Contacts of the helix formed by residues 278 - 293 (chain A) in PDB entry 2YEV
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 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277A PHE* 1.3 74.6 - - - +
279A TYR* 1.3 57.5 + - - +
280A ARG 3.3 2.9 - - - -
281A GLN* 3.2 20.9 + - - +
282A MET* 2.9 31.6 + - - +
331A ASN* 3.5 10.3 - - - +
78B HIS 2.7 18.5 + - - -
79B GLY* 4.6 3.6 - - - -
84B GLU* 4.1 4.0 - - - -
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Residues in contact with TYR 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A TRP* 3.4 46.2 - + - -
191A MET 2.7 29.8 + - - -
193A ILE* 4.4 14.4 - - + -
196A TRP* 2.9 28.0 + + - -
276A LEU* 3.8 27.8 + - + +
277A PHE 3.5 2.0 - - - -
278A GLY* 1.3 75.0 - - - +
280A ARG* 1.3 73.5 + - + +
282A MET* 3.2 12.5 + - - +
283A VAL* 3.1 23.1 + - + +
528A GLU* 3.9 29.8 - - + +
78B HIS 4.5 1.2 + - - -
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Residues in contact with ARG 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A TRP* 4.1 27.8 - - + -
278A GLY 3.3 0.8 - - - -
279A TYR* 1.3 86.4 - - + +
281A GLN* 1.3 68.5 + - - +
283A VAL* 3.1 4.5 + - - +
284A TRP* 2.9 74.1 + - + -
81B ASP* 3.7 28.5 + - - -
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Residues in contact with GLN 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A GLY* 3.2 21.8 + - - +
280A ARG* 1.3 89.5 + - - +
282A MET* 1.3 58.3 + - - +
284A TRP* 3.7 32.2 - - + +
285A ALA* 2.9 31.6 + - - +
327A VAL* 4.3 6.4 - - + +
331A ASN* 3.8 8.1 - - - +
81B ASP* 3.7 22.3 + - - +
84B GLU* 3.2 45.8 - - + +
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Residues in contact with MET 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ILE* 3.8 21.1 - - + -
265A ALA* 4.2 1.8 - - + -
276A LEU* 4.0 27.1 - - + -
277A PHE 3.3 19.5 - - - +
278A GLY 2.9 17.5 + - - +
279A TYR* 3.2 10.0 + - - +
281A GLN* 1.3 77.0 - - - +
283A VAL* 1.3 60.5 + - - +
285A ALA* 3.4 4.1 + - - +
286A GLN* 3.1 28.6 + - - +
328A LYS* 3.8 27.5 - - + +
331A ASN* 3.5 36.8 - - + +
332A ILE* 3.8 13.0 - - + +
335A THR* 3.6 11.4 - - - +
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Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A TRP* 3.6 32.1 - - + -
193A ILE* 4.0 7.6 - - + -
196A TRP* 3.7 48.9 - - + +
279A TYR* 3.1 18.0 + - + +
280A ARG 3.1 6.8 + - - +
282A MET* 1.3 72.1 - - - +
284A TRP* 1.3 66.5 + - - +
286A GLN* 3.1 10.1 + - - +
287A MET* 3.0 40.0 + - + +
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Residues in contact with TRP 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A TRP* 3.8 19.7 - + - -
280A ARG* 2.9 52.9 + - + +
281A GLN* 3.7 36.3 - - + +
283A VAL* 1.3 76.6 - - - +
285A ALA* 1.3 58.4 + - - +
287A MET* 3.3 23.5 + - - +
288A GLY* 2.8 26.0 + - - -
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Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A GLN 2.9 18.1 + - - +
282A MET* 3.7 5.8 - - - +
283A VAL 3.1 0.2 - - - -
284A TRP* 1.3 74.7 - - - +
286A GLN* 1.3 60.5 + - - +
288A GLY* 3.2 1.6 + - - -
289A ILE* 2.9 34.5 + - - +
324A PRO* 3.3 32.8 - - + +
327A VAL* 4.3 7.4 - - + -
328A LYS* 4.2 17.5 - - + +
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Residues in contact with GLN 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ILE* 3.7 12.9 - - - +
