Contacts of the helix formed by residues 267 - 280 (chain B) in PDB entry 3V6R
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 ASP 267 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B GLY 3.2 3.0 - - - -
266B ARG* 1.4 83.2 - - - +
268B TYR* 1.4 60.1 + - - +
269B ILE* 3.2 15.6 + - + +
270B ASP* 3.0 35.4 + - - +
271B GLN* 2.9 30.5 + - - +
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Residues in contact with TYR 268 (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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227B ARG* 3.4 54.6 + - + +
230B ARG* 3.5 18.8 + - + -
234B VAL* 5.1 2.1 - - - +
235B ILE* 3.6 57.7 - - + +
267B ASP* 1.4 71.7 - - - +
269B ILE* 1.3 60.4 + - + +
271B GLN* 3.3 14.6 - - - +
272B TRP* 2.7 36.7 + - - +
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Residues in contact with ILE 269 (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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267B ASP* 3.2 12.4 + - + +
268B TYR* 1.3 79.4 - - + +
270B ASP* 1.3 62.5 + - - +
272B TRP* 3.6 6.2 + - + +
273B ASN* 3.4 28.3 + - - +
297B TYR* 3.4 47.9 + - + +
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Residues in contact with ASP 270 (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 PRO 4.4 0.2 - - - -
265B GLY* 3.4 6.1 - - - -
266B ARG* 3.2 27.2 + - + +
267B ASP* 3.0 20.5 + - - +
269B ILE* 1.3 75.0 - - + +
271B GLN* 1.3 62.4 + - - +
273B ASN* 3.3 15.4 + - - +
274B LYS* 2.8 51.1 + - - +
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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
----------------------------------------------------------
227B ARG* 2.8 35.6 + - - +
228B TYR* 3.6 24.2 + - - +
230B ARG 4.4 2.0 + - - -
235B ILE* 3.5 25.4 - - + +
263B PHE* 3.4 23.0 - - + +
264B PRO 3.9 11.4 + - - +
265B GLY 5.2 1.7 - - - +
267B ASP 2.9 14.7 + - - +
268B TYR* 3.3 23.6 - - - +
270B ASP* 1.3 73.2 - - - +
272B TRP* 1.4 64.0 + - - +
274B LYS* 3.1 14.9 + - - +
275B VAL* 3.2 17.1 + - + +
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Residues in contact with TRP 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B PRO* 3.8 27.1 - - + -
235B ILE* 5.5 11.8 - - + +
236B LEU* 3.9 26.9 - - + -
268B TYR 2.7 19.4 + - - +
269B ILE* 3.9 7.2 - - + +
270B ASP 3.4 0.2 - - - -
271B GLN* 1.4 69.3 - - - +
273B ASN* 1.4 65.0 + - - +
275B VAL* 3.2 24.6 + - + +
276B ILE* 3.0 52.3 + - + +
282B PRO* 4.0 15.9 - - + -
286B PHE* 4.5 0.9 - + - -
297B TYR* 4.8 7.6 - + + -
298B VAL* 4.1 33.3 - - + +
301B ARG* 4.5 17.0 - - + +
342B ILE* 3.8 26.7 - - + -
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Residues in contact with ASN 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B ILE* 3.4 19.2 + - - +
270B ASP* 3.3 19.5 + - - +
271B GLN 3.2 0.4 - - - -
272B TRP* 1.4 77.5 - - - +
274B LYS* 1.4 52.4 + - + +
276B ILE* 3.2 11.3 + - + +
277B GLU* 2.8 57.3 + - - +
297B TYR* 4.2 4.6 + - - -
301B ARG* 3.6 36.9 + - - +
304B TYR* 5.9 0.6 - - - -
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Residues in contact with LYS 274 (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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263B PHE* 3.7 15.9 - - - -
264B PRO* 3.3 43.7 - - + +
265B GLY* 4.7 0.8 - - - -
270B ASP* 2.8 45.9 + - - +
271B GLN 3.1 10.4 + - - +
273B ASN* 1.4 77.7 - - + +
275B VAL* 1.3 60.6 + - - +
277B GLU* 3.9 12.6 - - - +
278B GLN* 2.8 40.2 + - - +
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Residues in contact with VAL 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B PRO* 5.0 1.3 - - + -
235B ILE* 5.7 6.1 - - + -
247B TRP* 3.9 19.5 - - + -
263B PHE* 3.7 30.5 - - + -
271B GLN* 3.4 18.8 - - + +
272B TRP* 3.2 25.2 + - + +
274B LYS* 1.3 76.7 - - - +
276B ILE* 1.3 58.8 + - - +
278B GLN 3.5 0.5 + - - -
279B LEU* 2.8 34.7 + - + +
342B ILE* 3.7 31.6 - - + -
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Residues in contact with ILE 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B TRP* 3.0 50.7 + - + +
273B ASN* 3.3 24.5 - - - +
275B VAL* 1.3 73.2 - - - +
277B GLU* 1.3 61.7 + - - +
280B GLY* 2.9 44.5 + - - +
281B THR* 4.3 6.3 - - + +
282B PRO* 4.1 8.7 - - + -
301B ARG* 4.0 32.5 - - + +
302B PRO* 4.2 1.8 - - + +
304B TYR* 3.2 37.2 - - + +
342B ILE* 4.6 0.9 - - + -
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Residues in contact with GLU 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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273B ASN* 2.8 45.8 + - - +
274B LYS* 3.9 15.7 + - - +
275B VAL 3.4 0.2 - - - -
276B ILE* 1.3 72.3 - - - +
278B GLN* 1.3 62.6 + - + +
304B TYR* 3.5 45.9 + - + -
306B GLY* 4.1 7.8 + - - -
307B LEU* 4.0 14.4 - - - +
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Residues in contact with GLN 278 (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 ARG* 3.2 25.8 + - - +
262B LEU* 2.9 25.5 + - - +
263B PHE* 3.6 13.9 - - + -
274B LYS* 2.8 31.9 + - - +
275B VAL 3.5 2.1 + - - +
276B ILE 3.2 0.2 - - - -
277B GLU* 1.3 81.5 - - + +
279B LEU* 1.3 62.1 + - + +
280B GLY 3.5 0.7 - - - -
307B LEU* 2.8 48.8 + - + +
312B LEU* 3.5 27.0 - - + +
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Residues in contact with LEU 279 (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 TRP* 3.6 33.0 - - + -
263B PHE* 3.7 22.2 - - + -
275B VAL* 2.8 21.9 + - + +
278B GLN* 1.3 74.9 - - + +
280B GLY* 1.3 63.6 + - - +
305B ALA 4.0 5.7 - - - +
306B GLY* 3.7 3.9 - - - -
307B LEU 4.8 1.9 - - - +
309B PHE* 3.8 32.9 - - + -
312B LEU* 3.8 17.0 - - + -
340B LEU* 4.0 20.6 - - + +
342B ILE* 4.3 10.8 - - + +
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Residues in contact with GLY 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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276B ILE* 2.9 23.7 + - - -
279B LEU* 1.3 82.3 - - - +
281B THR* 1.3 64.4 - - - -
304B TYR 3.4 11.7 - - - -
305B ALA 3.6 10.5 - - - -
306B GLY* 3.4 4.4 - - - -
342B ILE* 3.4 20.6 - - - +
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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