Contacts of the helix formed by residues 262 - 273 (chain B) in PDB entry 2QVS
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 GLU 262 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260B SER 3.6 7.6 + - - +
261B LEU* 1.3 78.4 - - - +
263B MET* 1.3 70.1 + - + +
264B SER* 3.3 10.1 - - - +
265B GLU* 2.7 36.1 + - + +
266B ARG* 3.1 14.2 + - - +
376B ARG* 4.7 3.8 + - - -
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Residues in contact with MET 263 (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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249B GLU* 4.7 4.5 - - - +
262B GLU* 1.3 76.0 + - + +
264B SER* 1.3 63.5 + - - +
266B ARG* 3.1 40.7 + - - +
267B MET* 3.1 36.6 + - + +
192E LYS* 4.9 10.5 - - - +
193E GLY* 4.8 10.3 - - - -
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Residues in contact with SER 264 (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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262B GLU* 4.3 8.2 - - - +
263B MET* 1.3 80.3 - - - +
265B GLU* 1.3 69.4 + - - +
267B MET* 3.4 11.1 + - - +
268B LYS* 3.2 32.1 + - - +
193E GLY 6.4 0.7 - - - -
194E ARG* 4.8 2.8 + - - +
217E LYS* 6.2 3.8 - - - -
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Residues in contact with GLU 265 (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* 3.4 10.4 - - + -
262B GLU* 2.7 43.9 + - + +
264B SER* 1.3 79.0 - - - +
266B ARG* 1.3 64.5 + - - +
268B LYS* 3.5 14.9 + - + +
269B ILE* 3.4 18.4 + - - +
367B LEU* 3.5 29.7 - - + +
376B ARG* 2.8 40.3 + - - -
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Residues in contact with ARG 266 (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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249B GLU* 2.7 38.8 + - - +
252B ILE* 4.3 12.0 - - + +
253B GLU* 4.0 39.2 + - - +
258B PHE 5.1 3.9 + - - -
259B LYS* 5.2 2.4 + - - +
261B LEU* 3.2 48.1 + - + +
262B GLU 3.1 8.8 + - - +
263B MET* 3.1 33.7 + - - +
265B GLU* 1.3 76.6 - - - +
267B MET* 1.3 58.5 + - - +
269B ILE* 3.2 11.5 + - - +
270B VAL* 3.0 31.6 + - - +
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Residues in contact with MET 267 (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 ARG* 4.3 8.0 + - + +
249B GLU* 4.8 15.5 - - + +
263B MET* 3.1 33.8 + - + +
264B SER* 3.7 10.1 - - - +
265B GLU 3.2 0.4 - - - -
266B ARG* 1.3 76.3 - - - +
268B LYS* 1.3 59.8 + - - +
270B VAL* 3.3 9.3 + - + +
271B ASP* 2.9 33.6 + - - +
193E GLY* 3.3 41.1 - - - -
194E ARG* 3.5 33.4 - - + +
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Residues in contact with LYS 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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264B SER* 3.2 20.8 + - - +
265B GLU* 3.7 10.3 - - - +
266B ARG 3.3 0.4 - - - -
267B MET* 1.3 75.7 - - - +
269B ILE* 1.3 63.3 + - + +
271B ASP* 3.3 22.5 - - - +
272B VAL* 3.6 13.2 + - - +
366B LEU* 3.9 34.4 - - + +
367B LEU* 4.8 8.3 - - + -
194E ARG* 4.6 6.8 - - - +
217E LYS* 6.3 1.4 - - - +
282E GLY 5.0 1.4 + - - -
283E ASN* 2.8 54.1 + - - +
284E LEU 5.1 3.1 - - - -
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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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252B ILE* 4.4 17.5 - - + -
258B PHE* 6.4 0.7 - - + -
261B LEU* 4.9 5.6 - - + -
265B GLU 3.4 14.4 - - - +
266B ARG* 3.3 10.8 - - - +
268B LYS* 1.3 76.9 - - - +
270B VAL* 1.3 62.0 - - + +
272B VAL* 3.0 4.3 + - - +
273B ILE* 2.8 55.5 + - + +
294B PHE* 5.7 2.7 - - + -
358B MET* 3.6 32.3 - - + -
363B PHE* 3.8 22.7 - - + -
366B LEU* 4.6 5.8 - - + -
367B LEU* 3.9 21.1 - - + -
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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
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245B ARG* 3.8 40.0 - - + +
248B PHE* 3.7 28.4 - - + -
249B GLU* 3.5 33.4 - - + +
252B ILE* 4.6 6.5 - - + -
266B ARG 3.0 17.4 + - - +
267B MET* 3.3 11.2 + - + +
269B ILE* 1.3 75.0 - - - +
271B ASP* 1.3 62.5 + - - +
272B VAL 3.3 0.3 + - - -
273B ILE* 3.6 19.3 - - - +
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Residues in contact with ASP 271 (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 ARG* 2.6 44.7 + - - +
267B MET 2.9 16.2 + - - +
268B LYS* 3.3 14.1 - - - +
270B VAL* 1.3 78.7 - - - +
272B VAL* 1.3 60.8 + - + +
273B ILE 5.3 0.4 - - - +
194E ARG* 2.8 28.0 + - - -
214E GLY 5.6 0.7 - - - -
215E TYR* 6.3 0.2 - - - -
277E LEU* 4.0 30.2 - - + +
283E ASN* 5.2 5.2 + - - +
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Residues in contact with VAL 272 (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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268B LYS 3.7 12.6 - - - +
269B ILE 3.0 10.2 + - - +
271B ASP* 1.3 82.2 - - + +
273B ILE* 1.3 70.5 + - - +
274B GLY* 3.6 1.4 + - - -
358B MET* 3.7 26.6 - - + +
362B ALA* 5.3 0.4 - - + -
366B LEU* 4.0 4.9 - - + -
276E ASP* 5.0 0.7 - - - +
277E LEU* 3.8 27.6 - - + +
278E THR* 3.4 32.5 - - + +
283E ASN* 5.9 0.4 - - - +
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Residues in contact with ILE 273 (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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248B PHE* 3.7 32.0 - - + -
252B ILE* 4.0 16.8 - - + -
269B ILE* 2.8 41.7 + - + +
270B VAL* 3.6 17.4 - - - +
271B ASP 3.8 0.4 - - - +
272B VAL* 1.3 75.7 - - - +
274B GLY* 1.3 68.5 + - - +
294B PHE* 5.3 1.1 - - + -
296B ILE* 5.0 4.3 - - + -
356B LEU* 4.0 22.0 - - + -
357B VAL 3.6 14.8 - - - +
358B MET* 4.0 23.3 - - + -
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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
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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