Contacts of the helix formed by residues 273 - 283 (chain V) in PDB entry 1MVW
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 273 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178V LEU* 4.6 1.3 - - - -
261V LEU 3.8 11.2 - - - -
262V PHE 4.0 12.2 + - - -
264V PRO* 4.0 11.4 - - - +
272V ALA* 1.3 75.8 - - - +
274V ILE* 1.3 66.9 + - - -
275V HIS* 3.3 6.6 - - - -
276V GLU* 2.9 23.0 + - - +
277V THR* 3.0 12.2 + - - -
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Residues in contact with ILE 274 (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* 3.6 28.4 - - + +
155V SER* 5.5 1.3 - - - +
160V THR* 3.6 21.3 - - + -
178V LEU* 3.4 26.0 - - + +
261V LEU* 3.2 40.5 + - + +
262V PHE* 3.6 25.6 - - + -
273V GLY* 1.3 67.2 - - - -
275V HIS* 1.3 58.7 + - - +
277V THR* 3.3 7.6 + - + -
278V THR* 2.9 31.1 + - - -
309V ILE* 6.2 2.7 - - + -
313V MET* 3.9 17.7 - - + -
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Residues in contact with HIS 275 (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* 3.4 34.4 - + + -
273V GLY* 2.9 8.4 + - - -
274V ILE* 1.3 72.0 - - - +
276V GLU* 1.3 98.4 + - + +
278V THR* 3.5 3.6 - - - -
279V TYR* 3.3 20.3 + - - +
313V MET* 3.4 29.6 - - - -
316V GLU* 3.2 53.6 + - + -
317V ILE* 3.8 9.1 - - + +
320V LEU* 4.9 6.8 - - + +
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Residues in contact with GLU 276 (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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272V ALA* 4.1 20.1 - - + +
273V GLY 2.9 11.8 + - - +
275V HIS* 1.3 101.5 + - + +
277V THR* 1.3 53.9 + - - +
279V TYR* 3.2 7.8 + - - +
280V ASN* 2.8 51.8 + - - +
320V LEU* 4.5 13.0 - - + -
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Residues in contact with THR 277 (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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160V THR* 6.1 0.4 - - + -
162V ASN* 2.9 32.1 - - - +
176V MET* 3.8 19.4 - - + +
177V ARG 6.0 0.2 - - - -
178V LEU* 5.2 15.8 - - + +
272V ALA* 4.0 19.1 + - - +
273V GLY 3.0 14.5 + - - -
274V ILE* 3.5 11.9 - - + +
276V GLU* 1.3 75.0 - - - +
278V THR* 1.3 63.2 + - - +
280V ASN* 3.8 8.1 + - - +
281V SER* 3.1 24.3 + - - -
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Residues in contact with THR 278 (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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151V ILE* 3.6 6.5 - - + +
153V LEU* 3.9 2.6 - - - +
162V ASN* 3.4 19.9 + - - +
274V ILE 2.9 15.7 + - - -
275V HIS 3.5 9.6 - - - -
277V THR* 1.3 73.1 - - - +
279V TYR* 1.3 63.3 + - - +
281V SER* 3.4 4.0 - - - -
282V ILE* 3.0 35.7 + - + +
297V ASN* 3.2 33.9 + - - +
313V MET* 3.0 17.4 - - + +
317V ILE* 4.1 15.3 - - + -
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Residues in contact with TYR 279 (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 3.3 9.1 + - - +
276V GLU 3.2 8.3 - - - +
277V THR 3.1 0.2 - - - -
278V THR* 1.3 80.0 - - - +
280V ASN* 1.3 79.7 + - - +
282V ILE* 2.9 24.8 + - - +
283V MET* 2.9 55.7 + - + +
294V TYR* 3.4 22.0 - + - -
317V ILE* 5.1 5.2 - - + -
320V LEU* 3.3 64.1 + - + +
321V ALA 4.3 0.7 - - - -
322V PRO* 5.7 0.2 - - - +
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Residues in contact with ASN 280 (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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176V MET* 4.8 13.2 - - + -
272V ALA* 4.9 4.7 - - - +
276V GLU* 2.8 40.9 + - - +
277V THR* 3.1 9.4 + - - +
279V TYR* 1.3 92.2 - - - +
281V SER* 1.3 61.7 + - - +
283V MET* 3.2 6.6 + - - +
284V LYS* 3.1 26.1 + - - +
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Residues in contact with SER 281 (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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151V ILE* 3.6 13.0 - - - -
162V ASN* 3.6 16.1 - - - +
164V PRO* 3.4 12.2 - - - +
174V ALA* 2.4 32.2 + - - +
176V MET* 3.8 6.8 - - - +
277V THR 3.1 12.0 + - - -
278V THR 3.4 11.2 - - - -
280V ASN* 1.3 74.2 - - - +
282V ILE* 1.3 59.7 - - - +
284V LYS* 3.1 24.5 + - - +
285V CYS* 3.4 15.3 + - - -
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Residues in contact with ILE 282 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151V ILE* 3.7 22.7 - - + -
278V THR* 3.0 33.9 - - + +
279V TYR* 2.9 11.1 + - - +
281V SER* 1.3 80.6 - - - +
283V MET* 1.3 56.6 + - - +
284V LYS 3.0 5.5 + - - -
285V CYS* 3.2 18.8 + - - +
290V ARG* 3.4 28.0 + - + +
293V LEU* 4.5 13.0 - - + -
294V TYR* 3.6 58.6 - - + +
297V ASN* 4.6 1.8 - - - +
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Residues in contact with MET 283 (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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279V TYR* 2.9 57.0 + - + +
280V ASN* 3.2 6.6 + - - +
282V ILE* 1.3 69.6 - - - +
284V LYS* 1.4 56.8 + - - +
285V CYS 3.5 0.4 - - - -
290V ARG* 3.9 43.8 + - - +
294V TYR* 3.4 24.9 - - + +
322V PRO* 4.0 23.8 - - + -
325V MET* 6.0 0.9 - - + -
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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