Contacts of the helix formed by residues 170 - 179 (chain A) in PDB entry 1UES
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 ARG 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A THR* 3.5 23.6 + - - +
167A TYR* 2.8 43.4 + - - +
168A GLN* 3.2 6.4 + - - +
169A ASN* 1.3 88.3 - - - +
171A ARG* 1.3 63.4 + - - +
172A ALA* 3.3 3.1 - - - +
173A ASP* 2.9 47.8 + - + +
174A HIS 3.2 15.9 + - - -
226B PHE* 6.3 0.4 - - - -
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Residues in contact with ARG 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLY 2.8 28.0 + - - -
116A THR* 3.8 17.7 + - + +
118A LEU 2.8 25.0 + - - -
120A GLY* 3.1 26.9 + - - +
158A VAL* 3.2 33.2 + - + +
160A GLU* 4.9 5.7 + - - +
163A TYR* 3.0 46.3 + - + +
169A ASN 2.8 12.4 + - - +
170A ARG* 1.3 72.1 - - - +
172A ALA* 1.3 64.8 + - - +
174A HIS* 3.1 4.6 + - - +
175A LEU* 3.0 29.6 + - + +
359B TRP* 5.6 3.2 - - - -
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ASN* 5.6 2.5 - - + +
116A THR* 3.7 30.2 + - + +
170A ARG* 3.3 1.0 - - - +
171A ARG* 1.3 78.4 - - - +
173A ASP* 1.3 62.7 + - - +
175A LEU* 3.2 6.3 + - - +
176A LYS* 3.0 29.5 + - - +
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Residues in contact with ASP 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A TYR* 3.8 2.7 - - + -
170A ARG* 2.9 53.1 + - - +
172A ALA* 1.3 80.2 - - - +
174A HIS* 1.3 63.2 + - - +
176A LYS* 2.9 55.6 + - - +
177A ASP* 3.2 6.6 + - - +
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Residues in contact with HIS 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 3.6 17.6 + - - +
19A ILE* 4.4 4.3 - - + -
77A TYR* 4.3 6.8 + - - -
157A ASP 4.5 5.8 + - - -
162A ALA 3.9 11.5 + - - -
163A TYR* 3.5 36.5 - + + +
167A TYR* 3.3 41.0 + + + -
170A ARG 3.2 7.3 + - - +
171A ARG 3.1 9.3 + - - +
173A ASP* 1.3 77.9 - - - +
175A LEU* 1.3 71.4 + - + +
177A ASP* 3.1 4.3 + - - +
178A LEU* 3.0 55.4 + - + +
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Residues in contact with LEU 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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112A ASN* 3.6 42.8 - - + +
115A GLY* 3.7 22.7 - - - +
116A THR* 3.8 11.0 - - - +
156A PHE* 3.8 29.6 - - + -
157A ASP 5.0 0.4 - - - +
158A VAL* 4.0 14.6 - - + -
171A ARG* 3.0 20.8 + - + +
172A ALA* 3.6 6.5 - - - +
174A HIS* 1.3 84.7 - - + +
176A LYS* 1.3 64.4 + - - +
178A LEU* 3.1 27.2 + - + +
179A TRP* 3.2 14.9 + - - -
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Residues in contact with LYS 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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112A ASN* 4.3 10.5 - - - +
167A TYR* 4.9 0.6 - - - -
172A ALA 3.0 10.5 + - - +
173A ASP* 2.9 56.4 + - - +
174A HIS 3.2 0.4 - - - -
175A LEU* 1.3 78.4 - - - +
177A ASP* 1.3 79.4 + - - +
179A TRP* 3.2 28.1 + - - +
180A SER* 4.7 0.7 + - - -
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Residues in contact with ASP 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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18A VAL* 3.6 19.6 - - + +
167A TYR* 2.6 40.4 + - - +
173A ASP 3.2 4.8 + - - +
174A HIS 3.1 7.6 + - - +
176A LYS* 1.3 93.9 + - - +
178A LEU* 1.3 64.4 + - - +
179A TRP 3.1 2.5 - - - -
180A SER* 2.8 30.5 + - - +
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Residues in contact with LEU 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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18A VAL* 3.8 12.8 - - + -
19A ILE* 4.2 6.1 - - + -
77A TYR* 4.7 2.7 - - + +
81A PHE* 4.0 14.1 - - + -
156A PHE* 3.3 53.2 - - + -
157A ASP 5.0 2.2 - - - +
174A HIS* 3.0 47.5 + - + +
175A LEU* 3.1 16.7 + - + +
177A ASP* 1.3 76.3 - - - +
179A TRP* 1.3 63.5 + - - +
181A ILE* 3.0 33.2 + - + +
182A VAL* 3.4 10.9 - - - +
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Residues in contact with TRP 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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86A GLY* 3.4 14.2 - - - -
87A GLY 4.5 3.7 + - - +
104A PHE* 4.2 5.4 - + + -
107A PHE* 3.6 33.0 - + - -
108A LYS* 3.7 50.3 - - + +
111A PHE* 3.6 20.4 - + + -
112A ASN* 2.8 35.8 + - - +
154A LEU* 3.8 10.1 - - + -
156A PHE* 3.5 18.4 - + - -
175A LEU 3.2 10.1 + - - -
176A LYS* 3.2 26.7 - - - +
177A ASP 3.1 0.8 - - - -
178A LEU* 1.3 78.8 - - - +
180A SER* 1.3 60.6 + - - +
181A ILE 3.3 1.0 + - - -
182A VAL* 3.4 16.5 + - + +
184A TRP* 3.8 26.0 + + - -
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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
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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