Contacts of the helix formed by residues 246 - 261 (chain V) in PDB entry 1UW9
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 THR 246 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111O GLY 5.6 1.3 - - - +
275O THR* 3.3 14.3 - - - +
278O THR* 3.8 20.0 - - + -
279O SER* 3.4 5.6 - - - +
282O ILE* 3.9 19.3 - - + -
244V ALA* 3.8 1.1 - - - +
245V GLY* 1.3 84.0 - - - +
247V CYS* 1.3 65.0 + - - +
248V GLU* 3.4 16.7 + - - +
249V GLU* 3.2 26.6 + - + +
250V MET* 3.0 19.2 + - - +
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Residues in contact with CYS 247 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247O CYS* 2.1 50.7 - - + -
251O MET* 6.1 0.9 - - + -
275O THR* 3.3 13.2 - - - +
276O ALA* 3.7 23.3 - - - -
279O SER* 2.7 19.6 + - - +
246V THR* 1.3 70.7 - - - +
248V GLU* 1.3 58.4 + - - +
250V MET* 3.3 9.1 + - + +
251V MET* 3.0 37.5 + - + +
276V ALA* 4.1 4.3 - - - -
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Residues in contact with GLU 248 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251O MET* 4.0 18.7 - - - +
279O SER* 2.7 31.6 + - - +
282O ILE* 5.8 3.3 - - - +
246V THR* 3.4 11.4 - - - +
247V CYS* 1.3 77.1 - - - +
249V GLU* 1.3 61.5 + - + +
251V MET* 4.0 5.1 - - - +
252V LYS* 3.1 31.0 + - + +
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Residues in contact with GLU 249 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109O GLU* 5.2 2.2 - - - +
214V TRP* 3.9 8.7 + - - -
244V ALA* 3.6 19.7 - - + -
245V GLY 4.9 1.3 - - - +
246V THR* 3.2 20.8 + - + +
248V GLU* 1.3 75.8 - - + +
250V MET* 1.3 67.2 + - - +
252V LYS* 2.8 38.0 + - - +
253V ARG* 2.9 57.7 + - - +
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Residues in contact with MET 250 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275O THR* 4.7 3.6 - - + -
242V ALA* 3.2 37.7 - - + +
244V ALA* 3.5 6.1 - - + +
246V THR 3.0 13.0 + - - +
247V CYS* 3.5 19.5 - - + +
249V GLU* 1.3 76.9 - - - +
251V MET* 1.3 85.1 + - + +
253V ARG* 3.3 5.7 + - - +
254V ALA* 3.1 23.0 + - - +
267V HIS* 3.9 21.1 - - + +
276V ALA* 3.5 38.8 - - + +
279V SER* 4.5 2.2 - - - -
280V LEU* 3.9 18.8 - - + -
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Residues in contact with MET 251 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247O CYS* 6.0 1.3 - - + -
248O GLU* 4.0 12.3 - - - +
247V CYS* 3.0 23.0 + - + +
248V GLU* 4.0 5.8 - - - +
250V MET* 1.3 93.8 - - + +
252V LYS* 1.3 60.7 + - - +
254V ALA* 3.2 3.9 + - - +
255V VAL* 2.9 39.9 + - + +
279V SER* 3.8 34.8 - - - +
280V LEU* 4.1 7.6 - - - +
283V TYR* 4.3 27.8 - - + -
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Residues in contact with LYS 252 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B ASP* 3.4 38.1 + - - -
214V TRP* 3.8 17.1 - - + +
248V GLU* 3.1 20.3 + - + +
249V GLU* 2.8 39.1 + - - +
251V MET* 1.3 74.9 - - - +
253V ARG* 1.3 62.5 + - - +
255V VAL* 3.5 8.1 + - - +
256V SMC 3.1 23.4 + - - +
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Residues in contact with ARG 253 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109O GLU* 2.7 42.8 + - - -
207V ASN* 3.9 4.0 - - - +
208V SER* 3.8 12.7 - - - +
214V TRP* 3.4 49.8 - - + -
218V PHE* 3.3 20.7 - - + -
241V ASN 4.2 9.4 + - - -
242V ALA* 4.0 24.5 - - - -
243V THR 3.5 14.8 + - - -
244V ALA* 3.9 7.5 - - - +
249V GLU* 2.9 44.2 + - - +
250V MET 3.5 7.0 - - - +
251V MET 3.1 0.2 - - - -
252V LYS* 1.3 74.3 - - - +
254V ALA* 1.3 64.4 + - - +
256V SMC 3.4 1.9 + - - +
257V ALA* 3.2 17.3 + - - +
265V ILE* 5.6 0.4 - - - -
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Residues in contact with ALA 254 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242V ALA* 4.4 1.6 - - + +
