Contacts of the helix formed by residues 266 - 285 (chain B) in PDB entry 1WVV
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 ASN 266 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A LEU* 4.2 21.2 - - - +
512A CL 3.3 26.1 - - - +
260B LEU* 3.6 9.2 + - + +
261B GLU* 3.1 22.6 + - + +
265B GLY* 1.3 80.1 + - - +
267B PRO* 1.3 66.8 - - - +
268B ALA* 3.7 8.1 + - - +
269B GLN* 3.1 34.6 + - - +
270B VAL* 3.1 14.9 + - - +
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Residues in contact with PRO 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A GLU* 3.9 7.5 - - - +
158A ASN* 6.3 1.1 - - - +
161A ASN* 3.2 41.7 - - + +
164A HIS* 4.0 17.7 - - + +
165A TYR* 3.4 13.5 - - - +
261B GLU 5.2 0.2 - - - +
264B GLY* 3.6 15.0 - - - +
265B GLY 4.0 1.1 - - - +
266B ASN* 1.3 87.1 - - - +
268B ALA* 1.3 61.6 + - - +
270B VAL* 3.4 9.7 + - + +
271B GLN* 3.1 23.7 + - - +
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Residues in contact with ALA 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A TYR* 5.1 0.8 + - - -
257A ASN* 4.1 24.9 - - - +
260A LEU* 5.6 2.7 - - + -
266B ASN* 3.2 8.4 + - - +
267B PRO* 1.3 79.6 - - - +
269B GLN* 1.3 61.3 + - - +
271B GLN* 3.4 5.9 + - - +
272B SER* 2.8 28.2 + - - -
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Residues in contact with GLN 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A HIS* 5.6 0.6 + - - -
257A ASN* 4.0 11.3 - - - +
261A GLU* 3.8 20.8 + - - -
266A ASN* 3.7 13.6 - - - +
269A GLN* 3.0 18.5 + - - +
512A CL 3.7 12.2 - - + +
146B HIS* 2.9 32.9 + - + +
261B GLU* 3.8 22.4 - - - +
266B ASN* 3.1 33.8 + - - +
268B ALA* 1.3 78.2 + - - +
270B VAL* 1.3 61.5 + - - +
272B SER* 3.8 1.6 - - - -
273B ARG* 2.9 35.5 + - - +
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ASN* 4.9 7.0 - - + +
253B ILE* 4.0 20.1 - - + +
261B GLU* 3.5 38.6 - - + +
266B ASN 3.1 9.8 + - - +
267B PRO* 3.6 11.0 - - + +
269B GLN* 1.3 77.9 - - - +
271B GLN* 1.3 62.7 + - - +
273B ARG* 3.3 2.6 + - - +
274B ILE* 3.1 29.9 + - + +
293B SER* 4.0 24.9 - - - -
294B CYS* 4.1 21.1 - - - +
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Residues in contact with GLN 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A GLN 4.4 8.2 + - - +
153A TYR* 3.7 24.5 - - - +
156A GLU* 3.7 17.9 - - + +
157A VAL* 2.9 41.0 + - - +
158A ASN 4.6 0.9 + - - -
188A GLN* 5.1 6.9 + - + +
267B PRO 3.1 16.3 + - - +
268B ALA* 3.8 5.8 - - - +
270B VAL* 1.3 77.1 - - - +
272B SER* 1.3 58.2 + - - +
274B ILE* 3.2 9.9 + - - +
275B ASN* 2.8 63.1 + - - +
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Residues in contact with SER 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A HIS* 3.8 15.4 + - - -
269A GLN* 2.6 34.9 + - - -
146B HIS* 4.2 2.9 + - - -
268B ALA 2.8 18.8 + - - -
269B GLN* 3.8 7.9 - - - -
270B VAL 3.3 0.2 - - - -
271B GLN* 1.3 74.1 - - - +
273B ARG* 1.3 65.0 + - - +
275B ASN* 3.2 14.7 + - - +
276B LYS* 3.0 24.4 + - - +
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Residues in contact with ARG 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ALA* 4.7 2.7 - - - +
143B ASN* 2.9 41.9 + - - +
146B HIS* 3.4 45.4 + - + +
147B GLN* 4.8 5.3 + - - -
249B PHE* 3.8 16.9 - - + -
253B ILE* 3.7 23.8 - - + +
256B ILE* 4.1 19.6 - - - +
257B ASN* 3.9 14.8 - - - +
261B GLU* 2.8 42.0 + - - -
269B GLN 2.9 20.9 + - - +
270B VAL 3.6 4.0 - - - +
272B SER* 1.3 71.8 - - - +
274B ILE* 1.3 58.0 + - - +
276B LYS* 3.3 4.9 + - - +
277B PHE* 2.9 30.7 + - - +
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Residues in contact with ILE 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A TYR* 3.5 27.8 - - + +
157A VAL* 4.1 19.7 - - + -
158A ASN 5.5 0.4 - - - +
249B PHE* 4.1 11.7 - - + -
253B ILE* 4.5 0.9 - - + -
270B VAL* 3.1 19.5 + - + +
271B GLN* 3.4 11.2 - - - +
273B ARG* 1.3 76.6 - - - +
275B ASN* 1.3 56.6 + - - +
277B PHE* 3.5 3.5 - - + +
278B THR* 2.7 39.4 + - - +
292B LEU* 3.5 52.7 - - + +
293B SER* 4.0 15.3 - - - -
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Residues in contact with ASN 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A HIS 3.1 25.3 + - - +
147A GLN 3.2 16.4 + - - -
148A THR* 3.7 1.2 - - - -
149A GLY* 3.3 22.5 + - - +
153A TYR* 3.3 16.4 - - - -
271B GLN* 2.8 46.6 + - - +
272B SER* 3.3 16.1 - - - +
273B ARG 3.2 0.2 - - - -
274B ILE* 1.3 73.1 - - - +
276B LYS* 1.3 57.1 + - - +
278B THR* 3.3 3.3 + - - -
279B GLN* 3.0 34.3 + - - +
