Contacts of the helix formed by residues 263 - 274 (chain C) in PDB entry 3M0V
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 ASN 263 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A PHE* 4.2 1.0 - - - -
222A MET* 5.0 0.8 - - - +
228A TYR* 2.9 46.7 + - - +
229A SER* 3.7 11.9 - - - -
233A GLN* 5.2 6.4 + - + -
286B LYS* 3.7 8.2 - - - +
287B TYR* 3.7 15.3 + - - +
261C ASN 3.5 1.6 + - - -
262C THR* 1.3 74.9 - - - +
264C ILE* 1.3 59.5 + - - +
265C GLU* 3.0 15.1 - - - +
266C MET* 2.8 48.4 + - + +
267C ILE* 3.6 14.2 + - - +
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Residues in contact with ILE 264 (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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253C VAL* 4.2 9.0 - - + -
255C LEU* 3.3 52.3 - - + +
258C HIS* 3.6 35.7 - - + +
262C THR* 3.2 16.4 + - + +
263C ASN* 1.3 68.7 + - - +
265C GLU* 1.3 73.7 + - - +
266C MET 3.1 1.8 - - - -
267C ILE* 3.0 17.6 + - + +
268C VAL* 3.1 14.4 + - + +
301C ARG* 4.4 28.7 - - - +
305C VAL* 4.8 4.7 - - + -
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Residues in contact with GLU 265 (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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192A PHE* 3.8 8.3 - - + -
228A TYR* 2.6 38.1 + - - +
286B LYS* 4.7 6.3 + - - -
263C ASN* 3.0 20.0 - - - +
264C ILE* 1.3 83.7 + - - +
266C MET* 1.3 59.6 + - - +
268C VAL* 3.4 11.4 + - - +
269C ALA* 3.1 17.0 + - - +
301C ARG* 4.3 15.9 - - - +
304C LEU* 3.5 44.1 - - + +
305C VAL* 4.2 8.2 - - - +
308C GLU* 3.6 15.4 - - + +
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Residues in contact with MET 266 (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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192A PHE* 3.6 37.7 - - + -
229A SER* 3.8 15.7 - - - +
230A THR 3.3 26.2 - - - +
231A VAL* 4.7 1.3 - - + -
233A GLN* 3.4 39.5 - - - +
263C ASN* 2.8 28.6 + - + +
264C ILE 3.1 0.4 - - - -
265C GLU* 1.3 74.6 - - - +
267C ILE* 1.3 67.6 + - - +
269C ALA* 3.2 2.1 + - - +
270C ARG* 2.9 50.0 + - + +
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Residues in contact with ILE 267 (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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233A GLN* 4.7 5.6 - - - +
234A ASP* 5.1 0.9 - - - +
235C TRP* 3.5 55.0 - - + +
253C VAL* 4.6 10.1 - - + -
258C HIS* 3.6 31.4 - - + +
262C THR* 3.9 19.1 - - + -
263C ASN 3.6 9.1 + - - +
264C ILE* 3.0 11.1 + - + +
266C MET* 1.3 78.4 - - - +
268C VAL* 1.3 62.5 + - - +
270C ARG* 3.2 7.7 + - - +
271C LEU* 2.9 36.1 + - + +
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Residues in contact with VAL 268 (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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253C VAL* 4.9 5.2 - - + -
264C ILE* 3.1 20.7 + - + +
265C GLU* 3.5 11.2 - - - +
267C ILE* 1.3 77.6 - - - +
269C ALA* 1.3 62.9 + - - +
271C LEU* 3.2 6.2 + - - +
272C ILE* 3.0 45.0 + - + +
277C LEU* 4.0 7.1 - - + +
280C PHE* 3.4 43.1 - - + -
305C VAL* 4.2 12.1 - - + +
308C GLU* 4.3 10.5 - - + -
309C LEU* 4.0 8.3 - - + -
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Residues in contact with ALA 269 (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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192A PHE* 3.9 22.2 - - + -
193A THR* 3.6 14.2 + - - +
265C GLU 3.1 7.9 + - - +
266C MET 3.2 7.6 + - - +
268C VAL* 1.3 81.0 - - - +
270C ARG* 1.3 58.5 + - - +
272C ILE* 3.2 11.0 + - - +
273C GLN* 2.9 29.5 + - - +
308C GLU* 3.5 24.4 - - - +
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Residues in contact with ARG 270 (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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192A PHE* 3.4 34.4 + - - +
193A THR* 4.3 1.2 - - - +
196A PHE* 3.7 40.8 - - - +
231A VAL* 2.8 33.1 + - - +
237A THR* 3.1 26.0 + - - +
240A LEU* 4.5 4.7 - - + -
235C TRP* 3.7 28.0 - - + -
266C MET* 2.9 44.2 + - + +
267C ILE 3.6 4.9 - - - +
269C ALA* 1.3 74.8 - - - +
271C LEU* 1.3 63.0 + - - +
273C GLN* 3.3 11.0 + - - +
274C PHE* 3.2 29.5 + - - +
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Residues in contact with LEU 271 (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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220C HIS* 5.4 0.2 - - + -
235C TRP* 3.9 28.3 - - + +
239C TYR* 4.7 8.3 - - + -
251C CYS* 3.9 36.3 - - + -
253C VAL* 3.6 31.2 - - + -
267C ILE* 2.9 27.3 + - + +
268C VAL 3.2 4.2 + - - +
270C ARG* 1.3 75.7 - - - +
272C ILE* 1.3 60.6 + - - +
274C PHE* 3.5 2.4 + - - -
275C GLY 3.1 3.3 + - - -
276C LYS* 2.7 41.2 + - + +
277C LEU* 3.4 20.6 + - + +
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Residues in contact with ILE 272 (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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193A THR* 6.1 0.4 - - - +
268C VAL* 3.0 36.7 + - + +
269C ALA* 3.5 11.0 - - - +
271C LEU* 1.3 76.0 - - - +
273C GLN* 1.3 67.4 + - - +
275C GLY* 2.9 15.6 + - - +
277C LEU* 3.5 13.2 - - + -
308C GLU 4.3 7.9 - - - +
309C LEU* 4.1 4.0 - - + -
312C ALA* 4.1 20.2 - - + -
317C VAL* 4.8 12.9 - - + +
318C LYS* 4.7 7.4 - - - +
320C PHE* 3.4 44.9 - - + -
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Residues in contact with GLN 273 (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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193A THR* 3.5 33.1 + - + +
196A PHE* 3.2 31.2 - - - +
197A GLU* 4.0 21.5 + - - +
200A LEU* 4.1 7.9 - - - +
269C ALA 2.9 17.6 + - - +
270C ARG* 3.5 12.5 + - - +
272C ILE* 1.3 78.9 - - - +
274C PHE* 1.3 84.8 + - + +
275C GLY 3.7 0.3 + - - -
318C LYS* 5.6 2.3 + - - +
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Residues in contact with PHE 274 (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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196A PHE* 3.9 11.9 - + - -
200A LEU* 4.8 4.0 - - + -
240A LEU* 3.6 40.6 - - + -
244A THR* 4.5 15.3 - - - -
239C TYR* 3.9 33.0 + - + +
243C GLN* 5.3 1.6 - - - +
270C ARG* 3.2 20.2 + - - +
271C LEU* 3.5 2.2 + - - +
272C ILE 3.1 0.4 - - - -
273C GLN* 1.3 111.5 - - + +
275C GLY* 1.3 62.0 + - - +
276C LYS* 3.3 14.1 + - - +
318C LYS* 4.5 5.0 + - - -
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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