Contacts of the helix formed by residues 277 - 298 (chain B) in PDB entry 1XV9
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 GLN 277 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B LEU* 4.8 4.0 - - + -
186B PRO* 3.3 30.5 - - + +
189B ASP* 3.1 14.1 + - - +
275B VAL* 5.0 0.2 - - - +
276B THR* 1.3 105.4 + - - +
278B ARG* 1.3 56.1 + - - +
279B ASP* 2.8 14.9 + - + +
280B GLU* 2.9 31.7 + - + +
281B ILE* 3.1 14.6 + - + +
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Residues in contact with ARG 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A THR* 3.5 27.7 + - - +
352A GLU* 2.7 43.9 + - - -
356A LYS* 3.7 16.6 - - - +
421A ARG* 3.9 5.9 - - - +
270B PRO* 3.4 35.2 - - + +
275B VAL* 4.4 14.6 - - + +
276B THR 3.3 6.6 + - - +
277B GLN* 1.3 74.6 - - - +
279B ASP* 1.3 55.9 + - - +
281B ILE* 4.5 6.1 - - - -
282B ASP* 2.7 80.1 + - - +
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Residues in contact with ASP 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B GLN* 2.8 4.3 + - + -
278B ARG* 1.3 80.9 + - - +
280B GLU* 1.3 65.1 + - - +
282B ASP* 3.4 6.8 + - - +
283B GLN* 3.2 34.2 + - - +
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Residues in contact with GLU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B VAL* 4.4 5.0 - - - +
184B SER* 3.8 19.0 + - - +
185B LEU* 3.2 30.0 - - + +
186B PRO* 5.1 0.9 - - - +
277B GLN* 2.9 22.8 + - + +
279B ASP* 1.3 78.0 - - - +
281B ILE* 1.3 58.6 + - - +
283B GLN* 3.1 9.2 + - - +
284B LEU* 2.8 44.7 + - + +
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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
----------------------------------------------------------
185B LEU* 4.3 19.3 - - + -
189B ASP* 4.6 15.3 - - + +
193B LEU* 3.8 24.9 - - + -
268B PHE* 4.0 14.4 - - + -
269B SER 3.6 6.1 - - - +
270B PRO* 3.2 33.4 - - + -
275B VAL* 4.0 28.0 - - + -
277B GLN 3.1 13.0 + - - +
278B ARG* 4.3 0.7 - - - +
280B GLU* 1.3 76.9 - - - +
282B ASP* 1.3 57.1 + - - +
284B LEU* 3.6 9.4 - - + +
285B GLN* 2.8 28.1 + - - +
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Residues in contact with ASP 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LYS* 3.1 35.8 + - - -
421A ARG* 4.1 0.2 + - - -
270B PRO* 3.7 10.3 - - - +
278B ARG* 2.7 50.3 + - - +
279B ASP* 3.5 7.1 - - - +
280B GLU 3.3 0.2 - - - -
281B ILE* 1.3 76.9 - - - +
283B GLN* 1.3 64.6 + - - +
285B GLN* 3.4 11.6 - - - +
286B GLU* 3.0 27.3 + - - +
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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
----------------------------------------------------------
279B ASP* 3.2 19.6 + - - +
280B GLU* 3.1 10.7 + - - +
282B ASP* 1.3 82.1 - - - +
284B LEU* 1.3 58.6 + - - +
285B GLN 3.1 1.6 - - - -
286B GLU* 3.6 21.4 - - - +
287B GLU* 2.8 34.2 + - - +
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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
----------------------------------------------------------
181B VAL* 3.4 38.1 - - + -
185B LEU* 4.5 6.3 - - + -
268B PHE* 4.0 31.0 - - + -
280B GLU* 2.8 38.5 + - + +
281B ILE* 3.6 11.2 - - - +
283B GLN* 1.3 76.9 - - - +
285B GLN* 1.3 57.8 + - - +
287B GLU* 3.2 23.3 - - - +
