Contacts of the helix formed by residues 285 - 292 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231P ALA 4.0 4.3 - - - +
232P PHE 2.8 25.1 - - - +
233P GLY* 3.3 20.9 - - - -
234P ASN 3.3 20.9 - - - -
235P ALA* 4.4 0.9 - - + -
245P ARG* 3.8 8.8 - - + +
270P LEU* 3.8 9.0 - - + +
271P GLU* 2.5 43.4 + - - +
274P ARG* 3.2 25.6 - - + -
275P VAL* 3.9 19.7 - - + -
284P SER* 1.4 97.6 + - - +
286P HIS* 1.3 64.6 + - - +
287P ILE* 3.4 0.9 - - + -
288P PHE* 4.0 14.7 + + + -
289P TYR* 3.2 11.6 - - - -
434P TYR* 3.7 21.5 - + - +
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Residues in contact with HIS 286 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230P GLU* 3.3 24.7 - - + -
231P ALA* 3.2 9.7 + - - +
234P ASN 3.2 8.5 + - - -
235P ALA* 3.4 28.2 + - - -
236P MLY 3.9 3.1 - - - -
241P ASP 3.9 9.0 - - - -
242P ASN* 2.5 29.8 + - - -
283P ARG* 3.5 23.9 + - - +
285P TYR* 1.3 69.6 - - - +
287P ILE* 1.3 57.4 + - - +
288P PHE 3.0 3.1 - - - -
289P TYR* 2.6 34.0 + - - +
290P GLN* 2.7 27.5 + - - +
325P ILE* 4.7 10.9 - - + +
327P ASP* 5.0 1.7 - - - +
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Residues in contact with ILE 287 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231P ALA* 2.7 30.5 + - + +
232P PHE* 3.0 44.2 - - + -
285P TYR* 4.4 1.1 - - + -
286P HIS* 1.3 71.0 - - - +
288P PHE* 1.3 78.8 + - + +
290P GLN* 2.9 16.0 + - - +
291P ILE* 2.8 35.3 + - + +
334P THR* 4.5 8.3 - - + -
351P ILE* 5.4 0.2 - - + -
352P TYR* 4.8 15.9 - - + -
355P THR* 4.3 15.5 - - + +
434P TYR* 4.0 18.6 - - - +
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Residues in contact with PHE 288 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275P VAL* 4.9 8.5 - - + -
284P SER* 4.0 16.4 - - - -
285P TYR* 4.0 24.2 - + + +
286P HIS 2.7 2.4 + - - -
287P ILE* 1.3 83.9 - - + +
289P TYR* 1.3 69.1 + - + +
291P ILE* 3.5 4.8 + - - +
292P MET* 3.2 28.8 + - - +
315P VAL* 4.0 32.3 - - + -
355P THR* 3.4 35.2 - - + -
358P VAL* 4.6 12.6 - - + -
359P MET* 3.8 29.6 - - + -
434P TYR* 3.9 31.2 - + - -
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Residues in contact with TYR 289 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278P GLN* 4.1 1.4 + - - -
283P ARG* 3.4 36.6 - - - +
284P SER* 3.3 30.5 + - - -
285P TYR 3.2 23.8 - - - -
286P HIS 2.6 10.8 + - - +
288P PHE* 1.3 73.8 - - + +
290P GLN* 1.3 67.4 + - - +
292P MET* 3.6 7.3 + - - +
293P SER* 3.3 17.2 + - - -
309P PRO* 4.7 8.1 - - + -
315P VAL* 2.3 46.9 + - + -
319P GLU 3.5 12.0 + - - -
320P ILE* 3.5 37.2 - - + +
327P ASP* 3.7 13.3 - - - +
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Residues in contact with GLN 290 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231P ALA* 3.5 17.5 - - - +
286P HIS* 2.7 29.1 + - - +
287P ILE* 3.0 17.4 - - + +
289P TYR* 1.3 76.6 - - - +
291P ILE* 1.3 52.4 + - + +
293P SER* 2.6 37.8 + - - -
327P ASP* 3.3 18.6 + - - +
330P GLU* 3.5 17.6 - - + +
331P LEU* 2.8 37.3 - - + +
334P THR* 2.4 39.7 + - - +
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Residues in contact with ILE 291 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287P ILE* 2.8 26.1 + - + +
288P PHE* 3.6 5.8 - - - +
290P GLN* 1.3 74.5 - - + +
292P MET* 1.3 60.7 + - + +
293P SER 3.0 1.6 + - - -
294P ASN* 3.8 2.9 + - - -
295P MLY 5.3 0.2 + - - -
296P MLY 5.5 0.2 - - - +
299P LEU* 4.9 9.7 - - + +
300P ILE* 3.1 20.5 - - + +
303P LEU* 3.6 26.2 - - + -
305P ILE* 4.0 23.8 - - + -
331P LEU* 3.2 13.1 - - + +
352P TYR* 3.7 32.5 - - + -
355P THR* 4.7 18.8 - - + -
359P MET* 4.6 5.6 - - + -
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Residues in contact with MET 292 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288P PHE 3.2 20.7 + - - +
289P TYR* 3.6 7.6 + - - +
291P ILE* 1.3 78.6 - - + +
293P SER* 1.3 64.8 + - - +
294P ASN* 3.2 2.4 + - - -
300P ILE* 4.2 7.2 - - - -
305P ILE* 4.3 12.3 - - + -
306P THR 3.8 13.7 - - - +
307P THR* 3.5 31.4 - - - +
308P ASN 3.4 7.2 - - - +
309P PRO* 3.0 57.7 - - + -
312P TYR* 4.4 7.4 - - + -
315P VAL* 4.8 6.5 - - - -
359P MET* 4.2 20.6 - - + +
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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