0 18.2 - - - +
221V LEU* 4.7 5.6 - - - +
307V PRO* 1.3 72.3 - - - +
309V ILE* 1.3 63.8 + - - +
310V ALA* 3.3 3.6 - - - +
311V ASP* 3.8 22.1 + - - +
312V ARG* 3.3 21.5 + - - +
335V ARG* 5.9 0.2 - - - +
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Residues in contact with ILE 309 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153V LEU* 5.7 4.0 - - + -
219V VAL* 3.9 15.5 - - + -
261V LEU* 4.3 13.9 - - + -
262V PHE* 4.6 8.8 - - + -
274V ILE* 6.2 2.9 - - + -
299V MET* 4.3 13.2 - - + -
303V THR 3.9 6.7 - - - +
304V THR* 3.2 52.5 - - + +
306V TYR* 3.2 26.2 - - + +
307V PRO 3.2 1.2 - - - -
308V GLY* 1.3 77.7 - - - +
310V ALA* 1.3 72.5 - - + +
312V ARG* 3.8 2.6 + - - +
313V MET* 3.0 33.0 + - + +
335V ARG* 3.5 14.1 - - - +
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Residues in contact with ALA 310 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299V MET* 4.0 22.4 - - + -
308V GLY* 5.7 0.9 - - - -
309V ILE* 1.3 83.0 - - + +
311V ASP* 1.4 54.3 + - - +
313V MET* 3.1 3.8 + - - +
314V GLN* 2.8 38.3 + - + +
329V ILE* 4.1 15.8 - - + +
331V ALA* 4.1 13.9 - - + -
335V ARG* 5.5 0.7 - - - +
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Residues in contact with ASP 311 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221V LEU* 3.8 32.1 - - + +
308V GLY* 3.8 17.0 + - - +
309V ILE 3.5 0.2 - - - -
310V ALA* 1.4 73.6 - - - +
312V ARG* 1.3 65.3 + - - +
314V GLN* 3.1 11.0 - - - +
315V LYS* 3.0 26.3 + - - +
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Residues in contact with ARG 312 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219V VAL* 3.6 12.8 - - + -
220V ALA 3.0 21.3 + - - +
221V LEU* 3.8 14.8 - - - +
222V ASP 4.9 2.9 - - - +
223V PHE* 2.9 41.0 - - - +
262V PHE* 3.3 26.2 - - + +
263V GLN* 3.4 27.1 + - - +
308V GLY 3.3 13.8 + - - +
309V ILE 3.9 3.4 - - - +
310V ALA 3.4 0.2 - - - -
311V ASP* 1.3 78.4 - - - +
313V MET* 1.3 52.5 + - - +
315V LYS* 3.6 3.5 - - - +
316V GLU* 2.7 76.4 + - - +
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Residues in contact with MET 313 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153V LEU* 4.5 9.2 - - + -
262V PHE* 4.2 11.2 - - + -
274V ILE* 3.9 17.0 - - + -
275V HIS* 3.4 35.2 - - - -
278V THR* 3.0 35.7 - - + +
297V ASN* 4.4 11.2 - - - +
299V MET* 4.8 9.2 - - - -
309V ILE* 3.0 23.1 + - + +
310V ALA* 3.1 4.9 + - - +
312V ARG* 1.3 71.9 - - - +
314V GLN* 1.3 59.2 + - - +
316V GLU* 3.6 2.5 - - - +
317V ILE* 2.9 39.2 + - + +
329V ILE* 4.1 16.4 - - + -
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Residues in contact with GLN 314 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310V ALA* 2.8 13.3 + - + +
311V ASP* 3.1 17.5 - - - +
313V MET* 1.3 75.9 - - - +
315V LYS* 1.3 62.2 + - + +
318V THR* 2.8 35.3 + - - +
327V ILE* 3.5 32.4 + - - +
328V LYS* 4.3 2.6 - - - +
329V ILE* 3.5 29.5 - - + +
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Residues in contact with LYS 315 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221V LEU* 6.3 4.9 - - + -
311V ASP 3.0 12.8 + - - +
312V ARG* 4.0 3.4 - - - +
314V GLN* 1.3 82.8 - - + +
316V GLU* 1.3 66.4 + - - +
318V THR* 3.1 34.2 + - + +
319V ALA* 3.5 30.4 - - - +
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Residues in contact with GLU 316 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262V PHE* 4.6 2.5 - - + -
275V HIS* 3.2 56.5 + - + +
312V ARG* 2.7 59.7 + - - +
313V MET* 3.2 7.4 + - - +
315V LYS* 1.3 81.8 - - + +
317V ILE* 1.3 62.5 + - - +
319V ALA* 3.9 3.5 + - - +
320V LEU* 3.8 16.8 + - - +
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Residues in contact with ILE 317 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275V HIS* 3.8 23.3 - - + +
278V THR* 4.1 16.2 - - + -
279V TYR* 5.1 6.1 - - + +
294V TYR* 4.0 24.9 - - + +
297V ASN* 3.9 13.5 - - - +
313V MET* 2.9 28.4 + - + +
316V GLU* 1.3 76.5 - - - +
318V THR* 1.3 66.3 + - - +
319V ALA 3.2 1.8 - - - -
320V LEU* 3.0 6.5 + - + +
321V ALA* 2.9 25.3 + - - +
327V ILE* 3.7 26.5 - - + -
329V ILE* 3.6 20.6 - - + -
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Residues in contact with THR 318 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314V GLN* 2.8 30.7 + - - +
315V LYS* 3.1 30.1 + - + +
317V ILE* 1.3 72.8 - - - +
319V ALA* 1.3 60.8 + - - +
320V LEU 3.1 5.7 + - - -
321V ALA* 3.1 20.6 - - - +
323V SER* 5.8 0.9 + - - -
325V MET 6.1 0.4 - - - +
327V ILE* 3.7 30.5 - - + -
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Residues in contact with ALA 319 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315V LYS* 3.5 28.2 + - - +
316V GLU* 4.0 4.9 - - - +
317V ILE 3.2 1.0 - - - -
318V THR* 1.3 80.1 + - - +
320V LEU* 1.3 58.6 + - - +
321V ALA 4.8 0.7 - - - -
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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