288B MET* 2.9 42.1 + - + +
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Residues in contact with GLN 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A LEU* 3.8 23.2 + - + +
421A ARG* 3.0 35.4 + - - +
424A ALA* 6.2 0.4 - - - +
265B MET* 5.1 7.8 - - + +
268B PHE 3.3 21.0 + - - +
269B SER* 4.4 5.5 + - - +
270B PRO* 3.1 25.7 - - + +
271B ASP* 4.7 5.1 + - - -
281B ILE 2.8 17.2 + - - +
282B ASP* 3.4 18.0 - - - +
284B LEU* 1.3 75.3 - - - +
286B GLU* 1.3 63.8 + - - +
288B MET* 3.9 5.0 - - - +
289B ALA* 3.0 28.3 + - - +
320B ARG* 5.6 1.4 - - - +
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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
----------------------------------------------------------
356A LYS* 4.6 13.7 + - - -
417A LYS* 4.5 18.4 + - + +
420A LEU* 4.5 15.5 - - + -
282B ASP* 3.0 20.7 + - - +
283B GLN* 3.6 22.7 - - - +
285B GLN* 1.3 75.9 - - - +
287B GLU* 1.3 58.6 + - - +
289B ALA* 3.7 2.2 - - - +
290B LEU* 3.0 43.4 + - + +
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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
----------------------------------------------------------
113B LEU* 4.6 10.2 - - - +
283B GLN 2.8 16.6 + - - +
284B LEU* 3.2 24.2 - - - +
286B GLU* 1.3 73.6 - - - +
288B MET* 1.3 84.7 + - + +
290B LEU* 3.3 8.8 + - - +
291B THR* 3.0 30.2 + - - +
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Residues in contact with MET 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LEU* 3.9 29.6 - - + -
117B LEU* 5.8 1.6 - - - -
261B LEU* 5.4 7.5 - - + +
264B ALA* 4.0 24.2 - - + -
265B MET* 3.8 21.3 - - + +
268B PHE* 4.2 25.6 - - + -
284B LEU* 2.9 38.1 + - + +
285B GLN* 3.9 4.9 - - - +
287B GLU* 1.3 96.6 - - + +
289B ALA* 1.3 68.0 + - - +
291B THR* 2.8 19.2 + - - -
292B LEU* 3.1 11.1 + - - +
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Residues in contact with ALA 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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420A LEU* 4.1 13.7 - - + -
265B MET* 3.8 19.8 - - + -
285B GLN 3.0 15.6 + - - +
286B GLU* 3.7 7.2 - - - +
288B MET* 1.3 79.3 - - - +
290B LEU* 1.3 60.3 + - + +
292B LEU* 3.4 1.4 + - - +
293B GLN* 3.0 33.6 + - - +
309B TYR* 3.1 25.5 - - - +
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Residues in contact with LEU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A GLY* 5.4 8.7 - - - +
417A LYS* 5.9 6.3 - - + +
110B GLN* 4.2 4.3 - - - +
286B GLU* 3.0 32.1 - - + +
287B GLU* 3.3 8.0 + - - +
288B MET 2.9 1.0 + - - -
289B ALA* 1.3 73.2 - - + +
291B THR* 1.3 66.1 + - - +
292B LEU 3.1 2.7 + - - -
293B GLN* 3.1 37.0 + - - +
294B SER* 3.0 17.8 + - - -
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Residues in contact with THR 291 (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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106B LEU* 3.8 6.3 - - + +
110B GLN* 3.4 43.8 + - + +
113B LEU* 3.3 33.5 - - + +
114B ILE* 4.7 5.3 - - + +
261B LEU* 4.2 17.0 - - + +
287B GLU* 3.0 17.6 + - - +
288B MET* 2.8 12.2 + - - -
290B LEU* 1.3 72.6 - - - +
292B LEU* 1.3 61.4 + - - +
294B SER* 3.6 13.5 - - - -
295B TYR* 3.7 4.3 + - - +
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B GLU* 4.4 11.4 - - + +
