Contacts of the helix formed by residues 281 - 293 (chain M) in PDB entry 5IYB
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 ALA 281 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279M GLY 3.8 1.2 + - - -
280M VAL* 1.3 74.0 - - - +
282M ASP* 1.3 62.5 + - - +
283M VAL* 4.1 14.1 - - + -
284M THR* 3.1 28.6 + - - +
285M ILE* 3.4 5.4 + - - +
86Y C 3.1 44.9 + - + +
87Y G 4.6 5.6 - - - +
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Residues in contact with ASP 282 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271M GLN* 3.7 39.0 - - + +
272M LYS* 4.0 30.3 + - - +
275M GLY* 4.9 1.7 - - - -
280M VAL 3.5 3.2 + - - -
281M ALA* 1.3 72.0 - - - +
283M VAL* 1.3 78.9 + - - +
285M ILE* 3.5 15.7 + - - +
286M ARG* 3.0 40.9 + - - +
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Residues in contact with VAL 283 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281M ALA* 4.1 15.9 - - + -
282M ASP* 1.3 92.0 + - - +
284M THR* 1.3 66.2 + - - +
286M ARG* 3.3 20.4 + - - +
287M GLN* 2.9 28.9 + - - +
3X G 6.5 0.7 - - + -
4X G 5.9 4.9 - - - +
5X G 6.1 1.3 - - - +
86Y C 5.1 15.9 - - + -
87Y G 5.6 4.9 - - - +
88Y C 6.3 1.1 - - - +
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Residues in contact with THR 284 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252M SER* 3.7 18.4 - - - +
280M VAL* 3.8 6.1 - - + -
281M ALA* 3.1 12.7 + - - +
283M VAL* 1.3 79.1 - - - +
285M ILE* 1.3 63.9 + - - +
287M GLN* 4.0 9.2 - - - +
288M SER* 2.9 29.1 + - - -
85Y G 3.3 43.4 - - + +
86Y C 2.7 27.1 + - - +
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Residues in contact with ILE 285 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252M SER* 5.4 3.1 - - - +
255M ALA* 3.9 27.6 - - + +
256M ALA* 4.1 24.2 - - - +
259M TYR* 4.4 20.0 - - + -
271M GLN* 4.1 11.7 - - + +
274M ILE* 4.2 7.2 - - + -
275M GLY* 4.1 19.5 - - - +
280M VAL* 4.0 16.4 - - + -
281M ALA 3.7 8.3 - - - +
282M ASP* 3.5 19.7 - - + +
284M THR* 1.3 76.5 - - - +
286M ARG* 1.3 57.9 + - - +
288M SER* 3.1 5.6 + - - -
289M TYR* 2.8 29.8 + - + +
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Residues in contact with ARG 286 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271M GLN* 2.9 39.0 + - - +
282M ASP* 3.0 27.5 + - - +
283M VAL* 3.3 21.8 + - - +
285M ILE* 1.3 76.3 - - - +
287M GLN* 1.3 60.4 + - - +
289M TYR* 3.6 8.3 + - + +
290M ARG* 3.1 43.4 + - - +
316M LEU* 3.5 30.2 - - + +
3X G 2.9 65.5 + - - +
4X G 3.8 10.3 + - - -
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Residues in contact with GLN 287 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248M ARG* 4.0 24.1 + - - +
283M VAL 2.9 16.4 + - - +
284M THR* 4.0 8.7 - - - +
285M ILE 3.3 0.2 - - - -
286M ARG* 1.3 76.8 - - - +
288M SER* 1.3 57.4 + - - +
290M ARG* 3.2 17.7 + - + +
291M LEU* 3.0 43.7 + - + +
84Y G 6.0 0.9 - - - +
85Y G 5.0 7.1 + - - -
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Residues in contact with SER 288 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245M VAL* 4.8 4.2 - - - +
248M ARG* 5.1 7.7 + - - +
252M SER* 3.8 23.8 - - - -
253M VAL* 5.3 2.6 - - - +
256M ALA* 4.1 17.0 - - - -
284M THR* 2.9 18.9 + - - +
285M ILE 3.1 4.6 + - - -
287M GLN* 1.3 78.2 - - - +
289M TYR* 1.3 61.7 + - - +
291M LEU* 3.3 17.1 + - - +
292M ILE* 3.2 27.6 + - - +
85Y G 4.9 2.4 + - - -
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Residues in contact with TYR 289 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256M ALA* 4.2 6.8 - - + +
259M TYR* 3.9 38.6 - + + -
260M MET* 3.6 30.7 - - + -
263M GLN* 5.5 1.5 - - + +
271M GLN* 6.0 2.5 - - - +
285M ILE* 2.8 21.5 + - + +
286M ARG* 3.8 8.3 - - + +
288M SER* 1.3 69.0 - - - +
290M ARG* 1.3 64.4 + - + +
291M LEU 3.1 2.0 - - - -
292M ILE* 3.1 21.1 + - + +
293M TYR* 2.9 45.7 + + + +
313M LEU* 3.2 24.8 - - - +
314M PRO* 2.7 29.8 + - - +
315M GLN* 4.3 9.0 - - + -
316M LEU* 4.9 7.2 - - + -
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Residues in contact with ARG 290 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286M ARG* 3.1 32.8 + - - +
287M GLN* 3.3 17.1 - - + +
289M TYR* 1.3 78.1 - - + +
291M LEU* 1.3 60.9 + - + +
293M TYR* 4.3 5.9 - - - +
294M PRO* 3.7 16.1 - - - +
316M LEU* 2.5 42.2 + - - +
4X G 2.4 49.0 + - - +
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Residues in contact with LEU 291 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244M LEU* 5.0 10.9 - - - +
245M VAL* 3.5 29.4 - - + +
248M ARG* 3.9 31.4 - - - +
287M GLN* 3.0 32.5 + - + +
288M SER* 3.3 16.8 - - - +
289M TYR 3.1 0.4 - - - -
290M ARG* 1.3 79.6 - - + +
292M ILE* 1.3 59.7 + - - +
294M PRO* 3.8 9.8 - - - +
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Residues in contact with ILE 292 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235M ILE* 5.5 4.5 - - + -
239M ALA* 5.2 11.9 - - + -
244M LEU* 5.1 12.7 - - + +
245M VAL* 4.6 20.0 - - + -
253M VAL* 6.3 1.3 - - + -
256M ALA* 4.0 25.1 - - + +
257M ALA* 4.9 2.2 - - - +
260M MET* 3.5 30.1 - - + -
288M SER* 3.2 12.3 + - - +
289M TYR* 3.1 28.9 - - + +
291M LEU* 1.3 77.8 - - - +
293M TYR* 1.3 64.8 + - - +
294M PRO* 3.4 2.5 - - - -
295M ARG* 3.3 14.7 + - - +
296M ALA* 3.5 8.8 + - - -
299M LEU* 4.6 11.3 - - + +
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Residues in contact with TYR 293 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260M MET* 4.7 1.8 - - - -
289M TYR* 2.9 39.1 + + + +
290M ARG* 4.3 6.3 - - - +
292M ILE* 1.3 77.6 - - - +
294M PRO* 1.3 73.4 - - + +
295M ARG 3.0 1.2 + - - -
296M ALA* 3.2 18.5 + - + +
297M PRO* 4.8 1.6 - - - +
310M VAL* 4.3 11.3 + - + +
313M LEU* 3.3 34.3 + - + -
314M PRO 3.7 18.6 - - - -
315M GLN* 3.2 34.0 + - + -
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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