Contacts of the helix formed by residues 273 - 290 (chain B) in PDB entry 3NBV
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 273 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B LEU* 4.0 1.3 - - - -
272B ARG* 1.3 75.5 - - - +
274B VAL* 1.3 65.9 + - - +
275B GLN* 3.6 8.1 + - - +
276B GLU* 2.7 43.0 + - - +
277B ALA* 2.9 21.7 + - - +
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Residues in contact with VAL 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B VAL* 4.2 30.7 - - + -
222B VAL* 5.7 1.1 - - + -
232B ALA* 3.8 23.8 - - + -
240B LEU* 3.6 24.2 - - + -
264B VAL* 6.6 0.7 - - + -
268B LEU* 3.9 21.9 - - + +
273B SER* 1.3 73.4 - - - +
275B GLN* 1.3 57.0 + - - +
277B ALA* 3.3 2.6 + - + +
278B LEU* 3.0 28.7 + - + +
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Residues in contact with GLN 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B LEU* 3.9 36.4 - - + +
241B HIS 3.4 28.6 + - - +
242B SER* 4.7 7.3 - - - -
273B SER* 3.1 8.7 + - - +
274B VAL* 1.3 75.2 - - - +
276B GLU* 1.3 67.4 + - + +
278B LEU* 3.6 5.7 + - - +
279B ARG* 3.3 20.8 + - - +
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Residues in contact with GLU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B SER* 4.2 2.0 - - - -
272B ARG* 2.9 51.3 + - + +
273B SER* 2.7 46.7 + - - +
275B GLN* 1.3 78.7 - - + +
277B ALA* 1.3 57.7 + - - +
279B ARG* 3.2 8.6 + - - +
280B PHE* 2.9 29.7 + - - +
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Residues in contact with ALA 277 (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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264B VAL* 3.6 23.7 - - + +
267B SER* 3.4 28.9 + - - +
268B LEU* 3.8 23.6 - - + -
273B SER 2.9 16.2 + - - +
274B VAL* 3.6 4.7 - - + +
276B GLU* 1.3 74.9 - - - +
278B LEU* 1.3 56.0 + - - +
280B PHE* 3.7 1.3 - - - +
281B GLY 2.8 29.3 + - - -
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Residues in contact with LEU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B VAL* 4.3 6.5 - - + -
230B ALA* 3.7 44.2 - - + +
231B ASP 3.9 12.3 - - - +
232B ALA* 3.8 13.2 - - + +
240B LEU* 3.7 34.3 - - + +
241B HIS* 3.8 9.0 - - - +
242B SER* 4.1 5.6 - - - -
260B PHE* 3.8 12.4 - - + -
264B VAL* 4.5 6.4 - - + +
274B VAL* 3.0 17.6 + - + +
275B GLN* 3.8 7.6 - - - +
277B ALA* 1.3 72.0 - - - +
279B ARG* 1.3 66.5 + - - +
281B GLY* 3.3 1.0 + - - -
282B CYS* 2.9 28.8 + - - +
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Residues in contact with ARG 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B SER* 3.7 15.7 + - - +
245B PHE* 3.9 27.6 - - + -
275B GLN* 3.3 15.1 + - - +
276B GLU* 3.2 12.0 + - - +
278B LEU* 1.3 79.8 - - - +
280B PHE* 1.3 57.6 + - - +
282B CYS* 3.1 5.0 + - - +
283B GLN* 2.9 54.5 + - - +
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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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53B LEU* 4.0 17.5 - - + -
263B SER* 3.7 26.2 - - - -
266B PHE* 4.2 22.2 - + - -
267B SER* 4.1 14.1 - - - +
276B GLU 2.9 16.3 + - - +
277B ALA 3.8 3.1 - - - +
279B ARG* 1.3 75.0 - - - +
281B GLY* 1.3 63.2 + - - +
283B GLN* 3.2 21.6 + - - +
284B VAL* 2.9 48.6 + - + +
298B VAL* 6.1 0.4 - - - -
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Residues in contact with GLY 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B PHE* 3.5 20.6 - - - -
263B SER* 3.7 19.3 - - - -
264B VAL* 4.2 3.1 - - - -
277B ALA 2.8 20.5 + - - -
278B LEU 3.7 1.6 - - - -
280B PHE* 1.3 73.8 - - - +
282B CYS* 1.3 57.7 + - - +
284B VAL* 3.5 0.9 + - - +
285B ALA* 3.0 32.6 + - - +
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Residues in contact with CYS 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B GLY* 4.0 1.8 - - - -
230B ALA* 3.9 35.4 - - - -
242B SER* 3.7 9.2 - - - +
243B ASP 3.5 26.2 - - - +
