Contacts of the helix formed by residues 169 - 181 (chain A) in PDB entry 1UOU
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 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A ILE* 5.5 0.4 - - - +
168A GLN* 1.3 74.8 - - - +
170A PRO* 1.3 68.9 - - - +
171A GLU* 3.4 16.2 - - - +
172A GLN* 2.9 36.3 + - - +
173A MET* 2.9 28.0 + - - +
190A GLN* 3.6 18.4 - - - +
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Residues in contact with PRO 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A GLN* 3.5 29.8 - - + +
102A LEU* 3.5 33.0 - - + +
104A TRP* 5.1 1.4 - - - -
168A GLN 4.6 0.9 - - - +
169A SER* 1.3 87.6 - - - +
171A GLU* 1.3 70.5 + - - +
173A MET* 3.3 8.0 + - + +
174A GLN* 3.2 28.2 + - - +
190A GLN* 3.9 20.0 - - + +
191A LEU* 4.2 12.1 - - + -
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Residues in contact with GLU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A GLN* 4.9 3.3 + - - -
169A SER* 3.4 19.2 + - - +
170A PRO* 1.3 88.0 - - - +
172A GLN* 1.3 63.7 + - + +
174A GLN* 3.1 25.7 + - - +
175A VAL* 3.4 14.1 + - - +
190A GLN* 4.5 6.8 - - - +
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Residues in contact with GLN 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ILE 4.6 2.4 + - - +
168A GLN* 3.7 30.1 + - + +
169A SER* 2.9 42.1 + - - +
171A GLU* 1.3 78.2 - - + +
173A MET* 1.3 57.6 + - - +
175A VAL* 3.2 11.5 + - - +
176A LEU* 2.9 31.0 + - + +
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Residues in contact with MET 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LEU* 3.7 28.3 - - + -
104A TRP* 4.3 9.0 - - + -
141A PRO* 3.8 19.5 - - + +
143A ILE* 4.5 3.8 - - + -
168A GLN* 4.2 8.7 - - + +
169A SER 2.9 16.7 + - - +
170A PRO* 3.6 9.0 - - + +
171A GLU 3.2 0.2 - - - -
172A GLN* 1.3 76.5 - - - +
174A GLN* 1.3 56.9 - - - +
176A LEU* 3.2 9.7 + - - +
177A LEU* 3.0 31.7 + - - +
183A CYS* 3.7 23.3 - - - -
185A VAL* 3.7 29.4 - - + -
191A LEU* 3.7 27.6 - - - -
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Residues in contact with GLN 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A GLU* 3.2 19.9 + - - +
104A TRP* 3.5 28.0 - - + -
105A PRO* 5.3 6.8 - - + +
108A TRP* 4.0 7.8 - - + -
170A PRO* 3.2 17.1 + - - +
171A GLU* 3.1 16.5 + - - +
173A MET* 1.3 73.2 - - - +
175A VAL* 1.3 66.1 + - + +
177A LEU* 3.5 1.2 + - - +
178A ASP* 3.1 29.0 + - - +
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Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A GLU 3.4 10.1 + - - +
172A GLN* 3.2 12.0 + - - +
174A GLN* 1.3 76.3 - - + +
176A LEU* 1.3 66.4 + - + +
178A ASP* 3.2 12.8 + - + +
179A GLN* 3.1 48.6 + - + +
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Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A GLN* 3.6 25.8 - - + +
172A GLN 2.9 17.2 + - - +
173A MET* 3.2 9.4 + - - +
175A VAL* 1.3 77.3 - - + +
177A LEU* 1.3 60.1 + - - +
179A GLN* 4.7 0.4 - - - +
180A ALA* 3.0 32.7 + - - +
181A GLY 3.6 0.2 + - - -
182A CYS 3.7 3.9 - - - +
183A CYS* 3.5 29.8 - - + -
346A MET* 4.7 1.6 - - - +
349A ALA* 3.1 50.9 - - + +
350A GLN* 3.5 26.0 - - + +
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A TRP* 3.6 29.6 - - + -
108A TRP* 3.5 25.1 - - + -
112A LEU* 4.0 7.0 - - + -
139A LYS* 2.7 49.7 + - + -
140A VAL 4.0 10.5 - - - +
141A PRO* 4.0 14.4 - - + -
173A MET 3.0 20.1 + - - +
174A GLN 3.5 1.1 + - - +
175A VAL 3.2 0.2 - - - -
176A LEU* 1.3 77.9 - - - +
178A ASP* 1.3 53.1 + - - +
181A GLY* 3.1 16.4 + - - +
182A CYS* 3.6 33.2 - - - +
183A CYS* 4.0 5.4 - - - +
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Residues in contact with ASP 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A TRP* 3.3 22.5 - - - -
139A LYS* 4.3 7.1 + - - +
174A GLN* 3.1 19.3 + - - +
175A VAL* 3.2 14.6 + - + +
177A LEU* 1.3 80.2 - - - +
179A GLN* 1.3 63.7 + - + +
180A ALA 3.9 0.2 + - - -
181A GLY 4.9 0.2 + - - -
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Residues in contact with GLN 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A VAL* 3.1 35.3 + - + +
176A LEU 4.3 1.3 - - - +
178A ASP* 1.3 84.8 - - + +
180A ALA* 1.3 58.7 + - - +
342A ARG* 3.3 17.3 + - - -
345A ARG* 3.6 16.4 - - + +
349A ALA* 3.4 32.7 + - + +
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Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ALA* 3.5 5.4 - - - +
176A LEU 3.0 12.3 + - - +
179A GLN* 1.3 78.4 - - + +
181A GLY* 1.3 59.3 + - - +
182A CYS* 3.2 21.3 + - - +
342A ARG* 3.2 31.5 - - - +
345A ARG* 3.6 10.8 - - + +
346A MET* 3.6 32.1 - - + +
349A ALA* 5.0 2.2 - - + -
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Residues in contact with GLY 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ALA* 3.7 10.6 - - - +
138A CYS 3.5 4.6 - - - +
139A LYS* 3.1 22.9 - - - +
140A VAL 2.8 22.5 + - - -
176A LEU 3.6 0.4 + - - -
177A LEU* 3.1 25.1 + - - -
178A ASP 4.7 0.4 + - - -
179A GLN 3.9 0.2 - - - -
180A ALA* 1.3 76.0 - - - +
182A CYS* 1.3 59.3 + - - +
342A ARG* 5.4 0.4 - - - -
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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