Contacts of the helix formed by residues 273 - 283 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178X LEU* 4.6 1.6 - - - -
261X LEU 3.8 11.2 - - - -
262X PHE 4.0 11.9 + - - -
264X PRO* 4.0 11.6 - - - +
272X ALA* 1.3 75.8 - - - +
274X ILE* 1.3 65.6 + - - -
275X HIS* 3.3 7.0 - - - -
276X GLU* 2.9 23.0 + - - +
277X THR* 3.0 12.5 + - - -
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Residues in contact with ILE 274 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153X LEU* 3.6 27.4 - - + +
155X SER* 5.7 1.1 - - - +
160X THR* 3.6 21.5 - - + +
178X LEU* 3.4 26.2 - - + +
261X LEU* 3.2 40.7 + - + +
262X PHE* 3.6 25.6 - - + -
273X GLY* 1.3 67.5 - - - -
275X HIS* 1.3 59.3 + - - +
277X THR* 3.3 7.1 + - + -
278X THR* 2.9 31.2 + - - -
309X ILE* 6.2 2.5 - - + -
313X MET* 3.9 18.2 - - + -
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Residues in contact with HIS 275 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262X PHE* 3.4 34.8 - + + -
273X GLY* 2.9 8.4 + - - -
274X ILE* 1.3 72.4 - - - +
276X GLU* 1.3 98.6 + - + +
278X THR* 3.5 3.8 - - - -
279X TYR* 3.3 21.0 + - - +
313X MET* 3.4 28.9 - - - -
316X GLU* 3.2 52.9 + - + -
317X ILE* 3.8 8.3 - - + +
320X LEU* 4.9 6.9 - - + +
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Residues in contact with GLU 276 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272X ALA* 4.1 20.1 - - + +
273X GLY 2.9 12.6 + - - +
275X HIS* 1.3 99.9 + - + +
277X THR* 1.3 53.9 + - - +
279X TYR* 3.2 8.9 + - - +
280X ASN* 2.8 50.9 + - - +
320X LEU* 4.5 13.7 - - + -
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Residues in contact with THR 277 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153X LEU* 5.9 0.4 - - + -
160X THR* 6.1 0.2 - - + -
162X ASN* 2.9 31.6 - - - +
176X MET* 3.8 20.2 - - + +
178X LEU* 5.2 17.0 - - + +
272X ALA* 4.0 18.5 + - - +
273X GLY 3.0 13.9 + - - -
274X ILE* 3.5 11.7 - - + +
276X GLU* 1.3 75.1 - - - +
278X THR* 1.3 63.3 + - - +
280X ASN* 3.8 8.2 + - - +
281X SER* 3.1 23.9 + - - -
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Residues in contact with THR 278 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151X ILE* 3.6 6.9 - - + +
153X LEU* 3.9 2.8 - - - +
162X ASN* 3.4 20.3 + - - +
274X ILE 2.9 15.6 + - - -
275X HIS 3.5 9.6 - - - -
277X THR* 1.3 74.3 - - - +
279X TYR* 1.3 62.3 + - - +
281X SER* 3.4 3.8 - - - -
282X ILE* 3.0 35.9 + - + +
297X ASN* 3.2 34.8 + - - +
313X MET* 3.0 17.0 - - + +
317X ILE* 4.1 15.5 - - + -
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Residues in contact with TYR 279 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275X HIS 3.3 10.0 + - - +
276X GLU 3.2 8.7 - - - +
277X THR 3.1 0.2 - - - -
278X THR* 1.3 80.0 - - - +
280X ASN* 1.3 79.2 + - - +
282X ILE* 2.9 24.6 + - - +
283X MET* 2.9 56.4 + - + +
294X TYR* 3.4 21.1 - + - -
317X ILE* 5.1 5.6 - - + -
320X LEU* 3.3 62.1 + - + +
321X ALA 4.3 0.7 - - - -
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Residues in contact with ASN 280 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176X MET* 4.8 12.3 - - + -
272X ALA* 4.9 5.0 - - - +
276X GLU* 2.8 41.3 + - - +
277X THR* 3.1 10.2 + - - +
279X TYR* 1.3 91.2 - - - +
281X SER* 1.3 62.5 + - - +
283X MET* 3.2 6.3 + - - +
284X LYS* 3.1 24.9 + - - +
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Residues in contact with SER 281 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151X ILE* 3.6 13.0 - - - -
162X ASN* 3.6 16.3 - - - +
164X PRO* 3.4 11.8 - - - +
174X ALA* 2.4 32.0 + - - +
176X MET* 3.8 7.2 - - - +
277X THR 3.1 11.6 + - - -
278X THR 3.4 10.8 - - - -
280X ASN* 1.3 74.6 - - - +
282X ILE* 1.3 60.2 + - - +
284X LYS* 3.1 24.8 + - - +
285X CYS* 3.4 14.8 + - - -
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Residues in contact with ILE 282 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151X ILE* 3.7 22.9 - - + -
278X THR* 3.0 32.5 - - + +
279X TYR* 2.9 10.0 + - - +
281X SER* 1.3 79.5 - - - +
283X MET* 1.3 56.2 + - - +
284X LYS 3.0 5.3 + - - -
285X CYS* 3.2 18.9 + - - +
290X ARG* 3.4 28.8 + - + +
293X LEU* 4.5 13.7 - - + -
294X TYR* 3.6 58.1 - - + +
297X ASN* 4.6 2.2 - - - +
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Residues in contact with MET 283 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279X TYR* 2.9 57.1 + - + +
280X ASN* 3.2 7.5 + - - +
282X ILE* 1.3 70.2 - - - +
284X LYS* 1.4 57.0 + - - +
285X CYS 3.5 0.9 - - - -
290X ARG* 3.9 43.2 + - - +
294X TYR* 3.4 24.7 - - + +
322X PRO* 4.0 24.7 - - + -
325X MET* 6.0 0.4 - - + -
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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