Contacts of the helix formed by residues 261 - 277 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183L LEU* 3.9 26.0 - - + -
186L ILE* 4.0 17.0 - - + -
187L PHE* 5.7 1.3 - - + -
221L PHE* 3.9 33.0 - - + -
224L LEU* 4.0 13.0 - - + -
247L LEU* 3.4 45.2 + - + +
248L PHE* 5.3 3.9 + - + +
250L ASN 4.2 5.7 + - - -
252L TYR* 4.2 9.1 - - + -
259L MET 3.9 1.0 + - - -
260L PHE* 1.3 73.9 - - - +
262L THR* 1.3 58.4 + - - +
264L ILE* 3.2 13.6 + - + +
265L ALA* 2.9 30.3 + - + +
286L PHE* 5.4 0.2 - - + -
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Residues in contact with THR 262 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1L MET* 4.2 13.0 - - + -
2L GLY 5.7 0.9 - - - +
38L ASP* 3.4 28.2 + - - +
186L ILE* 4.3 17.7 - - + +
189L ARG* 3.7 20.0 + - - +
190L GLU* 4.1 3.9 - - - +
248L PHE* 4.6 9.5 - - - +
260L PHE* 3.3 3.7 - - - +
261L LEU* 1.3 80.6 - - - +
263L ASN* 1.3 69.0 + - - +
265L ALA* 3.4 7.7 + - - +
266L THR* 2.9 31.8 + - - +
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Residues in contact with ASN 263 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1L MET* 5.4 5.7 - - - +
259L MET* 3.9 18.8 - - + +
260L PHE* 3.2 27.5 + - - +
262L THR* 1.3 84.7 - - - +
264L ILE* 1.3 66.7 + - - +
266L THR* 3.4 8.9 + - - -
267L ASP* 3.1 21.7 + - - +
21R T 4.9 1.2 + - - -
22R G 3.7 23.4 + - - +
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Residues in contact with ILE 264 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221L PHE* 3.9 25.6 - - + -
252L TYR* 3.9 22.4 - - + +
254L TYR* 3.7 51.3 - - + -
259L MET* 3.7 34.3 - - + +
260L PHE 3.0 13.8 + - - +
261L LEU* 3.5 14.6 - - + +
263L ASN* 1.3 76.0 - - - +
265L ALA* 1.3 54.3 + - - +
267L ASP* 3.0 4.0 + - - +
268L TYR* 2.7 32.6 + - + +
286L PHE* 4.3 5.8 - - + -
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Residues in contact with ALA 265 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186L ILE* 3.5 31.6 - - + -
187L PHE* 3.6 31.2 - - + -
190L GLU* 4.0 4.2 - - + +
261L LEU* 2.9 17.3 + - + +
262L THR 3.6 2.7 - - - +
263L ASN 3.3 0.2 - - - -
264L ILE* 1.3 76.4 - - - +
266L THR* 1.3 56.1 + - - +
268L TYR* 4.3 1.8 - - - -
269L THR* 2.7 36.8 + - - -
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Residues in contact with THR 266 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1L MET* 5.6 2.6 - - - +
190L GLU* 3.1 32.2 + - - +
194L THR* 5.9 0.3 - - - +
262L THR* 2.9 19.3 + - - +
263L ASN* 3.5 11.2 + - - -
264L ILE 3.1 0.4 - - - -
265L ALA* 1.3 77.8 - - - +
267L ASP* 1.3 63.2 + - - +
269L THR* 3.8 1.0 - - - -
270L LYS* 3.0 26.4 + - + +
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Residues in contact with ASP 267 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254L TYR* 2.7 35.5 + - + -
255L LYS* 2.9 19.7 + - - -
259L MET* 5.2 5.8 - - + -
263L ASN 3.1 8.1 + - - +
264L ILE 3.0 6.7 + - - +
266L THR* 1.3 79.8 - - - +
268L TYR* 1.3 63.0 + - - +
270L LYS* 3.3 11.0 + - - +
271L HIS* 3.0 43.4 + - - -
29Q A 5.3 2.1 + - - -
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Residues in contact with TYR 268 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108L ILE* 3.9 15.7 - - + +
111L GLN* 3.3 20.7 + - - -
187L PHE* 4.2 9.2 - + - -
217L LEU* 3.7 23.8 - - + -
220L PRO* 3.3 17.5 - - + +
221L PHE* 4.0 22.2 - + + -
254L TYR* 3.6 20.3 + + + +
264L ILE 2.7 23.5 + - - +
265L ALA* 3.9 5.2 - - - +
267L ASP* 1.3 74.9 - - - +
269L THR* 1.3 64.8 + - - +
271L HIS 3.4 0.2 + - - -
272L VAL* 3.0 44.0 + - + +
284L PRO* 3.3 39.3 + - + +
286L PHE* 4.2 10.1 - - + -
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Residues in contact with THR 269 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187L PHE* 3.4 23.0 - - - -
190L GLU* 3.7 25.4 - - + +
191L LEU* 3.8 23.6 - - + -
