Contacts of the helix formed by residues 156 - 173 (chain A) in PDB entry 1U5H
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 156 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ILE* 5.2 4.0 - - + -
147A SER* 2.9 38.9 + - - -
148A SER* 2.9 18.7 + - - +
149A ARG 3.3 18.5 + - - -
150A ARG* 3.8 28.9 - - + +
151A ALA 5.0 1.0 - - - +
155A TYR* 1.3 77.6 - - - +
157A ASP* 1.3 67.9 + - - +
158A VAL* 3.3 11.7 - - + +
159A ALA* 3.1 12.8 + - + +
160A ARG* 3.2 8.3 + - - +
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Residues in contact with ASP 157 (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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150A ARG* 5.9 0.7 + - - -
155A TYR 4.9 0.3 - - - +
156A ARG* 1.3 73.9 - - - +
158A VAL* 1.3 56.6 + - - +
160A ARG* 3.1 27.7 + - - +
161A HIS* 2.8 29.9 + - - +
274A FMT 5.1 7.2 - - - +
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Residues in contact with VAL 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 4.5 4.5 - - + -
140A ILE* 3.7 29.6 - - + -
143A LEU* 4.1 23.3 - - + -
156A ARG* 4.5 5.8 - - + +
157A ASP* 1.3 79.1 - - - +
159A ALA* 1.3 61.0 + - - +
161A HIS* 3.3 9.6 + - + +
162A VAL* 3.0 38.5 + - + +
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Residues in contact with ALA 159 (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 TRP* 3.5 24.2 - - + -
136A ALA* 4.2 7.6 - - + -
139A LEU* 4.2 10.3 - - + -
140A ILE* 5.5 1.6 - - + -
148A SER* 4.4 7.9 - - - +
155A TYR* 3.8 28.5 - - + -
156A ARG* 3.1 10.0 + - + +
158A VAL* 1.3 80.7 - - + +
160A ARG* 1.3 65.6 + - - +
162A VAL 3.3 1.4 + - - -
163A ARG* 2.9 20.3 + - - +
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Residues in contact with ARG 160 (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 TRP* 5.5 0.2 - - - -
150A ARG* 5.4 12.7 - - - +
154A ALA* 5.6 4.3 - - - +
155A TYR* 4.0 26.8 + - + +
156A ARG 3.2 10.9 + - - +
157A ASP* 3.1 27.1 + - - +
159A ALA* 1.3 77.2 - - - +
161A HIS* 1.3 61.2 + - - +
163A ARG* 3.4 11.6 + - - +
164A SER* 3.2 25.3 + - - -
274A FMT 3.8 37.4 + - - +
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Residues in contact with HIS 161 (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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157A ASP 2.8 17.3 + - - +
158A VAL* 3.4 12.3 - - + +
160A ARG* 1.3 74.4 - - - +
162A VAL* 1.3 64.7 + - + +
164A SER* 3.4 7.2 + - - -
165A THR* 2.9 43.8 + - - -
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Residues in contact with VAL 162 (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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111A VAL* 4.5 8.7 - - + +
112A GLU* 6.1 0.4 - - - -
117A ALA* 3.9 28.0 - - + -
134A TRP* 4.2 18.6 - - + -
135A GLY 5.7 0.2 - - - +
139A LEU* 3.6 28.0 - - + -
158A VAL* 3.0 26.4 + - + +
159A ALA 3.8 3.4 - - - +
161A HIS* 1.3 78.0 - - + +
163A ARG* 1.3 66.8 + - - +
165A THR* 3.2 7.4 + - - -
166A ILE* 2.9 36.5 + - + +
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Residues in contact with ARG 163 (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 TRP* 3.6 35.8 - - + +
155A TYR* 5.7 4.9 - - - -
159A ALA 2.9 16.7 + - - +
160A ARG* 3.6 11.4 - - - +
162A VAL* 1.3 76.3 - - - +
164A SER* 1.3 62.9 + - - +
166A ILE* 3.2 9.5 - - - +
167A LEU* 3.0 21.1 + - - +
179A ASP* 2.9 36.2 + - - -
194A GLU* 3.9 5.8 + - - +
197A ASP* 2.8 29.9 + - - -
198A ALA* 3.5 20.0 - - - +
201A VAL* 5.4 5.1 - - - +
203A PHE* 3.6 17.2 - - + -
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Residues in contact with SER 164 (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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160A ARG 3.2 11.5 + - - -
161A HIS* 3.8 8.1 - - - -
163A ARG* 1.3 76.5 + - - +
165A THR* 1.3 67.1 + - - +
167A LEU* 3.3 9.4 + - - +
168A LEU* 2.9 41.0 + - - +
