Contacts of the helix formed by residues 285 - 306 (chain B) in PDB entry 3VPM
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 SER 285 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B LYS 3.9 0.6 + - - -
284B PRO* 1.3 76.3 - - - +
286B GLU* 1.3 65.3 + - - +
287B GLU* 3.5 11.8 - - - +
288B ARG* 2.9 35.2 + - - +
289B VAL* 3.0 12.5 + - - +
337B PHE* 4.4 0.2 - - - -
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Residues in contact with GLU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B SER* 1.3 71.4 - - - +
287B GLU* 1.3 63.4 + - - +
289B VAL* 3.4 1.3 + - - +
290B ARG* 3.0 41.8 + - + +
332B MET* 4.6 0.9 - - - +
337B PHE* 3.4 46.3 - - + +
338B SER* 2.9 41.3 + - - +
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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 SER* 3.5 11.8 - - - +
286B GLU* 1.3 80.1 - - - +
288B ARG* 1.3 62.6 + - + +
290B ARG* 3.5 16.2 + - - +
291B GLU* 3.1 43.5 + - - +
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Residues in contact with ARG 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ARG* 4.7 5.5 - - - +
213B TRP* 3.4 28.3 - - - -
216B ASP* 5.6 1.2 + - - -
219B ALA* 5.8 0.6 - - - +
223B GLU* 2.7 31.5 + - + +
284B PRO* 4.3 11.4 - - + -
285B SER* 2.9 23.2 + - - +
287B GLU* 1.3 76.8 - - + +
289B VAL* 1.3 66.1 + - - +
291B GLU* 3.0 49.9 + - - +
292B ILE* 3.2 29.6 + - + +
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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
----------------------------------------------------------
226B VAL* 4.1 21.5 - - + -
277B PHE* 4.3 4.3 - - + -
284B PRO* 4.0 22.9 - - + -
285B SER 3.0 12.6 + - - +
286B GLU 3.8 5.8 - - - +
288B ARG* 1.3 72.4 - - - +
290B ARG* 1.3 67.2 + - - +
292B ILE* 2.9 14.4 + - + +
293B ILE* 2.9 23.6 + - + +
332B MET* 3.7 23.6 - - + -
335B LEU* 4.3 6.5 - - + -
337B PHE* 3.6 32.3 - - + -
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Residues in contact with ARG 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B GLU* 3.0 36.5 + - + +
287B GLU* 3.5 16.4 + - - +
289B VAL* 1.3 76.4 - - - +
291B GLU* 1.3 63.5 + - - +
293B ILE* 4.5 3.6 - - - +
294B ILE* 2.8 50.5 + - + +
332B MET* 3.8 12.8 - - + -
338B SER 5.6 0.2 - - - -
339B LYS 4.6 3.8 + - - -
340B VAL* 3.6 51.4 + - + +
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Residues in contact with GLU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B GLU* 3.1 32.0 + - - +
288B ARG* 3.0 44.0 + - - +
290B ARG* 1.3 77.0 - - - +
292B ILE* 1.3 59.5 + - - +
294B ILE* 4.1 5.6 - - - +
295B ASN* 3.1 25.1 + - - +
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Residues in contact with ILE 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B TRP* 3.6 29.5 - - + -
213B TRP* 3.8 28.5 - - + -
223B GLU* 4.1 21.5 - - + +
226B VAL* 4.5 15.0 - - + -
227B ALA* 4.3 11.0 - - - -
230B ALA* 5.0 1.6 - - + -
284B PRO* 6.4 0.2 - - + -
288B ARG* 3.4 41.5 - - + +
289B VAL* 2.9 10.8 + - + +
291B GLU* 1.3 69.4 - - - +
293B ILE* 1.3 61.3 + - - +
295B ASN* 3.3 7.2 + - - +
296B ALA* 2.9 27.4 + - - +
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Residues in contact with ILE 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B VAL* 4.0 19.5 - - + -
230B ALA* 4.1 11.0 - - + -
234B ILE* 3.8 9.9 - - + -
289B VAL* 2.9 26.1 + - + +
290B ARG* 3.9 2.9 - - - +
292B ILE* 1.3 69.4 - - - +
294B ILE* 1.3 62.1 + - + +
296B ALA* 3.0 5.7 + - - +
297B VAL* 2.8 29.3 + - + +
328B ALA* 3.6 30.3 - - + +
331B LEU* 3.9 26.2 - - + -
332B MET* 3.6 33.4 - - + -
335B LEU* 5.1 0.9 - - + -
340B VAL* 5.8 1.8 - - + -
341B PHE* 5.2 3.1 - - + -
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Residues in contact with ILE 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ARG* 2.8 48.9 + - + +
291B GLU* 4.1 3.6 - - - +
293B ILE* 1.3 71.0 - - + +
295B ASN* 1.3 64.2 + - - +
297B VAL* 3.0 9.2 + - - +
298B ARG* 2.9 48.1 + - + +
340B VAL* 3.9 32.5 - - + -
341B PHE* 4.0 10.1 - - + -
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Residues in contact with ASN 295 (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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209B TRP* 3.1 28.0 - - - +
213B TRP* 6.2 0.8 - - - -
291B GLU 3.1 22.1 + - - +
292B ILE* 3.4 7.3 - - - +
293B ILE 3.3 0.2 - - - -
294B ILE* 1.3 76.9 - - - +
296B ALA* 1.3 62.5 + - - +
298B ARG* 3.4 7.5 + - - +
299B ILE* 3.2 32.7 + - - +
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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
----------------------------------------------------------
209B TRP* 4.2 8.9 - - + -
230B ALA* 3.9 24.5 - - + -
234B ILE* 3.7 10.0 - - + +
235B PHE* 3.5 29.8 - - + -
292B ILE 2.9 14.2 + - - +
293B ILE* 3.5 7.6 - - - +
295B ASN* 1.3 73.0 - - - +