194L THR* 4.3 6.3 - - + -
217L LEU* 3.6 25.3 - - + +
265L ALA 2.7 20.9 + - - -
266L THR 3.8 2.5 - - - -
268L TYR* 1.3 77.6 - - - +
270L LYS* 1.3 62.6 + - - +
272L VAL* 3.2 2.7 + - - +
273L VAL* 3.0 23.9 + - + +
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Residues in contact with LYS 270 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194L THR* 4.6 13.6 - - + +
266L THR* 3.0 20.6 + - + +
267L ASP* 3.8 8.7 + - - +
269L THR* 1.3 74.9 - - - +
271L HIS* 1.3 79.7 + - + +
273L VAL* 3.4 8.0 + - - +
274L LYS* 3.0 44.7 + - + +
29Q A 4.1 4.4 + - - -
30Q T 2.5 34.3 + - - -
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Residues in contact with HIS 271 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255L LYS* 3.5 14.1 + - - -
267L ASP* 3.0 53.5 + - - +
270L LYS* 1.3 88.9 + - + +
272L VAL* 1.3 65.9 + - - +
274L LYS* 3.0 16.2 + - + +
275L VAL* 2.9 29.7 + - - +
280L GLU* 2.7 34.0 + - - +
284L PRO* 3.8 20.0 - - + -
29Q A 4.3 15.8 + - - -
30Q T 6.0 1.6 - - - -
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Residues in contact with VAL 272 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104L VAL* 4.0 15.7 - - + -
108L ILE* 4.3 7.6 - - + -
217L LEU* 3.8 26.7 - - + -
268L TYR* 3.0 45.1 + - + +
269L THR* 3.6 8.1 - - - +
271L HIS* 1.3 75.5 - - - +
273L VAL* 1.3 59.9 + - + +
275L VAL* 3.3 9.5 + - - +
276L LEU* 2.9 42.8 + - + +
283L VAL* 5.1 2.9 - - + -
284L PRO* 3.9 15.0 - - + +
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Residues in contact with VAL 273 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89L GLN* 3.6 31.6 - - - +
96L TRP* 4.5 6.1 - - + -
191L LEU* 4.2 15.5 - - + -
194L THR* 4.1 15.3 - - + +
196L CYS* 3.9 20.6 - - - -
217L LEU* 5.5 0.2 - - + -
269L THR* 3.0 19.4 + - + +
270L LYS* 3.5 11.0 - - - +
272L VAL* 1.3 80.5 - - + +
274L LYS* 1.3 57.9 + - + +
276L LEU* 3.3 8.7 + - + +
277L ASN* 2.9 35.0 + - - +
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Residues in contact with LYS 274 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270L LYS* 3.0 38.3 + - + +
271L HIS* 3.0 20.5 + - + +
273L VAL* 1.3 76.9 - - + +
275L VAL* 1.3 60.9 + - - +
277L ASN* 3.2 10.6 + - - +
278L GLN 3.1 4.0 + - - -
279L GLU* 2.9 51.8 + - + +
280L GLU* 3.8 31.3 + - + +
30Q T 4.1 17.2 + - - -
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Residues in contact with VAL 275 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100L ARG* 3.0 29.7 + - - +
104L VAL* 3.4 25.6 - - + -
271L HIS 2.9 20.8 + - - +
272L VAL* 4.0 3.6 - - - +
274L LYS* 1.3 73.7 - - - +
276L LEU* 1.3 66.4 + - - +
278L GLN 3.0 9.0 + - - -
280L GLU* 3.3 30.1 - - + +
282L GLY 3.7 27.4 - - - +
283L VAL* 3.9 19.3 - - + +
284L PRO* 4.5 0.2 - - + -
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Residues in contact with LEU 276 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96L TRP* 3.3 58.3 - - + +
100L ARG* 3.7 16.6 - - + +
101L LYS* 4.0 22.4 - - + +
104L VAL* 3.9 24.2 - - + -
202L LEU* 3.9 26.5 - - + -
213L LEU* 5.4 3.1 - - + -
217L LEU* 5.6 0.2 - - + -
272L VAL* 2.9 35.6 + - + +
273L VAL* 3.3 7.2 + - + +
275L VAL* 1.3 75.5 - - - +
277L ASN* 1.3 57.7 + - - +
278L GLN* 3.1 8.3 + - - +
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Residues in contact with ASN 277 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89L GLN* 3.1 34.3 + - - +
92L ARG* 3.6 20.7 - - - +
96L TRP* 2.8 29.9 + - - +
273L VAL* 2.9 27.3 + - - +
274L LYS* 3.2 8.2 + - - +
276L LEU* 1.3 73.9 - - - +
278L GLN* 1.3 70.8 + - - +
279L GLU* 3.4 32.1 + - + +
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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
------------------------------------------------------------
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