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Residues in contact with THR 165 (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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117A ALA* 3.6 29.3 - - + +
120A ALA* 3.8 13.2 - - + -
161A HIS* 2.9 35.7 + - - -
162A VAL* 3.4 12.5 - - - +
164A SER* 1.3 77.8 - - - +
166A ILE* 1.3 60.1 + - + +
168A LEU* 3.9 6.8 - - - +
169A ALA* 3.0 26.7 + - - +
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Residues in contact with ILE 166 (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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111A VAL* 3.9 37.7 - - + -
120A ALA* 4.6 9.2 - - + -
132A MET* 4.3 14.9 - - + +
133A MET 4.6 4.5 - - - +
134A TRP* 3.4 40.4 - - + +
162A VAL* 2.9 19.8 + - + +
163A ARG 3.2 13.7 - - - +
165A THR* 1.3 78.1 - - + +
167A LEU* 1.3 77.1 + - - +
169A ALA* 4.0 5.1 - - - +
170A ALA* 2.9 32.6 + - - +
177A ALA* 5.5 0.9 - - + -
178A LEU 4.3 4.7 - - - +
203A PHE* 3.6 17.3 - - + -
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Residues in contact with LEU 167 (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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163A ARG 3.0 17.7 + - - +
164A SER* 3.3 8.5 + - - +
166A ILE* 1.3 79.6 - - - +
168A LEU* 1.3 70.9 + - + +
170A ALA* 3.8 3.1 - - - +
171A SER* 3.0 31.7 + - - -
177A ALA* 3.8 22.0 - - + -
201A VAL* 3.1 39.5 - - + +
202A GLY 4.0 22.2 - - - +
203A PHE* 3.7 23.3 - - + +
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Residues in contact with LEU 168 (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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164A SER* 2.9 30.1 + - - +
165A THR* 3.9 6.3 - - - +
167A LEU* 1.3 85.2 - - + +
169A ALA* 1.3 57.1 + - - +
171A SER* 4.0 4.3 - - - -
172A ALA* 2.8 32.6 + - - +
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Residues in contact with ALA 169 (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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120A ALA* 3.8 37.0 - - + +
121A ALA* 4.1 7.6 - - + +
124A ALA* 3.4 7.5 - - + +
132A MET* 5.3 2.0 - - + -
165A THR* 3.0 18.5 + - + +
166A ILE* 4.0 3.6 - - - +
168A LEU* 1.3 78.4 - - - +
170A ALA* 1.3 64.1 + - - +
172A ALA* 3.4 5.0 + - - -
173A PHE* 3.2 26.6 - - - -
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Residues in contact with ALA 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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132A MET* 3.7 25.9 - - + +
166A ILE 2.9 18.4 + - - +
167A LEU 3.8 2.9 - - - +
169A ALA* 1.3 76.1 - - - +
171A SER* 1.3 62.4 + - - +
173A PHE 3.2 3.1 + - - -
174A GLY 3.1 3.6 + - - -
175A ARG* 2.8 35.8 + - + +
176A LEU 3.8 18.6 - - - +
177A ALA* 3.9 12.1 - - + -
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Residues in contact with SER 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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167A LEU* 3.0 23.8 + - - -
168A LEU* 4.0 5.4 - - - -
170A ALA* 1.3 76.0 - - - +
172A ALA* 1.3 62.9 + - - +
174A GLY* 3.1 14.2 + - - +
175A ARG 4.6 5.2 - - - +
177A ALA* 5.5 0.4 - - - +
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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
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168A LEU 2.8 18.1 + - - +
169A ALA* 3.7 6.7 - - - +
170A ALA 3.3 0.2 - - - -
171A SER* 1.3 77.7 - - - +
173A PHE* 1.3 79.1 + - + +
174A GLY 3.5 0.2 - - - -
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Residues in contact with PHE 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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121A ALA* 3.7 28.0 - - + -
124A ALA* 3.8 24.5 - - + +
125A ALA* 3.6 28.9 - - + -
169A ALA* 3.2 23.6 - - - +
170A ALA 3.2 2.2 + - - -
171A SER 3.1 0.4 - - - -
172A ALA* 1.3 92.4 - - + +
174A GLY* 1.3 62.1 - - - +
175A ARG* 3.3 27.0 + - + +
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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