Contacts of the helix formed by residues 165 - 175 (chain A) in PDB entry 4WUR
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 ASP 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A TYR* 4.3 2.3 - - - -
164A ASP* 1.3 81.9 + - - +
166A ALA* 1.3 80.9 + - - +
167A SER* 3.1 14.7 + - - -
168A ARG* 3.5 20.9 + - + +
169A LEU* 3.4 21.0 + - - +
279A TYR* 2.9 12.1 + - - -
42B ARG* 3.6 21.0 + - - -
71B LEU 4.2 0.5 - - - +
72B ARG* 3.8 8.6 - - + -
73B LEU* 2.9 49.9 + - - +
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Residues in contact with ALA 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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112A TYR* 3.5 26.0 - - + +
115A ALA* 4.3 7.6 - - + -
116A VAL* 3.4 12.5 - - + +
164A ASP 3.6 0.2 + - - -
165A ASP* 1.3 75.6 + - - +
167A SER* 1.3 59.5 + - - +
169A LEU 3.2 2.4 + - - -
170A LEU* 3.0 27.1 + - - +
267A ASN* 5.9 0.9 - - - +
279A TYR* 3.3 43.3 - - + -
309A ASP* 5.0 2.9 - - - +
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Residues in contact with SER 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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165A ASP* 3.1 8.4 + - - -
166A ALA* 1.3 78.1 - - - +
168A ARG* 1.3 60.8 + - - +
170A LEU* 3.5 4.0 + - - +
171A HIS* 3.1 33.3 + - - -
247A SER* 5.1 2.6 - - - -
248A GLY 4.8 2.8 + - - -
279A TYR* 4.1 3.5 + - - -
308A THR* 3.7 14.3 - - - -
309A ASP* 2.5 39.9 + - - -
42B ARG* 3.8 18.6 - - - -
73B LEU* 6.4 0.7 - - - -
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Residues in contact with ARG 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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156A GLY* 2.9 37.2 + - - -
157A ASN* 5.0 4.8 - - - +
158A CYS* 4.7 1.2 - - - -
164A ASP* 4.3 1.4 + - - -
165A ASP* 3.5 21.4 + - + -
166A ALA 3.2 0.2 - - - -
167A SER* 1.3 77.9 - - - +
169A LEU* 1.3 74.8 + - - +
171A HIS 3.5 1.9 + - - -
172A THR* 3.2 32.6 + - - +
39B ASP 5.6 0.6 + - - -
42B ARG* 3.8 24.9 - - + +
49B GLN* 3.5 28.3 + - - +
72B ARG* 3.2 50.9 - - - +
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Residues in contact with LEU 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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112A TYR* 3.8 27.4 - - + -
113A LEU* 3.9 9.4 - - + -
116A VAL* 4.1 9.2 - - + -
152A ILE* 3.6 46.7 - - + +
156A GLY* 3.6 20.9 - - - -
158A CYS* 4.0 11.0 - - - -
164A ASP* 5.8 0.2 - - - +
165A ASP 3.4 10.8 + - - +
166A ALA* 3.2 8.3 + - - +
168A ARG* 1.3 83.6 - - - +
170A LEU* 1.3 66.4 + - - +
172A THR* 3.0 12.7 + - - +
173A VAL* 3.0 28.9 + - + +
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Residues in contact with LEU 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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116A VAL* 3.9 25.5 - - + +
119A THR* 3.8 28.5 - - + +
120A LEU* 3.8 33.4 - - + -
123A LEU* 5.3 0.2 - - + -
166A ALA 3.0 12.8 + - - +
167A SER* 3.6 9.2 - - - +
168A ARG 3.3 0.2 - - - -
169A LEU* 1.3 77.9 - - - +
171A HIS* 1.3 60.1 + - + +
173A VAL* 3.4 3.5 + - - +
174A LEU* 3.1 31.3 + - + +
245A LEU* 3.9 23.3 - - + -
267A ASN* 4.8 2.0 - - - +
309A ASP* 4.3 22.4 - - - +
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Residues in contact with HIS 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 SER* 3.1 24.8 + - - +
169A LEU 3.2 0.2 - - - -
170A LEU* 1.3 79.8 - - + +
172A THR* 1.3 64.4 + - - +
173A VAL 3.2 1.1 - - - -
174A LEU* 3.8 8.3 - - - +
175A ALA* 3.2 17.0 + - - +
208A CYS* 4.4 21.4 - - + +
209A TYR 5.1 1.8 - - - -
210A VAL* 3.7 25.6 - - + +
245A LEU* 4.2 19.1 - - + +
247A SER* 3.1 31.8 + - - -
309A ASP* 4.4 1.3 + - - -
42B ARG* 5.4 2.0 - - - -
49B GLN* 3.9 28.5 + - + +
51B GLU* 3.4 8.4 - - - +
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Residues in contact with THR 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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155A TYR* 5.0 5.0 + - - +
156A GLY* 4.5 7.0 - - - -
168A ARG* 3.2 33.2 + - - +
169A LEU* 3.0 24.7 + - - +
171A HIS* 1.3 75.3 - - - +
173A VAL* 1.3 68.4 + - - +
175A ALA* 3.0 17.0 + - - +
176A LYS* 3.5 14.4 - - - +
49B GLN* 3.6 10.3 - - - +
51B GLU* 2.9 30.2 - - - +
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Residues in contact with VAL 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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116A VAL* 4.8 2.7 - - + -
120A LEU* 3.8 21.8 - - + -
128A PHE* 3.3 37.8 - - + -
133A LEU* 5.3 3.6 - - + -
148A PHE* 5.2 0.2 - - + -
152A ILE* 3.8 39.5 - - + +
155A TYR* 6.1 3.4 - - + -
169A LEU* 3.0 25.2 + - + +
170A LEU* 3.5 7.4 - - - +
172A THR* 1.3 82.6 + - - +
174A LEU* 1.3 56.6 + - - +
176A LYS* 3.0 22.7 + - - +
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Residues in contact with LEU 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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120A LEU* 4.1 19.3 - - + -
123A LEU* 4.1 20.2 - - + -
126A ILE* 4.6 6.1 - - + -
128A PHE* 5.1 0.9 - - + -
170A LEU* 3.1 23.2 + - + +
171A HIS* 4.1 11.4 - - - +
172A THR 3.2 0.2 - - - -
173A VAL* 1.3 71.8 - - - +
175A ALA* 1.3 58.2 + - - +
176A LYS 2.9 4.9 - - - -
177A ALA* 2.8 43.2 + - + +
204A LEU* 3.9 18.7 - - + +
208A CYS* 4.3 17.9 - - - -
243A TRP* 5.2 1.1 - - + -
245A LEU* 4.0 27.4 - - + -
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Residues in contact with ALA 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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129A VAL* 5.7 0.9 - - - +
171A HIS 3.2 14.2 + - - +
172A THR 3.0 13.9 + - - +
174A LEU* 1.3 76.9 - - - +
176A LYS* 1.3 60.4 + - + +
177A ALA 3.7 3.9 + - - +
51B GLU* 4.0 23.8 - - + +
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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