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Residues in contact with LYS 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A SER* 5.4 8.9 + - - -
276A LYS* 5.8 4.6 - - - +
101B MET 5.0 4.0 + - - -
142B ALA* 3.9 28.7 - - + +
145B SER* 3.8 16.6 + - - +
146B HIS* 5.1 4.0 - - + +
272B SER* 3.0 16.5 + - - +
273B ARG* 3.9 4.7 - - - +
275B ASN* 1.3 74.0 - - - +
277B PHE* 1.3 66.0 + - - +
279B GLN* 3.1 33.4 + - - +
280B PHE* 2.9 56.3 + - + -
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Residues in contact with PHE 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ARG* 3.6 20.9 - - + -
138B ALA 3.9 1.6 - - - -
139B ALA* 3.7 38.6 - - + -
142B ALA* 3.5 10.4 - - + +
243B ILE* 5.2 0.9 - - + -
249B PHE* 3.5 44.6 - + + -
273B ARG 2.9 18.2 + - - +
274B ILE* 3.5 6.5 - - - +
276B LYS* 1.3 75.8 - - - +
278B THR* 1.3 59.5 + - - +
280B PHE* 3.2 2.8 + - - +
281B THR* 2.8 43.9 + - + -
288B THR* 3.3 43.3 - - + -
292B LEU* 4.0 4.9 - - + -
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Residues in contact with THR 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A PHE* 3.6 51.4 - - + -
153A TYR* 2.6 25.8 + - - +
274B ILE* 2.7 21.1 + - - +
275B ASN 3.7 4.0 - - - -
277B PHE* 1.3 73.7 - - - +
279B GLN* 1.3 65.9 + - - +
280B PHE 3.1 1.1 - - - -
281B THR* 3.1 9.4 + - - +
282B GLN* 2.9 30.0 + - + +
288B THR* 3.6 18.9 - - + +
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Residues in contact with GLN 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ASN* 5.0 4.9 - - + +
145A SER* 4.2 1.4 + - - -
149A GLY* 3.7 19.9 - - - +
150A GLY* 3.6 17.6 - - - +
276A LYS* 4.8 8.3 - - - +
501A CL 3.6 24.6 - - - +
275B ASN* 3.0 15.3 + - - +
276B LYS* 3.1 43.2 + - + +
278B THR* 1.3 75.8 - - - +
280B PHE* 1.3 65.7 + - + +
282B GLN* 3.3 7.7 + - - +
283B ILE* 3.0 33.8 + - + +
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Residues in contact with PHE 280 (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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101B MET* 3.6 55.1 - - + +
102B PHE* 3.8 13.5 - + - -
138B ALA* 3.8 18.8 - - + +
141B LEU* 3.5 32.3 - - + -
142B ALA* 3.5 23.1 - - - -
145B SER* 4.1 3.8 - - - -
276B LYS* 2.9 40.4 + - + +
277B PHE 3.5 7.2 - - - +
279B GLN* 1.3 79.7 - - + +
281B THR* 1.3 64.3 + - - +
283B ILE* 3.2 10.7 + - + +
284B LEU* 3.0 27.9 + - - +
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Residues in contact with THR 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ARG* 4.6 1.6 - - + -
138B ALA* 3.8 7.4 - - + -
277B PHE* 2.8 48.9 + - + +
278B THR* 3.1 21.7 + - - +
280B PHE* 1.3 72.7 - - - +
282B GLN* 1.3 57.7 + - - +
284B LEU 3.3 0.7 + - - -
285B GLY 2.9 24.1 + - - -
286B THR* 2.9 46.8 + - + +
287B THR* 3.9 10.3 - - - +
288B THR* 3.6 10.1 - - - +
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Residues in contact with GLN 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ASN* 3.5 46.7 + - + +
152A PHE* 3.7 33.4 - - + -
278B THR* 2.9 26.8 + - + +
279B GLN* 3.4 8.1 - - - +
281B THR* 1.3 77.5 + - - +
283B ILE* 1.3 62.3 + - - +
285B GLY* 3.2 13.1 + - - +
286B THR 4.8 7.0 - - - +
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Residues in contact with ILE 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ASN* 5.3 5.6 - - - +
97B GLN* 3.5 35.9 + - + +
100B GLN* 3.5 33.3 - - + +
101B MET* 3.8 38.1 - - + +
279B GLN* 3.0 20.9 + - + +
280B PHE* 3.2 16.1 + - + +
282B GLN* 1.3 77.5 - - - +
284B LEU* 1.3 61.7 + - + +
285B GLY 3.5 0.3 + - - -
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Residues in contact with LEU 284 (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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92B VAL 4.1 3.8 - - - +
93B VAL* 4.0 20.0 - - + -
97B GLN* 3.5 39.1 + - + +
101B MET* 3.5 28.5 - - + -
134B LYS* 3.2 62.0 + - + +
138B ALA* 4.0 14.8 - - + +
280B PHE 3.0 16.3 + - - +
281B THR 4.1 3.1 - - - +
283B ILE* 1.3 76.4 - - - +
285B GLY* 1.3 61.1 + - - +
286B THR* 4.5 1.8 - - + -
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Residues in contact with GLY 285 (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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134B LYS* 4.8 6.1 + - - +
281B THR 2.9 5.6 + - - -
282B GLN* 3.2 11.3 + - - -
283B ILE 3.3 0.6 - - - -
284B LEU* 1.3 80.0 - - - +
286B THR* 1.3 60.3 + - - +
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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