Contacts of the helix formed by residues 181 - 195 (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 SER 181 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156B GLN* 3.8 28.5 - - - -
160B ASP* 4.4 5.8 + - - -
115C GLN* 2.9 26.2 + - - +
180V LEU* 1.3 75.7 - - - +
182V ALA* 1.3 57.9 + - - +
183V LYS* 3.8 3.5 + - - +
184V ASN* 3.2 30.0 + - - +
185V TYR* 2.9 28.4 + - - +
211V PHE 3.7 10.8 - - - -
212V MET* 3.8 0.7 - - - -
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Residues in contact with ALA 182 (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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156B GLN* 5.2 1.6 - - - +
157B VAL* 5.8 4.9 - - + -
181V SER* 1.3 72.7 - - - +
183V LYS* 1.3 63.5 - - - +
185V TYR* 3.1 4.7 + - - +
186V GLY 3.1 18.0 + - - -
211V PHE 4.5 0.4 + - - -
212V MET* 3.7 25.0 - - + +
216V ASP* 3.6 30.5 - - + -
217V ARG* 3.6 15.8 - - - +
220V PHE* 3.6 18.8 - - + +
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Residues in contact with LYS 183 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ASP* 3.5 43.5 + - + +
163B ASN* 2.9 27.5 - - - +
165B TYR* 2.8 32.6 + - - +
71C ARG* 4.9 6.7 + - - +
72C TYR* 2.5 48.9 + - + +
106C ARG* 5.9 0.4 - - - +
117C GLN* 5.1 0.4 + - - -
181V SER* 3.3 3.0 + - - +
182V ALA* 1.3 77.7 - - - +
184V ASN* 1.3 59.6 + - - +
187V ARG* 2.9 39.7 + - - +
220V PHE* 3.5 13.7 - - + -
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Residues in contact with ASN 184 (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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110C PHE* 5.0 4.6 - - - -
115C GLN* 3.0 39.0 + - - +
116C VAL* 6.1 0.4 - - - +
74O LEU* 3.7 33.8 + - + +
180V LEU* 4.1 14.6 - - + +
181V SER* 3.2 16.8 + - - +
183V LYS* 1.3 74.8 - - - +
185V TYR* 1.3 60.0 + - - +
187V ARG* 3.0 29.0 + - - +
188V ALA* 2.9 30.7 + - - +
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Residues in contact with TYR 185 (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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174V ILE* 3.5 36.9 + - + +
176V PRO 5.0 2.0 - - - -
177V LYS 4.7 4.4 + - - -
180V LEU* 4.0 21.5 - - + +
181V SER 2.9 11.7 + - - +
182V ALA* 3.3 10.3 - - - +
184V ASN* 1.3 77.7 - - - +
186V GLY* 1.3 56.8 + - - +
188V ALA* 3.3 3.0 + - - +
189V VAL* 2.9 33.6 + - + +
202V ASP* 3.3 24.0 - - - -
203V ASP 3.2 27.0 + - - -
206V VAL* 3.7 14.7 - - + +
212V MET* 3.6 31.6 - - + -
217V ARG* 3.7 16.4 - - + -
221V VAL* 4.2 7.4 - - + -
238V HIS* 3.8 10.5 - - - -
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Residues in contact with GLY 186 (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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72C TYR* 3.2 20.2 - - - -
182V ALA 3.1 11.6 + - - -
183V LYS 3.3 0.2 + - - -
185V TYR* 1.3 72.5 - - - +
187V ARG* 1.3 60.4 + - - +
189V VAL* 4.1 6.7 - - - -
190V TYR* 2.9 27.4 + - - +
220V PHE 4.1 17.0 - - - -
221V VAL* 4.4 3.5 - - - +
224V ALA* 3.1 10.6 - - - +
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Residues in contact with ARG 187 (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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43C GLU* 2.9 29.7 + - - -
72C TYR* 3.2 22.1 + - + -
75C MET* 3.8 29.7 - - + +
106C ARG* 5.8 1.0 - - - +
110C PHE* 3.8 29.2 - - - -
117C GLN* 4.4 5.7 + - - -
70O TRP* 5.2 3.1 - - + -
74O LEU* 4.6 10.3 - - + -
183V LYS* 2.9 49.2 + - - +
184V ASN* 3.0 30.9 + - - +
185V TYR 3.3 0.2 - - - -
186V GLY* 1.3 76.6 - - - +
188V ALA* 1.3 63.3 + - - +
190V TYR* 3.4 4.8 + - - +
191V GLU* 3.2 30.5 + - + +
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Residues in contact with ALA 188 (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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70O TRP* 5.2 2.7 - - + -
71O THR* 4.5 11.0 - - + -
174V ILE* 4.1 23.8 - - + -
180V LEU* 5.0 1.1 - - + -
184V ASN 2.9 17.4 + - - +
185V TYR 3.7 4.5 - - - +
