Contacts of the helix formed by residues 154 - 163 (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 GLY 154 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151V HYP 4.6 4.8 - - - -
153V HIS* 1.3 74.7 - - - +
155V ILE* 1.3 60.7 + - - -
156V GLN 3.5 2.2 - - - -
157V VAL 3.3 1.0 + - - -
158V GLU* 2.9 32.0 + - - +
324V ASP* 2.9 20.6 + - - -
372V PRO* 3.8 12.7 - - - +
373V GLY 3.2 15.0 - - - -
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Residues in contact with ILE 155 (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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154V GLY* 1.3 70.5 - - - -
156V GLN* 1.3 63.6 + - - +
158V GLU* 3.3 7.9 + - - +
159V ARG* 3.0 29.9 + - + +
350V ARG* 3.8 29.8 - - + +
373V GLY* 3.1 21.6 + - - +
374V VAL 3.6 21.5 - - - +
375V MET* 3.6 35.8 - - + +
376V PRO* 4.7 0.7 - - + -
397V ASP* 3.8 31.4 - - + +
114W LYS* 6.0 0.9 - - - -
116W VAL* 6.6 0.4 - - + -
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Residues in contact with GLN 156 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181H SER* 3.6 22.4 - - - -
182H ALA 5.0 2.2 - - - +
211H PHE 4.3 10.4 + - - +
154V GLY 3.5 0.4 - - - -
155V ILE* 1.3 81.1 - - - +
157V VAL* 1.3 77.1 + - + +
159V ARG* 3.4 2.8 + - - +
160V ASP* 3.0 43.1 + - - +
114W LYS* 3.1 17.7 - - + +
115W GLN* 3.0 34.0 - - - +
116W VAL* 4.2 16.3 - - + +
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Residues in contact with VAL 157 (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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182H ALA* 5.8 4.3 - - + -
216H ASP* 3.4 38.8 - - + +
220H PHE* 5.2 4.0 - - + -
153V HIS* 3.6 35.9 - - + +
154V GLY 3.3 2.4 + - - +
156V GLN* 1.3 94.9 - - + +
158V GLU* 1.3 58.1 + - - +
160V ASP* 3.2 7.3 + - - +
161V LYS* 2.9 42.7 + - + +
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Residues in contact with GLU 158 (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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153V HIS* 5.3 0.4 - - + -
154V GLY 2.9 18.3 + - - +
155V ILE* 3.5 5.9 - - - +
156V GLN 3.2 0.2 - - - -
157V VAL* 1.3 77.5 - - - +
159V ARG* 1.3 62.6 + - - +
161V LYS 3.4 0.3 + - - -
162V LEU* 3.0 46.3 + - + +
169V LEU* 3.7 12.9 - - + +
199V PHE* 3.9 2.8 - - - -
290V PHE* 3.4 31.2 - - + -
324V ASP* 3.9 10.7 - - + +
325V HIS* 2.5 45.6 + - - -
375V MET* 3.9 18.1 - - + +
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Residues in contact with ARG 159 (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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155V ILE* 3.0 26.5 + - + +
156V GLN 3.7 4.3 - - - +
158V GLU* 1.3 76.3 - - + +
160V ASP* 1.3 57.8 + - - +
162V LEU* 3.4 4.9 + - - -
163V ASN* 2.8 25.5 + - - -
164V LYS* 2.8 51.5 + - - +
165V TYR* 3.6 27.6 + - + +
166V GLY 4.7 3.1 - - - -
167V ARG* 2.8 29.0 + - - +
168V GLY* 4.5 0.6 - - - -
169V LEU* 4.1 20.1 - - + +
375V MET* 4.7 9.2 - - + +
396V ASP* 2.8 25.8 + - - +
397V ASP* 3.0 24.0 + - - +
398V ALA 4.8 0.4 - - - +
116W VAL* 4.4 13.2 - - + -
117W GLN 4.8 2.5 - - - -
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Residues in contact with ASP 160 (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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181H SER* 4.5 4.7 + - - -
183H LYS* 3.5 35.1 + - + +
220H PHE* 3.5 29.5 - - + -
156V GLN* 3.0 40.9 + - - +
157V VAL* 3.2 7.1 + - - +
159V ARG* 1.3 77.1 - - - +
161V LYS* 1.3 61.1 - - - +
163V ASN* 3.5 7.4 + - - +
165V TYR* 2.8 26.1 + - - -
71W ARG* 4.5 2.8 + - - -
115W GLN 4.8 1.4 - - - +
116W VAL* 3.8 7.3 - - - +
117W GLN 5.0 1.4 + - - -
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Residues in contact with LYS 161 (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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215H ARG* 5.0 3.0 + - - +
216H ASP* 3.0 35.0 + - - +
219H LEU* 4.4 18.6 - - + +
220H PHE* 3.8 16.6 - - + -
153V HIS* 3.2 20.0 - - - -
157V VAL* 2.9 28.6 + - + +
160V ASP* 1.3 72.8 - - - +
162V LEU* 1.3 62.4 + - - +
288V GLY* 4.0 14.6 + - - -
290V PHE* 3.8 19.7 - - + -
66W LEU* 3.8 32.8 - - + +
68W TYR* 4.3 8.3 - - - -
71W ARG* 2.8 31.6 + - - +
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Residues in contact with LEU 162 (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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158V GLU* 3.0 37.7 + - + +
159V ARG* 4.0 3.6 - - - +
161V LYS* 1.3 74.4 - - - +
163V ASN* 1.3 70.4 + - - +
164V LYS* 3.5 30.3 + - + +
169V LEU* 4.2 11.7 - - + -
199V PHE* 3.6 36.3 - - + -
235V VAL* 3.7 40.4 - - + +
236V LYS 5.8 0.9 - - - +
263V PRO* 5.0 4.3 - - + -
290V PHE* 3.7 18.8 - - + -
13W GLU* 4.8 1.0 - - - +
66W LEU* 4.2 7.0 - - + -
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Residues in contact with ASN 163 (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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183H LYS* 3.0 26.3 - - - +
159V ARG 2.8 8.6 + - - -
160V ASP 3.5 2.8 + - - -
161V LYS 3.3 3.6 - - - -
162V LEU* 1.3 80.1 - - - +
164V LYS* 1.3 60.6 + - - +
165V TYR* 3.6 15.2 - - - -
235V VAL* 5.3 2.0 - - + -
13W GLU* 4.1 14.7 - - - +
52W VAL* 5.9 0.9 - - + +
70W ASN 5.0 0.3 - - - +
71W ARG* 3.7 46.9 + - + +
106W ARG* 3.9 19.1 + - - +
117W GLN* 5.4 0.2 + - - -
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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