Contacts of the helix formed by residues 277 - 298 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D LEU* 4.0 1.6 - - + -
186D PRO* 3.4 35.0 - - + +
189D ASP* 2.7 15.1 + - - +
276D THR* 1.3 90.3 + - - +
278D ARG* 1.3 62.3 + - - +
279D ASP 3.5 2.4 + - - -
280D GLU* 3.5 25.8 + - + +
281D ILE* 3.5 22.7 + - - +
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Residues in contact with ARG 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351C THR* 3.7 17.3 + - - -
352C GLU* 2.9 41.2 + - - -
356C LYS* 4.2 13.1 - - - +
270D PRO* 3.6 28.3 + - + +
275D VAL* 3.8 17.3 - - + +
276D THR 2.8 13.4 + - - +
277D GLN* 1.3 72.4 - - - +
279D ASP* 1.3 71.6 + - - +
281D ILE* 3.3 7.9 + - - +
282D ASP* 3.0 51.2 + - - +
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Residues in contact with ASP 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D GLN 3.5 0.6 - - - -
278D ARG* 1.3 86.2 + - - +
280D GLU* 1.3 66.3 + - - +
281D ILE 3.0 2.0 - - - -
282D ASP* 3.0 19.9 + - - +
283D GLN* 3.1 22.3 + - - +
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Residues in contact with GLU 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D VAL* 4.7 2.6 - - - +
184D SER* 4.5 10.0 + - - -
185D LEU* 3.3 40.2 + - - +
186D PRO* 4.8 1.0 - - - +
277D GLN* 3.5 23.1 - - + +
278D ARG 3.4 0.2 - - - -
279D ASP* 1.3 78.0 - - - +
281D ILE* 1.3 55.6 + - - +
283D GLN* 3.4 28.5 - - - +
284D LEU* 3.3 28.0 - - + +
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Residues in contact with ILE 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D LEU* 3.8 28.5 - - + -
189D ASP* 3.7 22.7 - - + +
193D LEU* 3.8 26.2 - - + -
268D PHE* 4.7 6.7 - - + +
269D SER 4.0 9.6 - - - +
270D PRO* 3.6 31.6 - - + -
275D VAL* 4.0 11.9 - - + -
277D GLN 3.5 8.7 + - - +
278D ARG 3.3 8.3 + - - +
279D ASP 3.0 0.4 - - - -
280D GLU* 1.3 75.7 - - - +
282D ASP* 1.3 58.7 + - - +
283D GLN 3.1 2.0 - - - -
284D LEU* 3.7 8.8 + - + +
285D GLN* 3.1 24.6 + - - +
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Residues in contact with ASP 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C LYS* 2.8 31.8 + - - -
421C ARG* 5.1 0.2 + - - -
270D PRO* 3.5 3.1 - - - +
278D ARG* 3.0 38.8 + - - +
279D ASP* 3.0 13.6 + - - +
281D ILE* 1.3 77.4 - - - +
283D GLN* 1.3 62.0 + - + +
285D GLN* 3.0 26.4 + - - +
286D GLU* 3.4 24.6 + - - +
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Residues in contact with GLN 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D ASP* 3.1 11.2 + - - +
280D GLU* 3.4 32.6 - - - +
282D ASP* 1.3 73.8 - - + +
284D LEU* 1.3 70.9 + - + +
285D GLN 3.1 1.5 + - - -
286D GLU* 3.4 5.7 + - - +
287D GLU* 3.1 22.5 + - - +
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Residues in contact with LEU 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D VAL* 3.2 42.4 - - + +
185D LEU* 4.9 6.3 - - + -
268D PHE* 4.3 31.9 - - + -
280D GLU* 3.3 29.4 - - + +
281D ILE* 3.7 11.6 + - - +
283D GLN* 1.3 78.6 - - + +
285D GLN* 1.3 65.9 + - - +
287D GLU* 3.2 31.5 - - - +