187V ARG* 1.3 78.1 - - - +
189V VAL* 1.3 58.0 + - - +
191V GLU* 3.4 1.5 + - - -
192V CYS* 3.0 27.5 + - - -
407V LEU* 4.3 6.7 - - + -
413V ASN* 3.1 26.8 + - - +
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Residues in contact with VAL 189 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174V ILE* 3.8 16.8 - - + -
185V TYR* 2.9 24.0 + - + +
186V GLY* 3.6 6.3 - - - +
187V ARG 3.3 0.2 - - - -
188V ALA* 1.3 72.1 - - - +
190V TYR* 1.3 67.6 + - - +
192V CYS* 3.2 2.8 + - - +
193V LEU* 2.9 39.3 + - + +
200V THR* 3.4 17.7 - - - +
221V VAL* 4.2 16.2 - - + +
224V ALA* 3.8 12.6 - - + -
238V HIS* 3.3 33.0 - - + +
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Residues in contact with TYR 190 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C TYR* 4.8 9.2 - + + -
73C TRP 3.5 19.7 - - - -
74C THR* 2.8 21.3 + - - -
186V GLY 2.9 17.2 + - - +
187V ARG* 3.4 5.1 + - - +
189V VAL* 1.3 76.9 - - - +
191V GLU* 1.3 88.3 + - + +
193V LEU* 4.0 0.7 - - - +
194V ARG* 3.0 43.8 + - + +
224V ALA* 3.5 19.7 - - + +
227V LYS* 3.4 38.8 - - + -
228V ALA* 4.0 15.0 - - + -
231V GLU* 2.6 29.9 + - - -
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Residues in contact with GLU 191 (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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73C TRP 4.1 1.2 - - - +
74C THR* 3.8 0.3 - - - -
75C MET* 3.0 48.5 + - + +
70O TRP* 5.7 2.2 - - + -
187V ARG* 3.2 23.6 + - + +
188V ALA* 3.9 2.7 - - - +
190V TYR* 1.3 92.8 - - + +
192V CYS* 1.3 61.3 + - - +
194V ARG* 2.9 37.7 + - - +
195V GLY 3.7 0.2 + - - -
413V ASN* 3.6 22.2 - - + +
414V ALA* 3.1 32.0 + - - +
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Residues in contact with CYS 192 (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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172V CYS* 3.8 24.0 - - - -
174V ILE* 4.0 11.0 - - - -
188V ALA 3.0 24.1 + - - +
189V VAL 3.2 0.6 + - - +
191V GLU* 1.3 74.1 - - - +
193V LEU* 1.3 65.1 + - - +
195V GLY 3.4 1.7 + - - -
197V LEU* 3.7 13.4 - - + +
200V THR* 3.5 19.1 - - + -
406V THR* 4.0 6.1 - - - -
407V LEU* 4.1 2.9 - - - -
413V ASN* 3.5 29.2 - - - -
417V ALA* 3.0 25.1 - - - +
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Residues in contact with LEU 193 (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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189V VAL* 2.9 39.6 + - + +
192V CYS* 1.3 73.0 - - - +
194V ARG* 1.3 60.7 + - - +
195V GLY 3.2 1.0 + - - -
196V GLY 3.3 4.0 + - - -
197V LEU* 3.4 15.6 - - + +
198V ASP 3.8 5.2 - - - +
199V PHE 3.6 22.4 - - - +
200V THR* 3.7 7.4 - - + +
224V ALA 4.4 0.2 - - - +
225V ILE* 3.9 27.8 - - + +
228V ALA* 3.5 15.9 - - + -
236V LYS* 2.7 42.9 + - + -
237V GLY 3.6 24.0 - - - +
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Residues in contact with ARG 194 (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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74C THR* 3.4 20.4 - - - +
75C MET 4.7 1.8 + - - -
190V TYR* 3.0 52.6 + - + +
191V GLU* 2.9 30.5 + - - +
193V LEU* 1.3 77.5 - - - +
195V GLY* 1.3 61.2 + - - +
196V GLY 3.3 0.8 + - - -
228V ALA* 4.0 5.8 - - + -
231V GLU* 2.9 31.0 + - - +
232V THR* 3.5 23.0 - - + +
414V ALA* 3.7 10.4 - - + +
3W VAL* 4.6 4.8 - - - +
4W TRP* 2.6 60.6 + - - +
5W THR 3.8 2.0 - - - -
6W PRO* 3.6 11.3 - - - +
17W TYR* 4.3 1.7 + - - -
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Residues in contact with GLY 195 (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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191V GLU 3.7 0.8 + - - -
192V CYS 3.4 3.4 + - - -
193V LEU 3.1 1.6 - - - -
194V ARG* 1.3 81.3 - - - +
196V GLY* 1.3 55.2 + - - +
414V ALA* 3.5 24.5 - - - -
417V ALA* 3.6 11.7 - - - -
418V ALA* 3.1 26.3 + - - +
4W TRP* 4.1 10.9 - - - -
17W TYR* 3.3 13.4 - - - -
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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