244B ALA* 4.5 0.9 - - - -
245B PHE* 3.6 11.8 + - + +
260B PHE* 4.0 2.5 - - - -
278B LEU 2.9 19.0 + - - +
279B ARG 3.1 3.8 + - - +
281B GLY* 1.3 73.5 - - - +
283B GLN* 1.3 61.0 + - - +
286B GLY* 2.9 26.3 + - - -
299B ANP 3.6 22.2 + - - +
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Residues in contact with GLN 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B PHE* 3.5 37.0 - - + +
279B ARG* 2.9 43.1 + - - +
280B PHE* 3.2 32.2 + - - +
282B CYS* 1.3 76.4 - - - +
284B VAL* 1.3 65.1 + - + +
286B GLY* 4.0 0.3 - - - -
287B LYS* 3.1 23.9 + - - +
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Residues in contact with VAL 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B VAL* 4.8 2.5 - - + -
53B LEU* 4.6 9.0 - - + -
259B THR* 3.6 15.9 - - + -
263B SER* 3.3 27.1 - - - +
280B PHE* 2.9 47.8 + - + +
283B GLN* 1.3 78.6 - - + +
285B ALA* 1.3 57.8 + - - +
287B LYS* 3.4 6.2 + - - +
288B LYS* 2.9 25.8 + - - +
297B ILE* 4.4 28.7 - - + +
298B VAL* 5.7 2.2 - - - +
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Residues in contact with ALA 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B ALA* 3.7 19.1 - - - +
259B THR* 4.0 9.6 - - - +
260B PHE* 4.0 10.1 - - + +
281B GLY 3.0 19.1 + - - +
284B VAL* 1.3 77.7 - - - +
286B GLY* 1.3 57.0 + - - +
288B LYS* 3.3 4.5 + - - +
289B CYS* 3.0 32.1 + - - -
299B ANP 3.4 29.6 - - - +
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Residues in contact with GLY 286 (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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245B PHE 3.4 23.6 - - - -
247B PRO* 3.6 14.2 - - - +
282B CYS 2.9 17.4 + - - -
283B GLN 4.0 0.2 - - - -
285B ALA* 1.3 74.5 - - - +
287B LYS* 1.3 66.1 + - - +
289B CYS* 3.1 16.5 + - - +
299B ANP 4.0 17.0 - - - -
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Residues in contact with LYS 287 (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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245B PHE* 4.3 1.2 + - - +
247B PRO* 4.8 4.7 - - - +
283B GLN 3.1 13.2 + - - +
284B VAL* 3.5 11.2 - - - +
286B GLY* 1.3 74.2 - - - +
288B LYS* 1.3 61.8 + - - +
290B GLY* 3.1 12.8 + - - -
291B LEU* 3.7 19.1 - - + +
296B GLY 3.0 24.8 + - - -
297B ILE* 3.6 16.9 + - - +
298B VAL* 3.3 25.5 - - - +
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Residues in contact with LYS 288 (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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252B ASP* 2.9 31.9 + - - +
254B LEU 3.1 27.4 - - - -
256B ALA* 4.2 15.5 - - + -
259B THR* 3.8 24.5 - - + +
284B VAL 2.9 14.5 + - - +
285B ALA 3.5 8.3 - - - +
286B GLY 3.2 0.6 - - - -
287B LYS* 1.3 77.3 - - - +
289B CYS* 1.3 64.2 + - - +
291B LEU* 3.1 18.3 + - - +
293B GLY* 2.9 31.5 + - - +
294B PHE* 4.1 11.9 - - + -
297B ILE* 3.7 23.1 - - + +
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Residues in contact with CYS 289 (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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247B PRO* 4.0 12.3 - - + -
250B VAL* 3.7 4.4 - - + +
251B VAL 2.8 22.5 + - - -
252B ASP 3.0 15.7 + - - -
253B THR* 3.5 27.1 - - + -
256B ALA* 3.7 15.9 - - - -
285B ALA 3.0 18.0 + - - -
286B GLY* 3.1 12.4 + - - +
288B LYS* 1.3 78.9 - - - +
290B GLY* 1.3 54.7 + - - +
299B ANP 3.6 30.5 - - + +
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Residues in contact with GLY 290 (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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247B PRO* 3.6 10.0 - - - +
248B PRO* 5.9 0.4 - - - -
249B ARG 3.4 20.1 - - - +
251B VAL* 3.6 17.4 - - - +
286B GLY 3.6 3.4 + - - -
287B LYS 3.1 8.6 + - - -
288B LYS 3.1 1.2 - - - -
289B CYS* 1.3 77.6 - - - +
291B LEU* 1.3 69.4 + - - +
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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