Contacts of the helix formed by residues 261 - 277 (chain D) in PDB entry 5XVO
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 LEU 261 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183D LEU* 3.9 25.8 - - + -
186D ILE* 4.0 16.4 - - + -
187D PHE* 5.8 1.1 - - + -
221D PHE* 3.9 32.8 - - + -
224D LEU* 3.9 12.8 - - + -
247D LEU* 3.4 45.0 + - + +
248D PHE* 5.4 2.8 + - + +
250D ASN 4.2 4.8 + - - -
252D TYR* 4.2 9.3 - - + -
259D MET 3.9 0.8 + - - -
260D PHE* 1.3 73.8 - - - +
262D THR* 1.3 59.9 + - + +
264D ILE* 3.2 13.8 + - + +
265D ALA* 2.9 30.2 + - + +
286D PHE* 5.4 0.2 - - + -
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Residues in contact with THR 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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2D GLY 5.3 1.6 + - - -
38D ASP* 3.0 31.4 + - - +
39D VAL* 5.3 0.2 - - + -
186D ILE* 4.5 14.8 - - + -
189D ARG* 3.5 22.4 - - - +
190D GLU* 4.0 3.3 - - - +
248D PHE* 4.4 19.9 - - + +
260D PHE* 4.6 6.2 - - - +
261D LEU* 1.3 77.6 - - - +
263D ASN* 1.3 68.1 + - - +
265D ALA* 3.4 7.3 + - - +
266D THR* 2.9 30.4 + - - -
102F ARG* 5.0 6.6 + - - -
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Residues in contact with ASN 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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2D GLY 5.7 1.0 - - - +
259D MET* 3.9 20.7 - - + +
260D PHE* 3.2 24.6 + - - +
262D THR* 1.3 84.1 + - - +
264D ILE* 1.3 65.7 + - - +
266D THR* 3.4 9.0 + - - -
267D ASP* 3.2 21.3 + - - +
102F ARG* 6.2 0.4 - - - -
17Q A 4.8 3.0 + - - -
18Q T 4.1 18.6 + - - -
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Residues in contact with ILE 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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221D PHE* 3.9 24.7 - - + -
252D TYR* 3.9 21.8 - - + +
254D TYR* 3.6 52.9 - - + -
259D MET* 3.7 34.1 - - + +
260D PHE 3.0 17.7 + - - +
261D LEU* 3.5 12.6 - - + +
263D ASN* 1.3 75.7 - - - +
265D ALA* 1.3 56.1 + - - +
267D ASP* 3.0 4.0 + - - +
268D TYR* 2.7 32.4 + - - +
286D PHE* 4.3 6.1 - - + -
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Residues in contact with ALA 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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186D ILE* 3.5 32.5 - - + -
187D PHE* 3.6 28.5 - - + -
190D GLU* 4.0 4.5 - - + -
261D LEU* 2.9 17.4 + - + +
262D THR 3.7 2.5 - - - +
263D ASN 3.3 0.2 - - - -
264D ILE* 1.3 77.2 - - - +
266D THR* 1.3 56.1 + - - +
268D TYR* 3.8 2.4 - - - +
269D THR* 2.7 37.2 + - - -
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Residues in contact with THR 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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190D GLU* 3.1 31.5 + - - +
193D GLN* 5.3 6.1 - - - +
262D THR 2.9 17.2 + - - -
263D ASN* 3.5 11.1 + - - -
264D ILE 3.1 0.2 - - - -
265D ALA* 1.3 77.8 - - - +
267D ASP* 1.3 63.4 + - - +
269D THR* 3.9 1.0 - - - -
270D LYS* 3.0 57.0 + - + +
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Residues in contact with ASP 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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254D TYR* 2.7 36.0 + - + -
255D LYS* 2.9 19.7 + - - +
259D MET* 5.2 5.8 - - + -
263D ASN 3.2 8.7 + - - +
264D ILE 3.0 6.7 + - - +
266D THR* 1.3 79.7 - - - +
268D TYR* 1.3 64.1 + - - +
270D LYS* 3.8 5.1 - - - +
271D HIS* 3.0 48.1 + - - -
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Residues in contact with TYR 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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108D ILE* 3.9 16.3 - - + +
111D GLN* 3.3 21.0 + - - -
187D PHE* 4.2 9.0 - + - -
217D LEU* 3.7 24.5 - - + -
220D PRO* 3.3 17.7 - - + +
221D PHE* 3.9 21.5 - + + -
254D TYR* 3.6 19.4 + + + +
264D ILE 2.7 22.2 + - - +
265D ALA* 3.8 6.3 - - - +
267D ASP* 1.3 74.8 - - - +
269D THR* 1.3 65.6 + - - +
271D HIS 3.4 0.2 + - - -
272D VAL* 3.0 44.8 + - + +
283D VAL* 4.9 0.2 - - - +
284D PRO* 3.3 37.8 + - + +
286D PHE* 4.2 9.9 - - + -
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Residues in contact with THR 269 (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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187D PHE* 3.4 22.9 - - - -