288D MET* 3.3 15.9 - - + +
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Residues in contact with GLN 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420C LEU* 3.0 39.5 - - + +
421C ARG* 4.0 8.0 + - - +
265D MET* 4.8 8.4 - - + +
268D PHE* 3.7 27.3 - - - +
270D PRO* 3.3 21.5 - - + +
281D ILE 3.1 18.5 + - - +
282D ASP* 3.0 33.3 + - - +
283D GLN 3.1 0.4 - - - -
284D LEU* 1.3 79.3 - - - +
286D GLU* 1.3 64.4 + - - +
288D MET* 3.0 13.6 + - - +
289D ALA* 3.3 9.4 + - - +
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Residues in contact with GLU 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C LYS* 5.8 1.7 + - - -
417C LYS* 3.4 34.0 + - + +
420C LEU* 4.9 14.4 - - + +
282D ASP* 3.4 14.5 + - - +
283D GLN* 3.4 4.2 + - - +
285D GLN* 1.3 81.5 - - + +
287D GLU* 1.3 63.6 - - - +
289D ALA* 3.3 10.3 + - + +
290D LEU* 3.0 51.6 + - + +
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Residues in contact with GLU 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D GLU* 5.1 8.0 - - - +
113D LEU* 4.0 20.6 - - + +
283D GLN 3.1 12.3 + - - +
284D LEU* 3.2 29.1 - - - +
285D GLN 3.1 0.4 + - - -
286D GLU* 1.3 77.1 - - - +
288D MET* 1.3 68.7 + - + +
290D LEU* 3.9 7.1 - - - +
291D THR* 2.4 39.6 + - - +
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Residues in contact with MET 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D LEU* 3.8 29.6 - - + -
117D LEU* 4.8 2.2 - - - -
261D LEU* 4.8 6.0 - - + +
264D ALA* 3.8 30.5 - - + -
265D MET* 3.6 19.1 - - + -
268D PHE* 4.0 23.8 - - + -
284D LEU* 3.3 26.7 - - + +
285D GLN* 3.0 6.7 + - - +
287D GLU* 1.3 98.3 - - + +
289D ALA* 1.3 70.1 + - - +
290D LEU 3.1 1.3 - - - -
291D THR* 2.9 6.0 + - - -
292D LEU* 2.7 27.2 + - - +
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Residues in contact with ALA 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420C LEU* 3.7 11.2 - - + -
265D MET* 3.4 26.3 - - + +
285D GLN 3.3 3.6 + - - +
286D GLU* 3.3 16.4 + - + +
288D MET* 1.3 78.5 - - - +
290D LEU* 1.3 58.0 + - + +
292D LEU* 3.3 0.9 + - - +
293D GLN* 2.9 37.2 + - - +
309D TYR* 3.1 26.3 - - - +
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Residues in contact with LEU 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413C GLY* 5.5 7.0 - - - +
416C ALA* 5.4 0.7 - - + -
110D GLN* 4.4 8.3 - - - +
286D GLU* 3.0 40.1 + - + +
287D GLU* 3.9 5.6 - - - +
289D ALA* 1.3 72.2 - - + +
291D THR* 1.3 51.4 + - - +
292D LEU 2.9 4.9 - - - -
293D GLN* 2.8 43.9 + - - +
294D SER* 2.7 26.3 + - - -
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Residues in contact with THR 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D LEU* 4.1 2.6 - - + +
110D GLN* 3.5 43.7 + - + +
113D LEU* 3.0 33.8 - - + +
114D ILE* 4.2 11.4 - - + +
261D LEU* 3.6 12.9 - - + +
287D GLU* 2.4 27.5 + - - +
288D MET* 2.9 5.9 + - - -
290D LEU* 1.3 74.8 - - - +
292D LEU* 1.3 56.7 + - - +
294D SER* 3.7 10.2 + - - -
295D TYR* 3.8 13.7 + - - +
