Contacts of the helix formed by residues 261 - 277 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183K LEU* 3.9 26.7 - - + -
186K ILE* 4.1 15.5 - - + -
187K PHE* 5.8 1.6 - - + -
221K PHE* 3.9 32.8 - - + -
224K LEU* 4.0 12.1 - - + -
247K LEU* 3.4 44.3 + - + +
248K PHE* 5.3 4.1 + - + +
250K ASN 4.2 5.5 + - - -
252K TYR* 4.2 8.7 - - + -
259K MET 3.9 1.0 + - - -
260K PHE* 1.3 73.4 - - - +
262K THR* 1.3 58.2 + - + +
264K ILE* 3.2 13.3 + - + +
265K ALA* 2.9 29.0 + - + +
286K PHE* 5.4 0.4 - - + -
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Residues in contact with THR 262 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43K GLU* 5.8 0.7 - - - +
186K ILE* 4.5 13.0 - - + -
189K ARG* 4.5 18.4 - - - +
190K GLU* 4.3 4.9 - - - +
248K PHE* 4.4 23.1 - - + +
260K PHE* 4.6 5.0 - - - +
261K LEU* 1.3 77.8 - - - +
263K ASN* 1.3 68.0 + - - +
265K ALA* 3.4 7.4 + - - +
266K THR* 2.9 30.6 + - - -
26O T 5.5 1.1 - - - +
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Residues in contact with ASN 263 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259K MET* 3.8 21.2 - - + +
260K PHE* 3.2 26.4 + - - +
262K THR* 1.3 84.9 + - - +
264K ILE* 1.3 65.0 + - - +
266K THR* 3.4 8.2 + - - -
267K ASP* 3.2 21.8 + - - +
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Residues in contact with ILE 264 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221K PHE* 3.9 24.0 - - + -
252K TYR* 3.9 22.2 - - + +
254K TYR* 3.6 54.3 - - + -
259K MET* 3.7 34.7 - - + +
260K PHE 3.0 16.0 + - - +
261K LEU* 3.5 12.8 - - + +
263K ASN* 1.3 76.4 - - - +
265K ALA* 1.3 53.7 + - - +
267K ASP* 3.0 3.8 + - - +
268K TYR* 2.7 35.8 + - + +
286K PHE* 4.3 6.1 - - + -
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Residues in contact with ALA 265 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186K ILE* 3.5 33.0 - - + -
187K PHE* 3.6 30.3 - - + -
190K GLU* 4.0 4.2 - - + +
221K PHE* 5.2 0.2 - - - -
261K LEU* 2.9 16.5 + - + +
262K THR 3.7 2.7 - - - +
263K ASN 3.3 0.2 - - - -
264K ILE* 1.3 76.6 - - - +
266K THR* 1.3 56.7 + - - +
268K TYR* 4.2 1.8 - - - -
269K THR* 2.7 36.4 + - - -
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Residues in contact with THR 266 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190K GLU* 3.1 33.2 + - - +
193K GLN* 5.4 3.6 - - - +
262K THR 2.9 17.0 + - - -
263K ASN* 3.5 10.8 - - - -
264K ILE 3.1 0.2 - - - -
265K ALA* 1.3 78.9 - - - +
267K ASP* 1.3 63.4 + - - +
269K THR* 3.9 0.9 - - - -
270K LYS* 3.0 56.5 + - + +
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Residues in contact with ASP 267 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254K TYR* 2.7 35.1 + - + -
255K LYS* 2.9 19.9 + - - -
259K MET* 5.2 5.6 - - + -
263K ASN 3.2 8.7 + - - +
264K ILE 3.0 7.3 + - - +
266K THR* 1.3 77.9 - - - +
268K TYR* 1.3 67.2 + - - +
270K LYS* 3.9 5.5 - - - +
271K HIS* 3.0 48.1 + - - -
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Residues in contact with TYR 268 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108K ILE* 3.9 16.1 - - + +
111K GLN* 3.3 21.2 + - - -
187K PHE* 4.1 9.6 - + - -
217K LEU* 3.6 24.5 - - + -
220K PRO* 3.3 18.1 - - + +
221K PHE* 3.9 22.0 - + + -
254K TYR* 3.6 20.5 + + + +
264K ILE 2.7 22.6 + - - +
265K ALA* 3.8 5.8 - - - +
267K ASP* 1.3 75.7 - - - +
269K THR* 1.3 65.0 + - - +
271K HIS 3.3 0.2 + - - -
272K VAL* 3.0 44.6 + - + +
284K PRO* 3.3 38.7 + - + +
286K PHE* 4.2 9.0 - - + -
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Residues in contact with THR 269 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187K PHE* 3.4 22.3 - - - -
190K GLU* 3.7 23.2 - - + +
