Contacts of the helix formed by residues 285 - 304 (chain B) in PDB entry 1WVA
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 THR 285 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B GLY 3.7 2.0 - - - +
284B LYS* 1.3 88.9 - - + +
286B PRO* 1.3 74.5 - - + +
287B GLU* 3.8 10.1 + - - +
288B GLU* 3.2 36.6 + - - +
289B VAL* 3.5 17.3 + - - +
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Residues in contact with PRO 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B THR* 1.3 90.9 - - + +
287B GLU* 1.3 56.8 + - - +
289B VAL* 3.6 8.5 + - + +
290B THR* 3.2 24.5 + - - -
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Residues in contact with GLU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B THR* 3.3 8.5 + - - +
286B PRO* 1.3 78.3 - - - +
288B GLU* 1.3 62.3 + - - +
289B VAL 3.2 0.9 - - - -
290B THR* 3.8 14.1 - - + +
291B ARG* 2.3 75.4 + - - +
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Residues in contact with GLU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PRO* 3.4 31.1 - - + +
282B LEU 4.2 2.3 - - - +
283B GLY* 3.6 7.9 - - - -
284B LYS* 2.7 50.4 + - - +
285B THR* 3.2 26.8 + - - +
287B GLU* 1.3 89.8 + - - +
289B VAL* 1.3 55.8 + - - +
291B ARG* 3.7 12.2 + - - +
292B THR* 2.8 36.8 + - - -
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Residues in contact with VAL 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B VAL* 4.8 4.3 - - + -
243B ALA* 4.2 7.9 - - + -
280B PRO* 3.0 49.4 - - + +
283B GLY* 3.8 12.6 - - - +
285B THR 3.5 14.8 + - - +
286B PRO* 3.7 8.1 - - + +
288B GLU* 1.3 75.3 - - - +
290B THR* 1.3 66.7 + - - +
292B THR* 3.1 2.6 + - - -
293B VAL* 2.9 38.8 + - + +
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Residues in contact with THR 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B PRO 3.2 14.2 + - - -
287B GLU* 3.8 15.0 - - + +
288B GLU 3.4 0.2 - - - -
289B VAL* 1.3 81.5 - - - +
291B ARG* 1.3 59.9 + - - +
293B VAL* 3.5 5.4 + - - +
294B ASN* 2.9 52.1 + - - +
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Residues in contact with ARG 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B PRO 3.9 0.8 + - - -
239B SER* 2.8 48.9 + - - +
240B PHE* 3.2 13.6 - - - +
242B PRO* 3.8 18.1 - - - +
287B GLU* 2.3 53.8 + - - +
288B GLU* 3.7 15.9 + - - +
290B THR* 1.3 78.5 - - + +
292B THR* 1.3 59.6 + - - +
294B ASN* 4.1 5.4 - - - +
295B THR* 2.8 32.1 + - - +
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Residues in contact with THR 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B VAL* 4.3 18.6 - - + -
240B PHE 3.9 7.4 - - - -
241B THR* 4.2 3.5 - - - +
242B PRO* 3.3 6.2 - - - +
243B ALA* 2.8 39.1 + - + +
278B VAL* 3.6 27.1 - - + -
288B GLU 2.8 21.7 + - - -
289B VAL 3.4 5.2 - - - -
291B ARG* 1.3 75.4 - - - +
293B VAL* 1.3 60.6 + - - +
295B THR* 3.3 3.8 + - - -
296B ALA* 2.9 27.2 + - - +
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Residues in contact with VAL 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B VAL* 3.4 37.0 - - + +
31B LEU* 4.1 11.9 - - + -
34B ALA* 3.5 31.6 - - + -
278B VAL* 4.7 13.7 - - + -
280B PRO* 5.5 0.7 - - + -
289B VAL* 2.9 28.5 + - + +
290B THR* 3.9 6.1 - - - +
292B THR* 1.3 76.4 - - - +
294B ASN* 1.3 59.3 + - - +
296B ALA* 3.2 7.4 + - - +
297B VAL* 2.9 27.9 + - - +
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Residues in contact with ASN 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ALA* 5.1 5.5 - - - +
39B LYS* 5.2 6.9 + - - -
254B TYR* 4.0 4.9 + - - +
290B THR* 2.9 41.4 + - - +
291B ARG* 4.1 5.6 - - - +
293B VAL* 1.3 80.9 - - - +
295B THR* 1.3 57.5 + - - +
297B VAL* 3.5 6.4 + - - +
298B ALA* 3.0 27.9 + - - +
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Residues in contact with THR 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B LEU* 3.4 33.0 - - + -
240B PHE* 2.9 16.4 + - + +
241B THR* 3.7 9.2 - - + -
254B TYR* 3.2 38.0 - - + -
291B ARG* 2.8 22.7 + - - +
292B THR 3.6 3.1 - - - -
293B VAL 3.2 0.6 - - - -
294B ASN* 1.3 74.7 - - - +
296B ALA* 1.3 64.9 + - - +
298B ALA* 3.3 1.0 + - - +
299B ILE* 2.9 33.7 + - + +
