Contacts of the helix formed by residues 255 - 268 (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 255 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253D GLN 3.9 1.6 - - - +
254D LEU* 1.3 77.7 - - - +
256D GLU* 1.3 69.1 + - - +
257D PRO* 3.4 5.1 - - + +
258D GLU* 2.7 38.0 + - + +
259D TYR* 2.8 11.8 + - - -
295D TYR* 2.9 32.7 + - - -
299D GLN* 5.2 0.3 - - - -
300D GLN* 3.7 30.8 + - - +
301D ARG 5.4 0.9 + - - -
304D ARG* 2.9 25.9 + - - +
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Residues in contact with GLU 256 (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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118D LEU* 3.5 21.7 - - + +
121D HIS* 3.7 27.3 + - + +
122D THR* 3.2 23.5 + - - +
255D GLN* 1.3 70.5 - - - +
257D PRO* 1.3 73.1 - - + +
259D TYR* 2.8 22.6 + - - +
260D VAL* 2.9 15.1 + - - +
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Residues in contact with PRO 257 (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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114D ILE* 3.6 21.8 - - + -
118D LEU* 3.3 24.2 - - + -
255D GLN* 3.7 3.6 - - + -
256D GLU* 1.3 94.3 - - + +
258D GLU* 1.3 55.3 + - - +
260D VAL* 3.8 0.2 - - - +
261D LEU* 3.0 38.4 + - - +
295D TYR* 2.9 48.7 - - + +
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Residues in contact with GLU 258 (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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254D LEU* 3.0 30.5 - - + +
255D GLN* 2.7 47.4 + - + +
257D PRO* 1.3 73.7 - - - +
259D TYR* 1.3 60.2 + - - +
261D LEU* 4.6 5.2 - - - +
262D LEU* 3.5 15.1 + - - +
292D LEU* 4.9 10.1 - - + +
295D TYR* 3.7 36.5 - - + +
296D ILE* 4.7 11.2 - - + +
304D ARG* 3.1 32.4 + - - -
308D LEU* 4.4 11.2 - - - +
312D LEU* 5.2 0.7 - - - +
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Residues in contact with TYR 259 (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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121D HIS* 6.0 2.7 - - + +
204D ILE* 3.8 35.0 - - + +
205D VAL* 6.2 0.9 - - - -
207D ASN* 2.7 28.5 + - - -
208D THR* 3.7 27.1 - - + -
249D LEU* 3.6 15.1 + - + -
250D ARG* 3.6 30.5 + - - -
253D GLN* 5.4 0.2 - - - -
254D LEU* 3.2 46.1 + - + +
255D GLN 2.8 16.2 + - - -
256D GLU* 2.8 11.6 + - + +
258D GLU* 1.3 75.6 - - - +
260D VAL* 1.3 66.9 + - + +
262D LEU* 2.9 17.2 + - + +
263D ALA* 3.1 10.1 + - - +
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Residues in contact with VAL 260 (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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117D LEU* 3.1 44.4 - - + +
118D LEU* 3.2 27.6 - - + -
121D HIS* 3.2 43.3 - - + +
175D PHE* 4.6 7.4 - - + -
256D GLU 2.9 13.6 + - - +
257D PRO 3.8 0.4 - - - +
259D TYR* 1.3 76.3 - - + +
261D LEU* 1.3 60.6 + - + +
263D ALA* 3.5 8.5 + - - +
264D ALA* 3.2 17.2 + - - +
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Residues in contact with LEU 261 (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* 4.6 9.2 - - + -
114D ILE* 3.8 37.0 - - + -
117D LEU* 3.1 28.5 - - + -
257D PRO* 3.0 22.1 + - + +
258D GLU* 4.6 2.0 - - - +
260D VAL* 1.3 74.7 - - + +
262D LEU* 1.3 67.7 + - - +
264D ALA* 2.9 19.9 + - + +
265D MET* 3.3 12.1 + - - +
288D MET* 4.8 5.4 - - + +
291D THR* 3.6 29.2 - - + +
292D LEU* 3.9 26.4 - - + +
295D TYR* 4.8 6.3 - - + -
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Residues in contact with LEU 262 (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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204D ILE* 4.0 19.5 - - + +
249D LEU* 4.5 18.4 - - + -
254D LEU* 4.7 4.9 - - + -
