Contacts of the helix formed by residues 285 - 304 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283A GLY 4.6 0.7 - - - -
284A LYS* 1.3 96.8 - - + +
286A PRO* 1.3 70.4 - - + +
287A GLU* 3.1 27.6 + - - +
288A GLU* 2.9 30.6 + - + +
289A VAL* 3.3 12.3 + - - +
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Residues in contact with PRO 286 (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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285A THR* 1.3 90.0 - - + +
287A GLU* 1.3 56.9 + - - +
289A VAL* 3.6 11.9 + - + +
290A THR* 3.1 27.0 + - - -
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Residues in contact with GLU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A THR* 3.1 17.8 + - - +
286A PRO* 1.3 77.3 - - - +
288A GLU* 1.3 77.4 + - - +
289A VAL 3.1 1.6 - - - -
290A THR* 3.6 8.7 - - - -
291A ARG* 2.8 71.0 + - - +
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Residues in contact with GLU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PRO* 3.5 30.4 - - + +
243A ALA* 4.0 0.9 - - - +
282A LEU 4.7 0.9 - - - +
283A GLY* 3.6 6.5 - - - -
284A LYS* 2.6 55.5 + - + +
285A THR* 2.9 24.5 + - + +
287A GLU* 1.3 100.9 + - - +
289A VAL* 1.3 60.0 + - - +
291A ARG* 4.4 9.6 + - - +
292A THR* 2.8 29.6 + - - -
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Residues in contact with VAL 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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30A VAL* 4.8 5.2 - - + -
243A ALA* 4.4 6.7 - - + -
280A PRO* 3.2 50.7 - - + +
283A GLY* 4.0 9.9 - - - +
285A THR 3.5 14.1 - - - +
286A PRO* 3.6 11.4 - - + +
287A GLU 3.1 0.2 - - - -
288A GLU* 1.3 76.5 - - - +
290A THR* 1.3 61.8 + - - +
292A THR* 3.4 1.9 + - - -
293A VAL* 3.0 42.8 + - + +
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Residues in contact with THR 290 (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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286A PRO 3.1 15.8 + - - -
287A GLU* 3.3 8.9 + - + -
289A VAL* 1.3 78.1 - - - +
291A ARG* 1.3 59.9 + - - +
293A VAL* 4.6 4.3 - - - -
294A ASN* 3.0 50.5 + - - +
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Residues in contact with ARG 291 (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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238A PRO 4.1 0.6 + - - -
239A SER* 2.9 41.0 + - - +
240A PHE* 3.4 16.1 - - + +
242A PRO* 3.9 17.2 - - + +
287A GLU* 2.8 52.1 + - - +
288A GLU* 3.9 12.0 + - - +
290A THR* 1.3 79.1 - - - +
292A THR* 1.3 58.5 - - - +
294A ASN* 4.3 3.2 - - - +
295A THR* 2.7 37.2 + - - +
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Residues in contact with THR 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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233A VAL* 4.1 8.0 - - + +
240A PHE 3.8 8.1 - - - -
241A THR* 3.8 20.8 - - - +
242A PRO* 3.0 9.0 - - - +
243A ALA* 2.8 44.3 + - + +
278A VAL* 4.0 14.1 - - + -
288A GLU 2.8 21.9 + - - -
289A VAL 3.8 2.5 - - - -
291A ARG* 1.3 80.1 - - - +
293A VAL* 1.3 61.2 + - - +
295A THR* 3.9 2.6 - - - -
296A ALA* 3.2 21.0 + - - +
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Residues in contact with VAL 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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30A VAL* 3.2 37.7 - - + +
31A LEU* 4.4 10.5 - - + -
34A ALA* 3.6 29.6 - - + -
243A ALA* 6.4 0.2 - - + -
278A VAL* 4.4 17.3 - - + -
280A PRO* 5.3 1.3 - - + -
289A VAL* 3.0 27.8 + - + +
290A THR* 4.1 4.7 - - - +
292A THR* 1.3 75.9 - - - +
294A ASN* 1.3 64.6 + - - +
296A ALA* 3.1 7.8 + - - +
297A VAL* 2.9 26.0 + - - +
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Residues in contact with ASN 294 (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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34A ALA* 4.7 7.4 - - - +
39A LYS* 5.7 4.0 + - - -
254A TYR* 4.8 1.5 + - - -
290A THR* 3.0 38.9 + - - +
291A ARG* 4.3 3.3 - - - +
293A VAL* 1.3 79.8 - - - +
295A THR* 1.3 61.1 + - - +
297A VAL* 3.7 6.9 - - - +
298A ALA* 2.8 31.0 + - - +
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Residues in contact with THR 295 (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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236A LEU* 3.8 26.5 - - + -
240A PHE* 3.3 14.6 + - + +
241A THR* 3.9 10.8 - - + -
254A TYR* 3.5 39.8 - - + +
291A ARG* 2.7 25.5 + - - +
292A THR 3.9 3.4 - - - -
294A ASN* 1.3 78.5 - - - +
296A ALA* 1.3 57.2 + - - +
298A ALA* 3.8 1.5 - - - +
299A ILE* 3.0 36.9 + - + +
