Contacts of the helix formed by residues 261 - 277 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183B LEU* 3.9 25.8 - - + -
186B ILE* 4.1 16.6 - - + -
187B PHE* 5.8 1.1 - - + -
221B PHE* 3.9 33.0 - - + -
224B LEU* 3.9 12.8 - - + -
247B LEU* 3.4 45.6 + - + +
248B PHE* 5.3 3.2 + - + +
250B ASN 4.2 5.3 + - - -
252B TYR* 4.1 10.2 - - + -
259B MET 3.8 0.8 + - - -
260B PHE* 1.3 74.9 - - - +
262B THR* 1.3 58.4 + - + +
264B ILE* 3.2 10.8 + - + +
265B ALA* 2.9 29.3 + - + +
286B PHE* 5.4 0.4 - - + -
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Residues in contact with THR 262 (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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43B GLU* 5.8 0.7 - - - +
186B ILE* 4.5 17.7 - - + -
189B ARG* 4.6 8.7 - - - +
190B GLU* 4.0 6.6 - - - +
248B PHE* 4.4 26.2 - - + +
260B PHE* 4.7 6.2 - - - +
261B LEU* 1.3 77.2 - - - +
263B ASN* 1.3 68.8 + - - +
265B ALA* 3.4 8.1 + - - +
266B THR* 2.9 30.9 + - - -
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Residues in contact with ASN 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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259B MET* 4.9 11.5 - - + +
260B PHE* 3.2 29.8 + - - +
261B LEU 3.1 0.2 - - - -
262B THR* 1.3 84.4 + - - +
264B ILE* 1.3 65.3 + - - +
266B THR* 3.3 8.4 + - - -
267B ASP* 3.2 21.8 + - - +
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Residues in contact with ILE 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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221B PHE* 3.9 24.9 - - + -
252B TYR* 3.9 22.7 - - + +
254B TYR* 3.7 51.8 - - + -
259B MET* 3.7 35.0 - - + +
260B PHE 3.0 16.5 + - - +
261B LEU* 3.2 12.1 + - + +
263B ASN* 1.3 75.8 - - - +
265B ALA* 1.3 54.1 + - - +
267B ASP* 3.0 3.7 + - - +
268B TYR* 2.7 34.7 + - + +
286B PHE* 4.3 6.1 - - + -
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Residues in contact with ALA 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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186B ILE* 3.5 31.6 - - + -
187B PHE* 3.7 29.8 - - + -
190B GLU* 4.0 3.5 - - + +
261B LEU* 2.9 16.9 + - + +
262B THR 3.7 3.4 - - - +
264B ILE* 1.3 77.2 - - - +
266B THR* 1.3 56.6 + - - +
268B TYR* 3.8 2.6 - - - +
269B THR* 2.7 35.9 + - - -
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Residues in contact with THR 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B GLU* 3.1 32.3 + - - +
193B GLN* 5.3 3.1 - - - +
262B THR 2.9 17.5 + - - -
263B ASN* 3.5 11.3 + - - -
264B ILE 3.1 0.4 - - - -
265B ALA* 1.3 77.4 - - - +
267B ASP* 1.3 62.5 + - - +
269B THR* 3.9 1.2 - - - -
270B LYS* 3.0 54.0 + - + +
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Residues in contact with ASP 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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254B TYR* 2.7 35.2 + - + -
255B LYS* 2.9 20.3 + - - -
259B MET* 5.9 6.1 - - + -
263B ASN 3.2 8.8 + - - +
264B ILE 3.0 7.2 + - - +
266B THR* 1.3 77.0 - - - +
268B TYR* 1.3 66.9 + - - +
270B LYS* 3.8 5.3 - - - +
271B HIS* 3.0 48.5 + - - -
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Residues in contact with TYR 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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108B ILE* 3.9 17.1 - - + +
111B GLN* 3.3 21.8 + - - -
187B PHE* 4.2 9.4 - + - -
217B LEU* 3.7 23.6 - - + -
220B PRO* 3.3 13.4 - - + +
221B PHE* 4.0 23.8 - + + -
254B TYR* 3.6 20.8 + + + +
264B ILE 2.7 22.6 + - - +
265B ALA* 3.8 6.1 - - - +
267B ASP* 1.3 75.3 - - - +
269B THR* 1.3 65.0 + - - +
271B HIS 3.3 0.2 + - - -
272B VAL* 3.0 44.5 + - + +
284B PRO* 3.3 37.5 + - + +
286B PHE* 4.2 9.9 - - + -
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Residues in contact with THR 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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187B PHE* 3.4 23.2 - - - -
190B GLU* 3.7 25.3 - - + +
191B LEU* 3.8 22.4 - - + -