297B VAL* 1.3 65.5 + - - +
299B ILE* 3.4 1.2 + - - -
300B GLU* 3.0 22.2 + - - +
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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
----------------------------------------------------------
234B ILE* 4.1 14.1 - - + -
293B ILE 2.8 20.1 + - - +
294B ILE 3.0 8.0 + - - +
296B ALA* 1.3 71.6 - - - +
298B ARG* 1.3 61.2 + - - +
300B GLU* 3.1 2.9 + - - +
301B GLN* 2.8 60.5 + - - +
324B ILE* 3.8 13.7 - - + +
325B GLU* 4.0 13.9 - - + +
328B ALA* 3.4 32.1 - - + -
341B PHE* 4.1 15.0 - - + -
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Residues in contact with ARG 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ILE* 2.9 31.6 + - + +
295B ASN* 3.7 10.1 - - - +
297B VAL* 1.3 78.9 - - - +
299B ILE* 1.3 57.3 + - + +
301B GLN* 2.9 26.2 + - - +
302B GLU* 2.9 30.4 + - - +
325B GLU* 3.0 21.8 + - - -
341B PHE* 3.7 24.7 - - - -
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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
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205B LYS* 4.1 34.5 - - + +
206B LYS* 3.7 28.0 - - + +
209B TRP* 3.4 38.8 - - + +
235B PHE* 4.1 7.2 - - + -
295B ASN* 3.2 27.6 + - - +
296B ALA 3.8 4.0 - - - +
298B ARG* 1.3 75.4 - - + +
300B GLU* 1.3 60.1 + - - +
302B GLU* 3.2 8.9 + - - +
303B PHE* 2.8 28.8 + - + +
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Residues in contact with GLU 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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206B LYS* 2.5 32.2 + - - -
234B ILE* 3.4 24.2 - - + +
235B PHE* 3.2 13.9 - - + +
238B GLY* 3.0 30.1 + - - -
239B SER 4.1 1.4 + - - -
296B ALA 3.0 14.0 + - - +
297B VAL 3.5 7.0 - - - +
299B ILE* 1.3 77.0 - - - +
301B GLN* 1.3 57.8 + - - +
303B PHE* 2.9 8.4 + - - +
304B LEU* 2.9 42.8 + - + +
324B ILE* 3.8 21.3 - - + -
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Residues in contact with GLN 301 (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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297B VAL* 2.8 27.7 + - + +
298B ARG* 2.9 35.1 + - - +
300B GLU* 1.3 72.9 - - - +
302B GLU* 1.3 52.6 + - - +
304B LEU* 3.9 6.0 - - - +
305B THR* 2.7 40.8 + - - +
321B LYS* 2.7 61.3 + - + +
324B ILE* 4.2 7.8 - - + +
325B GLU* 3.2 25.7 + - - +
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Residues in contact with GLU 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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202B CYS 5.7 0.7 - - - +
205B LYS* 3.7 33.7 - - - +
298B ARG 2.9 19.7 + - - +
299B ILE* 3.6 7.8 - - - +
301B GLN* 1.3 70.0 - - - +
303B PHE* 1.3 65.6 + - - +
305B THR* 4.2 4.5 - - - -
306B GLU* 3.0 57.1 + - - +
307B ALA* 3.2 19.8 + - - +
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Residues in contact with PHE 303 (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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126B PHE* 6.4 0.2 - + - -
129B HIS 5.6 0.2 - - - -
130B VAL* 5.2 2.7 - - + -
133B PHE* 4.2 21.8 - + + -
202B CYS* 3.2 45.5 - - + +
203B VAL* 4.5 4.0 - - + -
206B LYS* 3.3 42.8 - - + -
239B SER* 4.0 14.6 - - - -
299B ILE* 2.8 13.6 + - + +
300B GLU* 2.9 10.1 + - - +
302B GLU* 1.3 84.0 + - - +
304B LEU* 1.3 74.6 + - + +
307B ALA* 4.1 3.8 - - - -
308B LEU* 3.0 53.9 + - + +
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Residues in contact with LEU 304 (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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126B PHE* 5.4 3.1 - - + -
238B GLY* 3.5 41.3 - - - -
239B SER* 4.3 2.2 - - - +
242B SER* 4.7 2.2 - - - +
300B GLU* 2.9 27.0 + - + +
301B GLN* 4.1 4.3 - - - +
302B GLU 3.2 0.2 - - - -
303B PHE* 1.3 93.7 - - + +
305B THR* 1.3 62.8 + - + +
308B LEU 4.0 3.8 - - - +
309B PRO* 3.2 3.0 - - - +
310B VAL* 3.0 51.1 + - + +
320B MET* 3.5 26.2 - - + -
324B ILE* 3.6 17.3 - - + -
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Residues in contact with THR 305 (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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301B GLN 2.7 22.8 + - - +
302B GLU* 4.2 2.9 - - - -
304B LEU* 1.3 82.5 - - + +
306B GLU* 1.3 71.8 + - - +
309B PRO* 3.6 18.4 - - - +
310B VAL* 5.6 0.4 - - + -
311B LYS* 4.8 4.7 + - - -
317B CYS* 3.7 37.3 - - + +
320B MET* 5.7 0.4 - - + -
321B LYS* 3.7 39.2 + - + +
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Residues in contact with GLU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B GLU* 3.0 40.8 + - - +
304B LEU 3.7 0.2 - - - -
305B THR* 1.3 89.7 + - - +
307B ALA* 1.3 65.3 + - - +
308B LEU 3.4 1.6 + - - -
309B PRO* 3.4 14.7 - - - +
321B LYS* 5.9 0.7 + - - -
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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