Contacts of the helix formed by residues 273 - 283 (chain W) 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 W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178W LEU* 4.6 1.3 - - - -
261W LEU 3.8 9.9 - - - -
262W PHE 4.0 11.7 + - - -
264W PRO* 4.0 12.4 - - - +
272W ALA* 1.3 76.6 - - - +
274W ILE* 1.3 66.5 + - - -
275W HIS* 3.3 6.8 - - - -
276W GLU* 2.9 23.7 + - - +
277W THR* 3.0 12.1 + - - -
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Residues in contact with ILE 274 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153W LEU* 3.6 28.2 - - + +
155W SER* 5.5 1.3 - - - +
160W THR* 3.6 20.6 - - + -
178W LEU* 3.4 25.6 - - + -
261W LEU* 3.2 40.5 + - + +
262W PHE* 3.6 25.8 - - + -
273W GLY* 1.3 66.8 - - - -
275W HIS* 1.3 59.1 + - - +
277W THR* 3.3 6.9 + - + -
278W THR* 2.9 31.5 + - - -
309W ILE* 6.2 2.7 - - + -
313W MET* 3.9 18.4 - - + -
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Residues in contact with HIS 275 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262W PHE* 3.4 34.8 - + + -
273W GLY* 2.9 8.2 + - - -
274W ILE* 1.3 72.2 - - - +
276W GLU* 1.3 99.5 + - + +
278W THR* 3.5 3.6 - - - -
279W TYR* 3.3 20.6 + - - +
313W MET* 3.4 28.7 - - - -
316W GLU* 3.2 53.4 + - + -
317W ILE* 3.8 8.4 - - + +
320W LEU* 4.9 7.1 - - + +
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Residues in contact with GLU 276 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272W ALA* 4.1 20.8 - - + +
273W GLY 2.9 11.5 + - - +
275W HIS* 1.3 100.5 + - + +
277W THR* 1.3 53.6 + - - +
279W TYR* 3.2 8.0 - - - +
280W ASN* 2.8 52.7 + - - +
320W LEU* 4.5 13.2 - - + -
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Residues in contact with THR 277 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160W THR* 6.1 0.2 - - + -
162W ASN* 2.9 32.5 + - - +
176W MET* 3.8 20.1 - - + +
177W ARG 6.0 0.2 - - - -
178W LEU* 5.2 16.0 - - + +
272W ALA* 4.0 18.2 + - - +
273W GLY 3.0 13.6 + - - -
274W ILE* 3.5 12.1 - - + +
276W GLU* 1.3 75.3 - - - +
278W THR* 1.3 64.0 + - - +
280W ASN* 3.8 8.1 + - - +
281W SER* 3.1 24.3 + - - -
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Residues in contact with THR 278 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151W ILE* 3.6 6.9 - - + +
153W LEU* 3.9 2.6 - - - +
162W ASN* 3.4 19.1 + - - +
274W ILE 2.9 14.6 + - - -
275W HIS 3.5 9.9 - - - -
277W THR* 1.3 72.7 - - - +
279W TYR* 1.3 62.4 + - - +
281W SER* 3.4 4.3 - - - -
282W ILE* 3.0 35.9 + - + +
297W ASN* 3.2 34.4 + - - +
313W MET* 3.0 17.4 - - + +
317W ILE* 4.1 15.5 - - + -
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Residues in contact with TYR 279 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275W HIS 3.3 9.8 + - - +
276W GLU* 3.2 8.5 - - - +
278W THR* 1.3 81.0 - - - +
280W ASN* 1.3 78.2 + - - +
282W ILE* 2.9 26.0 + - - +
283W MET* 2.9 54.8 + - + +
294W TYR* 3.4 22.0 - + - -
317W ILE* 5.1 5.4 - - + -
320W LEU* 3.3 64.2 + - + +
321W ALA* 4.4 0.7 - - - -
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Residues in contact with ASN 280 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176W MET* 4.8 13.9 - - - -
272W ALA* 4.9 4.9 - - - +
276W GLU* 2.8 40.6 + - - +
277W THR* 3.1 10.1 + - - +
279W TYR* 1.3 91.5 - - - +
281W SER* 1.3 63.6 + - - +
283W MET* 3.2 5.7 + - - +
284W LYS* 3.1 25.6 + - - +
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Residues in contact with SER 281 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151W ILE* 3.6 12.3 - - - -
162W ASN* 3.6 16.7 - - - +
164W PRO* 3.4 11.8 - - - +
174W ALA* 2.4 32.4 + - - +
176W MET* 3.8 8.1 - - - +
277W THR 3.1 11.7 + - - -
278W THR 3.4 10.8 - - - -
280W ASN* 1.3 74.6 - - - +
282W ILE* 1.3 58.5 + - - +
284W LYS* 3.1 24.9 + - - +
285W CYS* 3.4 15.1 + - - -
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Residues in contact with ILE 282 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151W ILE* 3.7 22.9 - - + -
278W THR* 3.0 31.6 - - + +
279W TYR* 2.9 11.1 + - - +
281W SER* 1.3 80.2 - - - +
283W MET* 1.3 56.0 + - - +
284W LYS 3.0 5.6 + - - -
285W CYS* 3.2 19.1 + - - +
290W ARG* 3.4 28.2 + - + +
293W LEU* 4.5 13.9 - - + -
294W TYR* 3.6 58.1 - - + +
297W ASN* 4.6 2.0 - - - +
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Residues in contact with MET 283 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279W TYR* 2.9 55.7 + - + +
280W ASN* 3.2 6.8 + - - +
282W ILE* 1.3 70.4 - - - +
284W LYS* 1.4 56.0 + - - +
285W CYS 3.5 0.6 - - - +
290W ARG* 3.9 42.5 + - - +
294W TYR* 3.4 24.2 - - + +
322W PRO* 4.0 24.7 - - + -
325W MET* 6.0 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