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Residues in contact with LEU 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258D GLU* 4.9 9.9 - - + +
261D LEU* 3.9 21.8 - - + -
262D LEU* 3.8 30.7 - - + +
265D MET* 3.9 22.2 - - + -
288D MET 2.7 13.6 + - - +
289D ALA* 3.5 6.1 - - - +
291D THR* 1.3 74.6 - - - +
293D GLN* 1.3 60.6 - - - +
294D SER 3.1 2.0 - - - -
295D TYR* 3.7 4.4 + - + +
296D ILE* 3.0 45.1 + - + +
309D TYR* 4.0 10.3 - - + -
312D LEU* 4.1 19.7 - - + -
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Residues in contact with GLN 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413C GLY* 4.1 11.1 - - - -
416C ALA* 3.0 35.8 - - + +
104D VAL* 4.0 0.6 - - - +
289D ALA* 2.9 26.8 + - - +
290D LEU* 2.8 38.7 + - - +
292D LEU* 1.3 77.7 - - - +
294D SER* 1.3 60.5 + - - +
296D ILE* 3.7 6.5 - - - +
297D LYS* 3.3 30.5 + - - +
309D TYR* 3.3 28.0 + - + -
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Residues in contact with SER 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D VAL* 2.9 23.4 - - - +
105D GLN 3.5 23.1 - - - -
106D LEU* 3.5 15.4 - - - +
110D GLN* 3.6 17.3 + - - -
290D LEU 2.7 16.7 + - - -
291D THR* 3.7 2.3 - - - -
293D GLN* 1.3 73.2 - - - +
295D TYR* 1.3 67.4 + - - +
296D ILE 3.0 1.3 + - - -
297D LYS 3.3 0.2 + - - -
298D GLY* 2.9 21.7 + - - -
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Residues in contact with TYR 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D LEU* 4.4 15.2 - - + +
114D ILE* 3.6 26.7 - - + -
255D GLN* 2.9 31.7 + - - -
257D PRO* 2.9 38.9 - - + +
258D GLU* 3.7 26.6 - - + +
261D LEU* 4.8 4.7 - - + -
291D THR 3.8 12.7 + - - +
292D LEU* 3.7 8.0 + - + +
294D SER* 1.3 80.2 - - - +
296D ILE* 1.3 63.7 + - - +
298D GLY* 3.5 20.1 - - - -
299D GLN* 3.6 4.1 + - - -
300D GLN* 4.2 9.4 + - + -
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Residues in contact with ILE 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258D GLU* 4.7 13.5 - - + +
292D LEU* 3.0 39.9 + - + +
293D GLN* 3.7 8.1 - - - +
294D SER 3.0 0.8 - - - -
295D TYR* 1.3 77.8 - - + +
297D LYS* 1.3 77.8 + - + +
299D GLN* 3.3 20.8 + - - +
306D ARG 4.8 8.5 - - - +
308D LEU* 3.6 22.7 - - + -
309D TYR* 3.0 48.0 - - + +
312D LEU* 4.7 2.7 - - + -
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Residues in contact with LYS 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401C GLU* 5.1 9.6 + - - -
405C LYS* 5.9 3.4 - - - +
103D PRO* 3.6 18.7 - - + +
104D VAL* 3.4 35.1 - - + +
293D GLN* 3.3 15.4 + - - +
294D SER 3.3 1.6 + - - -
296D ILE* 1.3 88.2 - - + +
298D GLY* 1.3 58.1 + - - +
299D GLN* 3.0 12.0 + - - +
306D ARG 6.1 1.3 - - - -
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Residues in contact with GLY 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D PRO* 3.9 20.2 - - - -
104D VAL 4.0 6.8 - - - +
294D SER 2.9 16.1 + - - -
295D TYR* 3.5 13.9 - - - +
297D LYS* 1.3 75.1 - - - +
299D GLN* 1.3 61.8 + - - -
300D GLN* 3.6 5.9 + - - +
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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