196A TRP* 3.5 18.8 + - - +
197A SER* 3.4 44.3 - - - +
200A ALA* 4.3 7.0 - - + +
258A LEU* 3.9 24.8 - - + +
261A LEU* 6.0 0.4 - - + -
282A MET 3.1 14.1 + - - +
283A VAL* 3.1 8.1 + - - +
285A ALA* 1.3 73.2 - - - +
287A MET* 1.3 66.7 + - + +
289A ILE* 3.2 5.5 + - + +
290A VAL* 3.0 28.6 + - - +
328A LYS* 2.8 32.9 + - + +
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Residues in contact with MET 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A TRP* 4.4 10.3 - - + -
196A TRP* 3.9 20.9 - - + -
200A ALA* 5.4 0.9 - - - +
283A VAL* 3.0 38.2 + - + +
284A TRP* 3.5 24.9 - - - +
286A GLN* 1.3 77.2 - - - +
288A GLY* 1.3 61.5 + - - +
290A VAL* 3.2 9.6 + - - +
291A VAL* 3.1 29.0 + - + +
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Residues in contact with GLY 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A TRP 2.8 13.9 + - - -
285A ALA* 3.2 5.1 + - - -
287A MET* 1.3 77.5 - - - +
289A ILE* 1.3 59.8 + - - +
291A VAL* 3.5 5.2 + - - +
292A LEU* 3.2 31.0 + - - +
324A PRO* 4.3 15.3 - - - -
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Residues in contact with ILE 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A TYR* 3.8 36.3 - - + +
257A LEU* 5.2 3.6 - - + -
258A LEU* 4.0 28.3 - - + -
261A LEU* 4.6 13.9 - - + -
285A ALA 2.9 21.4 + - - +
286A GLN* 3.6 7.4 - - + +
287A MET 3.2 0.2 - - - -
288A GLY* 1.3 74.3 - - - +
290A VAL* 1.3 60.2 + - - +
293A GLY* 2.9 28.1 + - - -
321A ILE* 4.2 9.9 - - + +
324A PRO* 3.9 10.3 - - + +
325A THR* 3.7 35.2 - - + +
328A LYS* 5.2 2.9 - - + -
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Residues in contact with VAL 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ALA* 3.6 36.3 - - + +
203A VAL* 4.9 10.1 - - + -
204A LEU* 3.9 30.7 - - + +
258A LEU* 4.0 9.6 - - + -
286A GLN 3.0 18.0 + - - +
287A MET* 3.2 10.1 + - - +
289A ILE* 1.3 78.4 - - - +
291A VAL* 1.3 68.8 + - + +
293A GLY 3.6 3.8 + - - -
294A THR* 3.7 16.4 - - + +
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Residues in contact with VAL 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A MET* 3.1 17.0 + - + +
288A GLY* 3.5 5.6 + - - +
289A ILE 3.3 0.2 - - - -
290A VAL* 1.3 81.5 - - + +
292A LEU* 1.3 65.5 + - + +
294A THR* 2.9 25.7 + - - +
295A MET* 3.7 21.0 - - - +
11C ALA* 5.3 3.8 - - + +
12C ALA* 6.2 0.4 - - - -
15C THR* 3.8 38.8 - - + +
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Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A GLY* 3.2 16.0 + - - +
291A VAL* 1.3 82.9 - - + +
293A GLY* 1.3 58.0 + - - +
294A THR 3.0 0.4 - - - -
295A MET* 2.9 38.0 + - + -
296A VAL* 3.4 15.9 - - - +
317A PHE* 4.3 26.9 - - + +
320A LEU* 4.0 28.3 - - + +
321A ILE* 3.5 25.6 - - + +
324A PRO* 4.0 22.0 - - + -
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Residues in contact with GLY 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A LEU* 5.0 2.5 - - - -
250A HIS* 3.4 15.5 - - - -
251A PRO* 3.3 22.1 - - - +
254A TYR* 4.2 18.8 - - - -
289A ILE 2.9 20.7 + - - -
290A VAL* 3.9 2.7 - - - -
291A VAL 3.1 0.8 - - - -
292A LEU* 1.3 77.4 - - - +
294A THR* 1.3 60.1 + - - +
295A MET 3.5 0.4 - - - -
296A VAL* 4.0 2.9 - - - +
297A TRP* 5.4 0.5 + - - +
321A ILE* 3.8 5.1 - - - +
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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