191K LEU* 3.8 25.8 - - + +
194K THR* 4.3 6.5 - - + -
217K LEU* 3.7 24.2 - - + +
265K ALA 2.7 23.0 + - - -
266K THR 3.9 2.0 - - - -
268K TYR* 1.3 73.8 - - - +
270K LYS* 1.3 67.3 + - - +
271K HIS 3.2 0.2 + - - -
272K VAL* 3.2 2.6 + - - +
273K VAL* 3.0 23.0 + - + +
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Residues in contact with LYS 270 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190K GLU* 5.8 0.7 - - - +
193K GLN* 6.0 1.3 - - - -
194K THR* 4.4 19.3 - - + -
266K THR* 3.0 45.3 + - + +
267K ASP* 3.9 5.8 - - - +
269K THR* 1.3 76.9 - - - +
271K HIS* 1.3 62.9 + - + +
273K VAL* 3.4 7.5 + - - +
274K LYS* 3.0 34.1 + - + +
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Residues in contact with HIS 271 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255K LYS* 3.5 14.1 + - - -
267K ASP* 3.0 53.8 + - - +
270K LYS* 1.3 81.4 - - + +
272K VAL* 1.3 66.3 + - - +
274K LYS* 3.1 11.4 + - + +
275K VAL* 2.9 26.3 + - - +
280K GLU* 2.7 35.0 + - - +
284K PRO* 3.8 22.0 - - + -
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Residues in contact with VAL 272 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104K VAL* 4.0 15.5 - - + -
108K ILE* 4.3 7.9 - - + -
217K LEU* 3.8 28.0 - - + -
268K TYR* 3.0 45.8 + - + +
269K THR* 3.2 7.2 + - - +
271K HIS* 1.3 74.3 - - - +
273K VAL* 1.3 58.6 + - + +
275K VAL* 3.2 7.5 + - - +
276K LEU* 2.9 42.8 + - + +
283K VAL* 5.1 4.3 - - + -
284K PRO* 3.9 16.8 - - + +
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Residues in contact with VAL 273 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89K GLN* 3.7 22.2 - - - +
96K TRP* 4.5 5.8 - - + -
191K LEU* 4.2 16.2 - - + -
194K THR* 4.1 15.3 - - + +
196K CYS* 4.0 20.0 - - - -
269K THR* 3.0 18.8 + - + +
270K LYS* 3.6 10.3 - - - +
272K VAL* 1.3 80.5 - - + +
274K LYS* 1.3 57.4 + - + +
276K LEU* 3.2 8.8 + - + +
277K ASN* 2.8 45.4 + - - +
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Residues in contact with LYS 274 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270K LYS* 3.0 20.4 + - + +
271K HIS* 3.1 16.6 + - + +
273K VAL* 1.3 76.8 - - + +
275K VAL* 1.3 61.7 + - - +
277K ASN* 3.2 4.8 + - - +
278K GLN 3.1 4.0 + - - -
279K GLU* 2.9 57.8 + - + +
280K GLU* 3.9 29.4 - - + +
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Residues in contact with VAL 275 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100K ARG* 3.1 40.0 + - - +
104K VAL* 3.6 22.9 - - + -
271K HIS 2.9 18.5 + - - +
272K VAL* 3.6 8.3 - - - +
274K LYS* 1.3 73.9 - - - +
276K LEU* 1.3 65.7 + - - +
278K GLN 3.0 9.0 + - - -
280K GLU* 3.4 25.4 - - + +
282K GLY 3.6 34.5 - - - +
283K VAL* 4.1 12.1 - - + +
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Residues in contact with LEU 276 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96K TRP* 3.3 56.0 - - + +
100K ARG* 3.7 17.1 - - + +
101K LYS* 4.0 22.9 - - + +
104K VAL* 3.9 23.8 - - + -
202K LEU* 3.9 28.0 - - + -
213K LEU* 5.4 2.7 - - + -
217K LEU* 5.6 0.7 - - + -
272K VAL* 2.9 35.3 + - + +
273K VAL* 3.6 7.0 - - + +
275K VAL* 1.3 77.3 - - - +
277K ASN* 1.3 58.9 + - - +
278K GLN* 3.2 8.5 + - - +
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Residues in contact with ASN 277 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89K GLN* 3.1 34.8 + - - +
92K ARG* 3.6 23.0 - - - +
96K TRP* 2.8 29.6 + - - +
273K VAL* 2.8 27.5 + - - +
274K LYS* 3.5 6.0 - - - +
275K VAL 3.2 0.2 - - - -
276K LEU* 1.3 74.4 - - - +
278K GLN* 1.3 69.0 + - - +
279K GLU* 3.4 26.3 + - + +
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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