250V MET 3.1 9.3 + - - +
251V MET* 3.2 9.2 + - - +
253V ARG* 1.3 76.1 - - - +
255V VAL* 1.3 56.2 + - - +
257V ALA* 3.3 6.9 + - - +
258V LYS* 3.0 23.4 + - - +
265V ILE* 3.9 18.6 - - + -
280V LEU* 3.8 30.1 - - + -
283V TYR* 3.8 20.4 - - + -
289V LEU* 3.7 7.8 - - + +
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Residues in contact with VAL 255 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251V MET* 2.9 24.9 + - + +
252V LYS* 3.6 8.5 - - - +
254V ALA* 1.3 73.4 - - - +
256V SMC 1.3 60.5 + - - +
258V LYS* 3.1 6.2 + - + +
259V GLU* 2.9 52.6 + - - +
283V TYR* 3.5 28.7 - - + +
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Residues in contact with SMC 256 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C VAL* 4.1 12.8 - - + -
214V TRP* 3.6 35.0 - - + -
215V ARG* 3.8 37.5 - - + +
218V PHE* 3.8 10.8 - - - -
219V LEU* 4.6 2.2 - - + -
252V LYS 3.1 10.5 + - - +
253V ARG 3.7 1.8 - - - +
254V ALA 3.3 0.4 - - - -
255V VAL* 1.3 77.2 + - - +
257V ALA* 1.3 61.8 + - - +
259V GLU* 3.1 6.0 + - - +
260V LEU* 3.0 52.4 + - + +
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Residues in contact with ALA 257 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218V PHE* 4.3 8.0 - - + -
240V LEU* 4.6 2.5 - - + -
253V ARG 3.2 8.7 + - - +
254V ALA 3.5 6.3 - - - +
255V VAL 3.3 0.2 - - - -
256V SMC 1.3 78.7 + - - +
258V LYS* 1.3 62.9 + - - +
260V LEU* 3.2 5.9 + - - -
261V GLY 3.2 16.1 + - - -
262V VAL* 3.5 31.0 + - + +
265V ILE* 3.5 32.1 - - + -
289V LEU* 4.4 6.3 - - + -
65W CYS* 4.1 0.5 - - - -
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Residues in contact with LYS 258 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ARG 5.1 0.9 - - - +
215H ARG* 4.7 4.4 - - - +
259H GLU* 5.1 2.8 + - - -
254V ALA 3.0 9.1 + - - +
255V VAL* 3.1 10.5 + - + +
257V ALA* 1.3 74.8 - - - +
259V GLU* 1.3 64.6 + - + +
261V GLY* 3.1 15.4 + - - -
283V TYR* 3.3 25.8 - - + +
287V ASN* 2.9 33.8 + - + +
289V LEU* 4.2 8.8 - - + +
62W SER* 3.1 42.2 + - - +
63W VAL* 4.2 12.3 - - - +
64W SER 5.5 0.3 + - - -
65W CYS* 3.6 21.9 + - - -
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Residues in contact with GLU 259 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B LYS* 5.1 2.8 + - - -
59C ARG 4.6 0.4 - - - -
60C PHE* 3.1 8.5 - - - -
61C GLY* 2.8 33.6 + - - +
62C SER 5.0 2.2 - - - +
63C VAL* 3.3 35.0 - - + +
255V VAL* 2.9 39.5 + - - +
256V SMC 3.1 8.3 + - - +
258V LYS* 1.3 82.3 - - + +
260V LEU* 1.3 56.0 + - - +
261V GLY 3.3 0.2 - - - -
62W SER* 4.3 20.6 - - - +
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Residues in contact with LEU 260 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ARG 4.0 0.9 - - - +
60C PHE* 3.3 40.5 - - + -
63C VAL* 3.7 20.0 - - + +
67C TYR* 5.3 0.4 - - + -
218V PHE* 4.0 18.2 - - + +
219V LEU* 4.2 19.3 - - + -
222V THR* 3.5 28.3 - - + +
226V TYR* 2.7 25.5 + - - -
240V LEU* 5.4 0.4 - - + -
256V SMC 3.0 43.4 + - + +
257V ALA* 3.2 8.5 + - - +
258V LYS 3.2 0.2 - - - -
259V GLU* 1.3 76.7 - - - +
261V GLY* 1.3 51.4 + - - +
262V VAL* 3.2 6.0 + - + +
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Residues in contact with GLY 261 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ARG* 2.9 27.8 + - - -
226V TYR* 3.2 8.6 + - - -
257V ALA 3.2 0.8 + - - -
258V LYS 3.1 16.5 + - - -
259V GLU 3.3 1.2 + - - -
260V LEU* 1.3 75.7 - - - +
262V VAL* 1.3 63.8 + - - +
263V PRO* 4.0 1.4 - - - +
64W SER* 3.5 22.4 - - - -
65W CYS* 3.8 11.0 - - - -
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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
------------------------------------------------------------
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