Contacts of the helix formed by residues 274 - 285 (chain B) in PDB entry 3GV5
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 GLY 274 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270B GLU* 3.0 17.3 + - - -
272B GLU 3.7 1.0 - - - -
273B LEU* 1.3 78.3 - - - +
275B ILE* 1.3 65.7 + - - -
276B SER 3.5 2.5 - - - -
277B VAL* 3.6 2.0 + - - -
278B ALA* 3.0 25.1 + - - +
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Residues in contact with ILE 275 (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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270B GLU* 3.8 23.6 + - + +
274B GLY* 1.3 70.7 - - - +
276B SER* 1.3 73.6 + - - +
279B GLN* 3.0 78.9 + - - +
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Residues in contact with SER 276 (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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274B GLY 3.5 0.4 - - - -
275B ILE* 1.3 87.1 - - - +
277B VAL* 1.3 68.9 + - - +
279B GLN* 4.4 3.3 - - - +
280B ARG* 3.0 29.6 + - - +
847T C 5.1 5.5 + - - -
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Residues in contact with VAL 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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246B THR* 5.6 5.4 - - + +
273B LEU* 3.8 38.4 - - + +
274B GLY 3.6 1.6 + - - -
275B ILE 3.4 0.2 - - - -
276B SER* 1.3 82.2 + - - +
278B ALA* 1.3 58.9 + - - +
280B ARG* 3.3 3.2 + - - +
281B ILE* 2.9 44.1 + - + +
847T C 5.8 3.8 - - - +
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Residues in contact with ALA 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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266B PRO 4.7 0.4 - - - +
269B LEU* 3.5 39.0 - - + +
270B GLU* 3.5 20.2 - - + +
273B LEU* 4.3 3.8 - - + +
274B GLY 3.0 19.1 + - - +
277B VAL* 1.3 77.2 - - - +
279B GLN* 1.3 62.8 + - - +
281B ILE* 3.8 4.5 - - - +
282B GLN* 3.0 29.8 + - - +
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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
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270B GLU* 3.0 31.5 + - - +
275B ILE* 3.0 41.1 + - - +
276B SER* 4.4 3.4 - - - +
278B ALA* 1.3 75.3 - - - +
280B ARG* 1.3 58.0 + - - +
282B GLN* 3.9 4.2 - - - +
283B LYS* 3.0 51.7 + - + +
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Residues in contact with ARG 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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240B PRO* 5.0 4.9 + - - +
276B SER 3.0 23.6 + - - +
277B VAL* 3.7 5.2 - - - +
279B GLN* 1.3 76.5 - - - +
281B ILE* 1.3 69.1 + - + +
283B LYS* 3.1 10.2 + - - +
284B LEU* 3.0 55.1 + - + +
288B GLU 5.1 0.2 + - - -
289B ASP* 2.4 40.8 + - - +
290B ASN* 4.5 4.8 - - - +
291B SER* 3.7 18.5 + - - +
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Residues in contact with ILE 281 (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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239B ILE* 4.5 2.1 - - + +
240B PRO 5.1 2.2 - - - +
241B GLY* 5.0 7.2 - - - +
242B ILE* 3.8 38.8 - - + -
246B THR* 4.5 4.3 - - + -
250B LEU* 4.0 12.1 - - + -
261B LEU* 3.7 24.0 - - + +
269B LEU* 4.6 1.6 - - + -
273B LEU* 3.6 27.6 - - + -
277B VAL* 2.9 35.1 + - + +
278B ALA* 3.8 6.3 - - - +
280B ARG* 1.3 80.2 - - + +
282B GLN* 1.3 63.8 + - - +
284B LEU* 3.5 15.3 + - + +
285B SER* 3.4 15.6 + - - -
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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
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261B LEU* 2.7 32.8 + - + +
262B GLN 4.3 3.2 + - - -
264B PHE* 2.7 30.8 + - - +
266B PRO* 3.4 31.0 - - - +
269B LEU* 3.8 17.9 - - + +
278B ALA 3.0 19.2 + - - +
279B GLN* 4.0 5.0 - - - +
281B ILE* 1.3 76.8 - - - +
283B LYS* 1.3 63.7 + - - +
285B SER* 2.9 22.5 + - - +
286B PHE* 3.4 21.2 - - + -
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Residues in contact with LYS 283 (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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279B GLN* 3.0 40.7 + - - +
280B ARG* 3.6 7.0 - - - +
282B GLN* 1.3 75.2 - - + +
284B LEU* 1.3 63.5 + - - +
286B PHE* 3.0 15.2 + - - +
288B GLU* 3.0 56.5 + - + +
290B ASN* 5.2 13.7 - - - +
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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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204B LEU* 3.6 33.4 - - + +
230B ILE* 4.8 1.7 - - - +
233B LEU* 6.1 1.4 - - - +
239B ILE* 3.6 20.0 - - + +
240B PRO* 3.2 32.5 - - + +
280B ARG* 3.0 57.3 + - + +
281B ILE* 3.6 16.2 - - + +
282B GLN 3.3 0.2 - - - -
283B LYS* 1.3 77.4 - - - +
285B SER* 1.3 53.2 + - - +
287B GLY* 2.8 24.3 + - - -
288B GLU 3.4 14.6 + - - +
289B ASP* 3.9 7.0 - - + -
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Residues in contact with SER 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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230B ILE* 3.3 10.0 - - - +
233B LEU* 6.4 1.6 - - - -
239B ILE* 4.0 25.1 - - - +
258B VAL* 4.1 10.8 - - - +
261B LEU* 4.0 9.2 - - - -
262B GLN* 2.6 57.4 + - - +
281B ILE 3.4 6.5 + - - -
282B GLN* 2.9 21.7 + - - -
283B LYS 3.2 0.2 + - - -
284B LEU* 1.3 77.1 - - - +
286B PHE* 1.3 51.5 + - - +
287B GLY 3.4 1.6 - - - -
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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