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Residues in contact with ALA 296 (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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31A LEU* 4.0 17.9 - - + -
233A VAL* 4.5 7.9 - - + -
241A THR* 5.5 0.2 - - - +
275A ILE* 4.3 10.7 - - + +
278A VAL* 4.3 16.2 - - + -
292A THR 3.2 14.8 + - - +
293A VAL* 3.1 10.7 + - - +
294A ASN 3.1 0.4 - - - -
295A THR* 1.3 77.0 - - - +
297A VAL* 1.3 58.0 - - - +
299A ILE* 3.4 8.5 - - - +
300A THR* 2.9 31.4 + - - -
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Residues in contact with VAL 297 (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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31A LEU* 4.2 17.0 - - + +
34A ALA* 4.0 24.5 - - + -
36A LEU* 3.9 25.1 - - + -
39A LYS* 4.1 22.9 - - + +
293A VAL 2.9 19.5 + - - +
294A ASN* 3.3 7.4 + - - +
296A ALA* 1.3 75.5 - - - +
298A ALA* 1.3 66.1 + - - +
300A THR* 3.2 6.7 + - - -
301A LEU* 2.9 38.8 + - + +
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Residues in contact with ALA 298 (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* 3.4 26.2 - - + +
258A LEU* 3.7 17.5 - - + +
294A ASN 2.8 18.8 + - - +
295A THR* 3.8 5.6 - - - +
297A VAL* 1.3 77.2 - - - +
299A ILE* 1.3 61.6 + - - +
301A LEU* 3.4 10.5 + - - +
302A ALA* 3.2 17.5 + - - +
306A LEU* 5.1 3.7 - - - +
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Residues in contact with ILE 299 (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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231A PHE* 3.7 37.2 - - + -
236A LEU* 4.6 4.0 - - + -
254A TYR 5.5 0.4 - - - +
257A GLY* 3.4 37.0 - - - +
258A LEU* 4.2 9.2 - - + +
261A THR* 3.9 14.3 - - + +
275A ILE* 4.2 17.0 - - + -
295A THR* 3.0 34.0 + - + +
296A ALA* 3.4 8.7 - - - +
297A VAL 3.1 0.2 - - - -
298A ALA* 1.3 73.4 - - - +
300A THR* 1.3 68.4 + - - +
302A ALA* 3.2 13.5 + - - +
303A CYS* 3.4 14.4 + - - -
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Residues in contact with THR 300 (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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31A LEU* 5.9 1.2 - - - +
36A LEU* 4.0 24.9 - - + +
40A LEU* 4.7 1.8 - - + -
95A LEU* 4.0 19.1 - - + -
97A LEU* 5.2 0.5 - - - +
273A LEU* 4.2 8.1 - - + -
275A ILE* 3.4 21.1 - - - +
296A ALA 2.9 18.8 + - - -
297A VAL* 3.7 4.8 - - - -
299A ILE* 1.3 77.3 - - - +
301A LEU* 1.3 62.2 + - - +
303A CYS* 3.1 17.2 + - - +
304A PHE* 3.1 39.7 - - + -
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Residues in contact with LEU 301 (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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36A LEU* 4.4 6.5 - - + -
39A LYS* 3.9 28.5 - - + +
40A LEU* 3.5 29.4 - - + -
43A GLN* 3.1 29.6 - - - +
297A VAL* 2.9 37.4 + - + +
298A ALA* 3.7 6.7 - - - +
300A THR* 1.3 74.6 - - - +
302A ALA* 1.3 61.3 + - - +
304A PHE 3.1 5.4 + - - -
306A LEU* 3.0 50.3 + - + -
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Residues in contact with ALA 302 (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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258A LEU* 4.3 8.5 - - + -
261A THR* 3.3 27.3 - - - +
262A GLU* 3.8 17.6 - - + +
265A TYR* 3.2 18.2 - - - +
298A ALA 3.2 10.7 + - - +
299A ILE 3.2 5.6 + - - +
301A LEU* 1.3 72.2 - - - +
303A CYS* 1.3 64.6 + - - +
304A PHE 3.0 2.3 + - - -
305A GLY* 3.4 4.3 + - - -
306A LEU* 3.4 23.1 - - + +
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Residues in contact with CYS 303 (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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229A LEU* 4.1 12.3 - - - -
261A THR* 3.3 39.3 - - - -
264A ILE* 6.0 1.6 - - + -
265A TYR* 3.3 20.0 - - - +
270A LEU* 3.6 27.0 - - + +
273A LEU* 3.8 30.1 - - + -
299A ILE* 3.4 10.3 - - - -
300A THR* 3.1 12.0 + - - +
302A ALA* 1.3 78.5 - - - +
304A PHE* 1.3 61.3 - - + +
305A GLY 3.5 0.2 - - - -
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Residues in contact with PHE 304 (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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6A ARG* 5.2 2.2 - - + -
8A ILE* 3.3 37.0 - - + -
40A LEU* 3.5 18.4 - - + -
43A GLN* 3.5 25.2 - - + +
44A GLU* 5.1 4.9 - - - +
45A CYS* 4.6 19.9 - - + -
93A ILE* 3.9 36.6 - - + -
95A LEU* 3.9 24.9 - - + -
265A TYR* 3.8 11.6 + + - -
270A LEU* 3.9 13.9 - - + -
273A LEU* 4.1 11.7 - - + -
300A THR* 3.1 28.9 - - + -
301A LEU 3.1 6.0 + - - +
302A ALA 3.0 0.8 - - - -
303A CYS* 1.3 82.2 - - + +
305A GLY* 1.3 55.2 + - - +
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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