194B THR* 4.3 7.0 - - + -
217B LEU* 3.6 24.0 - - + +
265B ALA 2.7 22.9 + - - -
266B THR 3.9 2.2 - - - -
268B TYR* 1.3 75.0 - - - +
270B LYS* 1.3 66.8 + - - +
272B VAL* 3.2 2.9 + - - +
273B VAL* 2.9 23.4 + - + +
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Residues in contact with LYS 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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5B THR* 5.5 3.8 + - - -
190B GLU* 5.7 0.4 + - - -
193B GLN* 5.0 11.9 + - - +
194B THR* 4.6 22.3 - - + +
266B THR* 3.0 41.8 + - + +
267B ASP* 3.8 6.7 - - - +
269B THR* 1.3 77.9 - - - +
271B HIS* 1.3 63.8 + - + +
273B VAL* 3.3 7.1 + - - +
274B LYS* 3.0 34.4 + - + +
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Residues in contact with HIS 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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255B LYS* 3.5 14.3 + - - -
267B ASP* 3.0 54.6 + - - +
270B LYS* 1.3 79.3 - - + +
272B VAL* 1.3 65.4 + - - +
274B LYS* 3.1 14.4 + - + +
275B VAL* 2.8 29.6 + - + +
280B GLU* 2.5 36.2 + - - +
284B PRO* 3.8 20.4 - - + -
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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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104B VAL* 4.0 15.9 - - + -
108B ILE* 4.4 7.9 - - + -
217B LEU* 3.8 26.5 - - + -
268B TYR* 3.0 45.9 + - + +
269B THR* 3.6 8.1 - - - +
271B HIS* 1.3 75.7 - - - +
273B VAL* 1.3 58.5 + - + +
275B VAL* 3.2 9.5 + - - +
276B LEU* 2.9 43.0 + - + +
283B VAL* 5.1 3.6 - - + -
284B PRO* 3.9 13.6 - - + +
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Residues in contact with VAL 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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89B GLN* 3.7 21.5 - - - +
96B TRP* 4.5 5.6 - - + -
191B LEU* 4.2 15.7 - - + -
194B THR* 4.1 16.2 - - + +
196B CYS* 4.0 20.0 - - - -
269B THR* 2.9 18.4 + - + +
270B LYS* 3.6 9.9 - - - +
272B VAL* 1.3 80.3 - - + +
274B LYS* 1.3 56.8 + - + +
276B LEU* 3.3 9.3 + - + +
277B ASN* 2.9 51.5 + - - +
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Residues in contact with LYS 274 (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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270B LYS* 3.0 22.2 + - + +
271B HIS* 3.1 18.8 + - + +
273B VAL* 1.3 76.8 - - + +
275B VAL* 1.3 57.2 + - - +
277B ASN* 3.2 11.1 + - - +
278B GLN 3.1 7.3 + - - -
279B GLU* 2.9 53.0 + - + +
280B GLU* 3.6 35.4 - - + +
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Residues in contact with VAL 275 (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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100B ARG* 3.0 29.3 + - - +
104B VAL* 3.4 26.0 - - + -
271B HIS 2.8 22.1 + - - +
272B VAL* 4.0 3.6 - - - +
274B LYS* 1.3 72.1 - - - +
276B LEU* 1.3 67.2 + - - +
278B GLN 3.0 8.8 + - - -
280B GLU* 3.4 29.6 - - + +
282B GLY 3.7 26.9 - - - +
283B VAL* 3.9 18.6 - - + +
284B PRO* 4.5 0.2 - - + -
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Residues in contact with LEU 276 (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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96B TRP* 3.3 56.5 - - + +
100B ARG* 3.7 16.7 - - + +
101B LYS* 4.0 22.4 - - + +
104B VAL* 3.9 23.6 - - + -
202B LEU* 3.9 26.5 - - + -
213B LEU* 5.4 2.9 - - + -
217B LEU* 5.6 0.2 - - + -
272B VAL* 2.9 36.3 + - + +
273B VAL* 3.6 7.4 - - + +
275B VAL* 1.3 76.7 - - - +
277B ASN* 1.3 60.0 + - - +
278B GLN* 3.0 8.4 + - - +
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Residues in contact with ASN 277 (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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89B GLN* 3.1 35.1 + - - +
92B ARG* 3.6 19.8 - - - +
96B TRP* 2.8 29.7 + - - +
273B VAL* 2.9 27.5 + - - +
274B LYS* 3.2 7.8 + - - +
276B LEU* 1.3 73.6 - - - +
278B GLN* 1.3 69.3 + - - +
279B GLU* 3.4 30.7 + - + +
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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