Contacts of the helix formed by residues 289 - 295 (chain Y) 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 ILE 289 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2041 ALA* 4.1 6.1 - - + -
166Y TYR* 3.7 40.2 - - + -
171Y LEU* 3.6 32.5 - - + -
285Y CYS* 4.0 7.6 - - + -
286Y ASP* 3.1 41.7 + - + +
287Y ILE 3.2 0.8 - - - -
288Y ASP* 1.4 75.8 - - - +
290Y ARG* 1.3 65.7 + - - +
291Y LYS* 3.3 5.8 - - - +
292Y ASP* 3.0 16.0 + - - +
293Y LEU* 3.3 30.2 + - + +
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Residues in contact with ARG 290 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1991 SER* 5.6 0.8 - - - -
2011 VAL* 3.2 36.0 - - - +
2461 GLN* 6.2 0.7 - - + -
282Y ILE* 3.4 36.3 + - + +
283Y MET* 3.9 47.3 + - - +
285Y CYS* 2.4 32.5 + - + -
286Y ASP 3.3 11.9 + - - +
287Y ILE* 3.8 14.5 - - - +
288Y ASP 3.4 1.4 - - - -
289Y ILE* 1.3 79.4 - - - +
291Y LYS* 1.4 61.6 + - - +
292Y ASP 3.3 0.5 + - - -
293Y LEU* 4.1 7.7 - - - +
294Y TYR* 3.1 33.2 + - + -
325Y MET* 4.7 5.4 - - + -
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Residues in contact with LYS 291 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2431 PRO* 1.6 45.5 + - + +
2441 ASP* 0.4 306.9 + - + +
2451 GLY 2.7 9.0 - - - +
288Y ASP 3.0 14.5 + - - +
289Y ILE* 3.2 0.8 + - - +
290Y ARG* 1.4 75.1 - - - +
292Y ASP* 1.4 91.3 + - - +
294Y TYR* 3.4 3.3 + - - +
295Y ALA* 3.2 23.2 + - - +
325Y MET* 3.7 8.0 - - - +
326Y LYS* 4.5 2.3 - - - +
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Residues in contact with ASP 292 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2431 PRO 4.2 4.9 - - - +
2441 ASP* 3.2 4.5 - - - +
149Y THR* 3.9 23.3 - - + +
150Y GLY* 5.2 0.2 - - - -
166Y TYR* 4.0 19.9 + - - -
289Y ILE* 3.0 9.5 + - - +
291Y LYS* 1.4 102.7 + - - +
293Y LEU* 1.3 68.6 + - - +
295Y ALA* 3.1 5.4 + - - -
296Y ASN* 2.9 30.8 + - - +
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Residues in contact with LEU 293 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149Y THR* 3.8 22.7 - - + -
150Y GLY* 3.8 20.2 - - - +
151Y ILE* 3.4 30.9 - - + +
164Y PRO* 4.4 6.7 - - + -
165Y ILE 4.3 4.9 - - - +
282Y ILE* 4.5 17.5 - - + -
285Y CYS* 4.0 22.0 - - + -
289Y ILE* 3.3 42.3 + - + +
290Y ARG* 4.1 7.4 - - - +
292Y ASP* 1.3 77.3 - - - +
294Y TYR* 1.3 58.2 + - - +
296Y ASN 3.0 26.2 + - - -
297Y ASN* 3.7 1.2 + - - +
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Residues in contact with TYR 294 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279Y TYR* 3.4 19.4 - + - -
282Y ILE* 3.6 37.7 - - + +
283Y MET* 3.4 32.8 - - + +
290Y ARG* 3.1 28.4 + - + +
291Y LYS 3.7 3.4 - - - +
292Y ASP 3.2 1.2 - - - -
293Y LEU* 1.3 79.3 - - - +
295Y ALA* 1.3 59.5 + - - +
296Y ASN 3.1 1.1 + - - -
297Y ASN* 4.6 1.5 + - - +
317Y ILE* 4.0 20.7 - - + +
321Y ALA* 3.6 20.7 - - + +
322Y PRO* 4.7 0.2 - - + -
325Y MET* 3.4 31.4 - - + -
326Y LYS 3.2 15.7 - - - +
327Y ILE* 3.4 16.1 - - + -
328Y LYS 2.8 22.3 + - - +
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Residues in contact with ALA 295 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291Y LYS 3.2 11.7 + - - +
292Y ASP* 3.1 4.1 + - - +
294Y TYR* 1.3 78.1 - - - +
296Y ASN* 1.4 74.3 + - - +
326Y LYS* 3.8 32.3 - - + +
328Y LYS* 3.2 33.8 - - - +
330Y ILE* 3.8 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