261B LEU* 3.3 43.9 - - + +
262B LEU* 3.9 16.4 - - + +
265B MET* 4.5 12.1 - - - -
288B MET 3.1 8.3 + - - +
289B ALA 3.7 7.4 - - - +
290B LEU 3.1 0.8 - - - -
291B THR* 1.3 74.5 - - - +
293B GLN* 1.3 63.4 + - - +
294B SER 3.0 5.4 - - - -
295B TYR* 2.9 15.3 + - + +
296B ILE* 3.0 40.6 + - + -
309B TYR* 3.5 15.7 - - + -
312B LEU* 4.3 13.0 - - + -
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Residues in contact with GLN 293 (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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413A GLY* 4.8 6.8 - - - +
416A ALA* 2.8 34.7 - - - +
417A LYS* 6.2 0.2 - - - +
289B ALA* 3.0 30.9 + - - +
290B LEU* 3.1 30.3 + - - +
292B LEU* 1.3 79.1 - - - +
294B SER* 1.3 60.0 + - - +
296B ILE* 3.9 6.1 - - - +
297B LYS* 3.4 28.2 + - - +
309B TYR* 3.3 33.1 + - + -
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Residues in contact with SER 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B VAL* 3.0 29.3 - - - +
105B GLN 3.7 13.2 - - - -
106B LEU* 3.6 17.6 - - - +
110B GLN* 3.3 14.2 + - - -
290B LEU 3.0 13.7 + - - -
291B THR 3.6 9.2 - - - -
292B LEU 3.0 0.2 - - - -
293B GLN* 1.3 76.1 - - - +
295B TYR* 1.3 64.9 + - - +
297B LYS* 3.3 1.8 + - - -
298B GLY* 3.1 7.6 + - - -
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Residues in contact with TYR 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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106B LEU* 4.0 26.8 - - + +
114B ILE* 4.1 18.2 - - + -
255B GLN* 2.8 33.4 + - - -
257B PRO* 3.2 30.0 - - + +
258B GLU* 3.6 30.1 - - + -
261B LEU* 4.8 8.1 - - + -
291B THR 3.7 7.7 + - - +
292B LEU* 2.9 12.6 + - + +
294B SER* 1.3 80.3 - - - +
296B ILE* 1.3 65.3 + - + +
298B GLY* 2.9 23.1 + - - +
299B GLN* 4.6 0.5 - - - -
300B GLN* 4.4 11.5 + - - -
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Residues in contact with ILE 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B GLU* 4.5 12.2 - - + +
292B LEU* 3.0 33.2 + - + +
293B GLN* 3.9 9.0 - - - +
294B SER 3.3 0.2 - - - -
295B TYR* 1.3 79.2 - - + +
297B LYS* 1.3 70.1 + - + +
299B GLN* 3.4 25.3 + - - +
305B ASP 5.7 1.6 - - - +
306B ARG 4.6 11.0 - - - +
308B LEU* 4.0 29.1 - - + +
309B TYR* 3.1 47.3 - - + +
312B LEU* 4.4 4.9 - - + -
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Residues in contact with LYS 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A GLU* 4.4 16.4 + - - -
405A LYS* 4.8 12.1 - - - +
103B PRO* 2.8 23.1 - - - +
104B VAL* 3.5 29.6 - - + -
293B GLN* 3.4 15.7 + - - +
294B SER* 3.3 1.5 + - - +
295B TYR 3.2 0.4 - - - -
296B ILE* 1.3 79.8 - - + +
298B GLY* 1.3 57.9 + - - +
299B GLN* 2.9 16.3 + - - +
306B ARG 5.4 6.5 - - - +
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Residues in contact with GLY 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B PRO* 3.6 20.0 - - - -
104B VAL* 3.8 8.7 - - - +
294B SER 3.1 9.4 + - - -
295B TYR* 2.9 22.5 + - - +
297B LYS* 1.3 73.3 - - - +
299B GLN* 1.3 58.0 + - - -
300B GLN* 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
------------------------------------------------------------
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