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Residues in contact with ALA 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.8 18.8 - - + -
231B PHE* 6.6 0.2 - - - -
233B VAL* 4.4 9.0 - - + -
241B THR* 5.0 1.3 - - - +
275B ILE* 4.2 14.1 - - + +
278B VAL* 4.0 20.0 - - + -
292B THR 2.9 16.4 + - - +
293B VAL* 3.7 4.7 - - - +
295B THR* 1.3 78.8 - - - +
297B VAL* 1.3 58.3 + - - +
299B ILE* 3.7 6.8 + - - +
300B THR* 2.8 26.7 + - - -
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Residues in contact with VAL 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.9 22.7 - - + +
34B ALA* 4.0 22.0 - - + -
36B LEU* 4.4 18.8 - - + -
39B LYS* 4.3 21.3 - - + +
293B VAL 2.9 18.8 + - - +
294B ASN* 3.8 6.5 - - - +
296B ALA* 1.3 74.3 - - - +
298B ALA* 1.3 62.1 + - - +
300B THR* 3.0 8.6 + - - -
301B LEU* 2.9 47.7 + - + +
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Residues in contact with ALA 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B TYR* 3.2 31.6 - - + +
258B LEU* 3.5 19.2 - - + +
294B ASN 3.0 13.9 + - - +
295B THR 3.5 4.5 - - - +
297B VAL* 1.3 79.6 - - - +
299B ILE* 1.3 61.0 + - + +
301B LEU* 3.5 8.3 + - - +
302B ALA* 3.2 16.8 + - - +
306B LEU* 5.7 1.4 - - - +
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Residues in contact with ILE 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B PHE* 3.5 50.7 - - + -
236B LEU* 4.0 6.5 - - + -
254B TYR* 5.1 3.6 - - + +
257B GLY* 4.2 13.5 - - - +
258B LEU* 4.2 17.0 - - + -
261B THR* 3.7 8.4 - - + +
275B ILE* 4.1 14.8 - - + -
295B THR* 2.9 48.3 + - + +
296B ALA* 3.9 6.1 - - - +
298B ALA* 1.3 79.9 - - + +
300B THR* 1.3 63.0 + - - +
302B ALA* 3.4 4.8 - - - +
303B CYS* 3.1 22.5 + - - -
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Residues in contact with THR 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LEU* 6.0 0.5 - - - +
36B LEU* 3.5 30.2 - - + +
40B LEU* 4.5 1.1 - - + -
95B LEU* 4.1 15.7 - - + -
97B LEU* 5.6 0.3 - - - +
273B LEU* 4.4 6.1 - - + -
275B ILE* 3.5 20.1 - - - +
296B ALA 2.8 18.4 + - - -
297B VAL* 3.0 9.6 + - - -
299B ILE* 1.3 77.2 - - - +
301B LEU* 1.3 64.6 + - - +
303B CYS* 3.2 16.9 + - - +
304B PHE* 3.3 33.3 - - + -
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Residues in contact with LEU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 4.3 7.2 - - + -
39B LYS* 4.0 32.1 - - + +
40B LEU* 3.5 27.1 - - + -
43B GLN* 3.3 28.4 - - - +
297B VAL* 2.9 28.9 + - + +
298B ALA* 4.0 6.3 - - - +
299B ILE 3.4 0.2 - - - -
300B THR* 1.3 72.2 - - - +
302B ALA* 1.3 63.3 + - - +
304B PHE 3.2 7.6 + - - +
306B LEU* 2.9 50.3 + - + +
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Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B LEU* 4.0 11.0 - - + -
261B THR* 3.0 42.0 - - - +
262B GLU* 4.0 10.2 - - + +
265B TYR* 3.4 9.4 - - - +
298B ALA 3.2 14.8 + - - +
299B ILE 3.4 6.3 - - - +
300B THR 3.2 0.2 - - - -
301B LEU* 1.3 77.9 - - - +
303B CYS* 1.3 59.7 + - - +
304B PHE 3.3 0.2 + - - -
305B GLY* 3.5 4.9 + - - -
306B LEU* 3.6 19.6 - - - +
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Residues in contact with CYS 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B LEU* 3.9 14.4 - - - -
261B THR* 3.5 29.6 - - - -
264B ILE* 5.8 0.9 - - - -
265B TYR* 3.1 23.9 - - - +
270B LEU* 3.7 25.9 - - + +
273B LEU* 3.8 24.9 - - + -
299B ILE* 3.1 23.8 - - - -
300B THR 3.2 9.8 + - - +
302B ALA* 1.3 78.5 - - - +
304B PHE* 1.3 63.1 + - + +
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Residues in contact with PHE 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ARG* 5.2 7.0 - - + -
8B ILE* 3.9 35.0 - - + -
40B LEU* 3.5 20.2 - - + -
43B GLN* 3.3 24.4 - - + +
44B GLU* 4.7 7.3 - - - +
45B CYS* 4.7 11.7 - - + -
93B ILE* 4.0 35.9 - - + -
95B LEU* 4.0 25.6 - - + -
265B TYR* 3.8 11.2 - + - -
270B LEU* 4.2 9.0 - - + -
273B LEU* 4.1 13.5 - - + -
300B THR* 3.3 29.3 + - + -
301B LEU 3.2 6.6 + - - +
302B ALA 3.2 0.8 - - - -
303B CYS* 1.3 81.0 - - + +
305B GLY* 1.3 55.9 + - - +
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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
------------------------------------------------------------
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