258D GLU 3.5 12.2 + - - +
259D TYR* 2.9 11.4 + - + +
261D LEU* 1.3 80.6 - - - +
263D ALA* 1.3 61.6 + - - +
265D MET* 3.4 9.1 + - + +
266D ALA* 3.4 7.6 + - - +
292D LEU* 3.8 12.5 - - + +
312D LEU* 3.6 38.8 - - + +
315D LEU* 5.8 3.6 - - + -
316D LEU* 3.3 37.2 - - + -
319D LEU* 5.7 2.2 - - + -
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Residues in contact with ALA 263 (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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125D MET* 5.8 1.3 - - + -
175D PHE* 5.7 9.9 - - + -
201D ILE* 4.2 19.5 - - + +
204D ILE* 3.2 36.9 - - + +
205D VAL* 5.1 3.6 - - + -
259D TYR 3.1 6.3 + - - +
260D VAL* 3.8 10.5 - - - +
262D LEU* 1.3 75.5 - - - +
264D ALA* 1.3 65.0 - - - +
266D ALA* 3.2 2.8 + - - +
267D LEU* 3.0 23.7 + - - +
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Residues in contact with ALA 264 (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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117D LEU* 3.8 23.8 - - + -
175D PHE* 6.1 2.9 - - - -
260D VAL 3.2 10.8 + - - +
261D LEU* 2.9 18.7 + - - +
263D ALA* 1.3 78.4 - - - +
265D MET* 1.3 55.4 + - - +
267D LEU* 3.4 10.0 - - - +
268D PHE* 2.9 37.9 + - + +
288D MET* 3.8 20.6 - - + -
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Residues in contact with MET 265 (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* 3.9 16.2 - - + -
261D LEU 3.3 7.3 + - - +
262D LEU 3.7 6.5 - - - +
263D ALA 3.2 0.4 - - - -
264D ALA* 1.3 75.1 - - - +
266D ALA* 1.3 67.7 + - - +
268D PHE* 3.3 15.3 - - - +
269D SER* 3.2 11.4 + - - -
285D GLN* 4.8 9.4 - - + +
288D MET* 3.6 20.6 - - + -
289D ALA* 3.4 38.4 - - + +
292D LEU* 3.9 24.0 - - - -
309D TYR* 4.0 8.1 - - - +
313D LEU* 4.5 10.3 - - + -
316D LEU* 4.3 20.3 - - + +
320D ARG* 4.8 2.1 + - - -
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Residues in contact with ALA 266 (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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197D ALA* 2.9 24.2 - - + +
200D GLU* 4.4 11.2 - - + +
201D ILE* 4.3 5.4 - - + -
204D ILE* 3.9 22.2 - - + -
262D LEU 3.4 3.2 + - - -
263D ALA 3.2 10.2 + - - +
265D MET* 1.3 76.3 - - - +
267D LEU* 1.3 60.0 + - - +
269D SER* 2.7 22.8 + - - -
272D ARG* 3.2 6.0 + - - +
316D LEU* 4.0 19.9 - - + +
320D ARG* 5.4 0.4 - - - +
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Residues in contact with LEU 267 (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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175D PHE* 5.3 3.8 - - + -
176D THR* 3.8 27.1 - - + -
179D LEU* 5.1 8.5 - - + -
182D PHE* 3.2 46.4 - - + -
193D LEU* 3.7 30.2 - - + +
194D LEU* 4.8 4.7 - - + -
197D ALA* 3.4 8.6 - - - +
201D ILE* 4.2 12.5 - - + +
263D ALA 3.0 9.9 + - - +
264D ALA* 3.4 10.1 - - - +
266D ALA* 1.3 81.2 - - - +
268D PHE* 1.3 76.6 + - + +
269D SER* 3.2 7.8 + - - -
272D ARG* 5.2 0.3 - - - +
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Residues in contact with PHE 268 (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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117D LEU* 6.2 3.4 - - + -
179D LEU* 6.1 4.5 - - + -
181D VAL* 4.4 20.4 - - + -
182D PHE* 3.6 35.4 - + + -
185D LEU* 5.0 0.9 - - + -
193D LEU* 4.6 10.1 - - + -
264D ALA* 2.9 27.6 + - + +
265D MET* 3.3 10.3 - - - +
266D ALA 3.4 0.2 - - - -
267D LEU* 1.3 87.1 - - + +
269D SER* 1.3 60.9 + - - +
270D PRO* 4.1 0.9 - - - -
281D ILE* 4.7 9.2 - - + +
284D LEU* 4.3 28.9 - - + -
285D GLN* 3.7 35.0 - - + +
288D MET* 4.0 27.1 - - + -
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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