190D GLU* 3.7 24.8 - - + +
191D LEU* 3.8 22.4 - - + -
194D THR* 4.3 7.2 - - + -
217D LEU* 3.6 25.1 - - + +
265D ALA 2.7 23.5 + - - -
266D THR 3.9 2.2 - - - -
268D TYR* 1.3 76.1 - - - +
270D LYS* 1.3 64.4 + - - +
271D HIS 3.2 0.2 + - - -
272D VAL* 3.2 2.3 + - - +
273D VAL* 2.9 23.2 + - + +
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Residues in contact with LYS 270 (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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193D GLN* 5.9 6.7 - - - +
194D THR* 4.4 18.8 - - + -
266D THR* 3.0 44.1 + - + +
267D ASP* 3.8 6.5 - - - +
269D THR* 1.3 76.6 - - - +
271D HIS* 1.3 60.6 + - + +
273D VAL* 3.4 6.8 + - - +
274D LYS* 3.0 38.3 + - + +
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Residues in contact with HIS 271 (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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255D LYS* 3.5 14.1 + - - -
267D ASP* 3.0 52.8 + - - +
270D LYS* 1.3 78.9 - - + +
272D VAL* 1.3 65.9 + - - +
274D LYS* 3.1 9.9 + - + +
275D VAL* 2.9 26.7 + - - +
280D GLU* 2.7 33.3 + - - +
284D PRO* 3.8 22.4 - - + -
33R T 4.4 20.3 + - - -
34R A 4.7 12.6 - - - -
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Residues in contact with VAL 272 (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* 4.0 15.9 - - + -
108D ILE* 4.3 6.7 - - + -
217D LEU* 3.8 26.9 - - + -
268D TYR* 3.0 46.7 + - + +
269D THR* 3.6 7.9 - - - +
271D HIS* 1.3 74.5 - - - +
273D VAL* 1.3 59.5 + - + +
275D VAL* 3.2 6.7 + - - +
276D LEU* 2.9 42.3 + - + +
283D VAL* 4.7 4.3 - - + -
284D PRO* 3.9 17.2 - - + +
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Residues in contact with VAL 273 (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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89D GLN* 3.6 22.2 - - - +
96D TRP* 4.5 5.8 - - + -
191D LEU* 4.2 15.7 - - + -
194D THR* 4.1 15.9 - - + +
196D CYS* 3.9 20.4 - - - -
217D LEU* 5.5 0.2 - - + -
269D THR* 2.9 19.8 + - + +
270D LYS* 3.5 9.9 - - - +
272D VAL* 1.3 77.2 - - + +
274D LYS* 1.3 60.6 + - + +
276D LEU* 3.2 8.5 + - + +
277D ASN* 2.8 49.8 + - - +
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Residues in contact with LYS 274 (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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270D LYS* 3.0 24.9 + - + +
271D HIS* 3.1 14.3 + - + +
273D VAL* 1.3 76.6 - - + +
275D VAL* 1.3 59.2 + - - +
277D ASN* 3.2 10.8 + - - +
278D GLN 3.1 4.0 + - - -
279D GLU* 2.9 51.4 + - + +
280D GLU* 3.9 29.2 - - + +
34R A 3.4 27.0 + - - +
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Residues in contact with VAL 275 (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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100D ARG* 2.8 36.7 + - - +
104D VAL* 3.7 22.2 - - + -
271D HIS 2.9 18.3 + - - +
272D VAL* 3.6 7.4 - - - +
274D LYS* 1.3 71.9 - - - +
276D LEU* 1.3 66.7 + - - +
278D GLN 3.0 3.1 + - - -
280D GLU* 3.4 24.7 - - + +
281D GLU 3.2 27.8 - - - +
282D GLY 3.6 16.8 - - - +
283D VAL* 3.8 14.4 - - + +
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Residues in contact with LEU 276 (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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96D TRP* 3.3 56.6 - - + +
100D ARG* 3.9 10.6 - - + +
101D LYS* 4.0 33.7 - - + +
104D VAL* 3.9 22.7 - - + -
202D LEU* 4.3 15.3 - - + -
213D LEU* 5.0 2.9 - - + -
272D VAL* 2.9 35.5 + - + +
273D VAL* 3.6 7.2 - - + +
275D VAL* 1.3 76.9 - - - +
277D ASN* 1.3 59.3 + - - +
278D GLN* 3.1 18.1 + - - +
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Residues in contact with ASN 277 (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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89D GLN* 3.1 34.5 + - - +
92D ARG* 3.6 21.5 - - - +
96D TRP* 2.8 29.8 + - - +
273D VAL* 2.8 27.1 + - - +
274D LYS* 3.5 7.8 - - - +
275D VAL 3.2 0.4 - - - -
276D LEU* 1.3 74.4 - - - +
278D GLN* 1.3 70.4 + - - +
279D GLU* 3.4 30.2 + - + +
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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