Contacts of the helix formed by residues 285 - 292 (chain D) 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 TYR 285 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D ALA 4.0 4.0 - - - +
232D PHE 2.8 24.7 - - - +
233D GLY* 3.3 20.4 - - - -
234D ASN 3.3 19.5 - - - -
235D ALA* 4.0 1.1 - - + +
245D ARG* 3.8 8.1 - - + +
270D LEU* 3.8 9.0 - - + +
271D GLU* 2.5 43.6 + - - +
274D ARG* 3.2 25.6 - - + -
275D VAL* 3.9 19.3 - - + -
284D SER* 1.4 98.4 + - - +
286D HIS* 1.3 64.9 + - - +
287D ILE* 3.4 1.1 - - + -
288D PHE* 4.0 14.3 + + + -
289D TYR* 3.2 12.3 - - - -
434D TYR* 3.7 20.2 - + - +
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Residues in contact with HIS 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230D GLU* 3.3 25.6 - - + -
231D ALA* 3.2 7.3 + - - +
234D ASN 3.2 8.3 + - - -
235D ALA* 3.4 29.2 + - - -
236D MLY 3.9 3.1 - - - -
241D ASP 3.9 8.5 - - - -
242D ASN* 2.5 29.2 + - - -
283D ARG* 3.5 24.6 + - - +
285D TYR* 1.3 71.1 - - - +
287D ILE* 1.3 57.1 - - - +
288D PHE 3.0 3.1 - - - -
289D TYR* 2.6 34.5 + - - +
290D GLN* 2.7 27.8 + - - +
325D ILE* 4.7 10.9 - - + +
327D ASP* 5.4 1.3 - - - +
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Residues in contact with ILE 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231D ALA* 2.7 30.9 + - + +
232D PHE* 3.0 44.4 - - + -
285D TYR* 4.4 1.3 - - + -
286D HIS* 1.3 72.3 - - - +
288D PHE* 1.3 80.5 + - + +
290D GLN* 2.9 16.8 + - + +
291D ILE* 2.8 35.7 + - + +
334D THR* 4.5 8.3 - - + -
352D TYR* 4.8 15.5 - - + -
355D THR* 4.3 13.7 - - + -
434D TYR* 4.0 17.9 - - - +
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Residues in contact with PHE 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D VAL* 4.9 7.9 - - + -
284D SER* 4.0 18.4 - - - -
285D TYR* 4.0 22.7 - + + +
286D HIS 2.7 3.0 + - - -
287D ILE* 1.3 84.4 - - + +
289D TYR* 1.3 70.3 + - + +
291D ILE* 3.5 5.0 + - - +
292D MET* 3.2 28.1 + - - +
315D VAL* 4.0 33.0 - - + -
355D THR* 3.4 35.2 - - + -
358D VAL* 4.6 12.8 - - + -
359D MET* 3.8 29.6 - - + +
434D TYR* 3.9 31.6 - + - -
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Residues in contact with TYR 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278D GLN* 4.1 1.2 + - - -
283D ARG* 3.4 36.1 - - - +
284D SER* 3.3 30.0 + - - -
285D TYR 3.2 24.2 - - - -
286D HIS 2.6 11.1 + - - +
288D PHE* 1.3 72.1 - - + +
290D GLN* 1.3 66.7 + - - +
292D MET* 3.6 6.3 + - - +
293D SER* 3.3 17.5 + - - -
309D PRO* 4.7 9.4 - - + -
315D VAL* 2.3 47.8 + - + -
319D GLU 3.5 11.1 + - - -
320D ILE* 3.5 35.9 - - + +
327D ASP* 3.7 12.7 - - - +
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Residues in contact with GLN 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D ALA* 3.5 17.2 - - - +
286D HIS* 2.7 28.1 + - - +
287D ILE* 2.9 17.6 + - + +
289D TYR* 1.3 76.6 - - - +
291D ILE* 1.3 51.6 + - + +
293D SER* 2.6 37.9 + - - -
327D ASP* 3.3 18.3 + - - +
330D GLU* 3.5 17.3 - - + +
331D LEU* 2.8 37.4 - - + +
334D THR* 2.4 40.0 + - - +
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Residues in contact with ILE 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287D ILE* 2.8 27.2 + - + +
288D PHE* 3.6 5.6 - - - +
290D GLN* 1.3 75.0 - - + +
292D MET* 1.3 60.3 + - + +
293D SER 3.0 1.4 + - - -
294D ASN* 3.8 2.9 + - - -
296D MLY 5.5 0.2 - - - +
299D LEU* 4.9 10.3 - - + +
300D ILE* 3.1 20.2 - - + +
303D LEU* 3.6 24.7 - - + -
305D ILE* 4.0 24.0 - - + -
331D LEU* 3.1 14.2 - - + +
352D TYR* 3.7 33.4 - - + -
355D THR* 4.7 18.8 - - + -
359D MET* 4.6 6.1 - - + -
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Residues in contact with MET 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288D PHE 3.2 20.7 + - - +
289D TYR* 4.0 7.4 - - - +
291D ILE* 1.3 79.5 - - + +
293D SER* 1.3 63.4 + - - +
294D ASN* 3.2 2.1 + - - -
300D ILE* 4.2 7.2 - - - -
305D ILE* 4.3 12.3 - - + -
306D THR 3.8 13.5 - - - +
307D THR* 3.5 31.3 - - - +
308D ASN 3.4 6.5 - - - +
309D PRO* 3.0 57.4 - - + -
312D TYR* 4.4 7.9 - - + -
315D VAL* 4.8 6.1 - - - -
359D MET* 4.2 20.4 - - + +
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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
------------------------------------------------------------
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