Contacts of the helix formed by residues 171 - 184 (chain A) in PDB entry 1WCP
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 ALA 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A VAL* 4.5 19.3 - - + -
165A GLU* 4.8 2.9 - - - +
166A CYS* 2.7 34.8 - - - +
169A GLY 3.4 3.0 + - - -
170A LEU* 1.3 70.7 - - - +
172A GLN* 1.3 80.7 + - + +
173A ASP 3.5 1.4 - - - +
174A VAL* 3.4 6.1 + - - +
175A ILE* 3.1 28.2 + - - +
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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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139A GLY* 3.0 31.7 + - - -
140A GLY* 5.2 0.4 - - - -
148A VAL* 4.1 10.1 - - - +
166A CYS* 5.5 0.2 - - - -
171A ALA* 1.3 82.1 - - + +
173A ASP* 1.3 65.2 + - - +
175A ILE* 3.0 19.1 + - - +
176A SER* 3.0 15.5 + - - -
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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
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24A HIS* 5.9 0.7 + - - -
36A TYR* 2.9 31.2 + - + -
170A LEU* 4.4 20.7 - - + +
171A ALA 3.5 0.8 - - - +
172A GLN* 1.3 76.3 - - - +
174A VAL* 1.3 60.7 + - - +
176A SER* 3.1 17.1 + - - -
177A THR* 2.9 22.0 + - - -
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Residues in contact with VAL 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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36A TYR* 3.6 42.8 - - + -
38A VAL* 4.8 7.0 - - + -
108A LEU* 3.8 24.5 - - + -
110A VAL* 5.2 0.7 - - + -
164A LEU* 5.5 5.2 - - + -
170A LEU* 3.5 41.1 - - + +
171A ALA* 3.6 5.2 - - - +
172A GLN 3.3 0.8 - - - -
173A ASP* 1.3 73.1 - - - +
175A ILE* 1.3 58.9 + - + +
177A THR* 3.2 4.2 + - - -
178A ILE* 3.0 40.3 + - + +
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Residues in contact with ILE 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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137A ALA* 4.0 11.1 - - + +
138A SER 3.8 9.0 - - - +
139A GLY* 3.8 23.8 - - - +
148A VAL* 3.7 36.8 - - + -
149A ALA 3.8 21.3 - - - +
150A TYR* 5.6 2.5 - - + -
164A LEU* 4.9 6.7 - - + -
171A ALA 3.1 15.1 + - - +
172A GLN* 3.0 11.1 + - - +
174A VAL* 1.3 73.9 - - + +
176A SER* 1.3 67.0 + - - +
178A ILE* 3.4 15.1 + - + +
179A GLY* 3.1 20.3 + - - -
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Residues in contact with SER 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A GLN 3.0 11.9 + - - -
173A ASP* 3.1 13.6 + - - -
175A ILE* 1.3 76.5 - - - +
177A THR* 1.3 64.3 + - - +
179A GLY* 3.4 1.3 + - - -
180A GLN* 2.9 39.3 + - - +
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Residues in contact with THR 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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24A HIS* 5.2 3.7 - - + +
25A PRO* 5.0 13.9 - - + +
29A VAL* 4.0 20.3 - - + +
34A VAL* 4.0 25.1 - - + -
36A TYR* 3.1 17.4 + - - +
110A VAL* 4.2 7.6 - - + -
173A ASP* 2.9 17.4 + - - -
174A VAL* 3.2 8.3 + - - -
176A SER* 1.3 77.8 - - - +
178A ILE* 1.3 55.2 + - - +
180A GLN* 3.7 8.6 + - - +
181A ALA* 3.0 31.5 + - - +
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Residues in contact with ILE 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 LEU* 4.5 11.4 - - + -
110A VAL* 4.2 19.5 - - + -
115A LEU* 4.8 14.6 - - + -
137A ALA* 4.3 8.1 - - + -
150A TYR* 5.0 16.2 - - + -
164A LEU* 5.6 4.7 - - + -
174A VAL* 3.0 38.3 + - + +
175A ILE* 3.8 17.9 - - + +
176A SER 3.3 0.4 - - - -
177A THR* 1.3 72.1 - - - +
179A GLY* 1.3 68.5 + - - +
181A ALA* 3.2 6.8 + - - +
182A PHE* 3.1 53.6 + - + -
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Residues in contact with GLY 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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137A ALA* 3.8 15.4 - - - +
175A ILE 3.1 14.4 + - - -
176A SER* 3.7 3.8 - - - -
178A ILE* 1.3 77.2 - - - +
180A GLN* 1.3 60.4 + - - +
182A PHE* 3.2 21.7 + - - +
183A GLU* 3.6 8.1 + - - +
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Residues in contact with GLN 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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22A TRP* 5.5 6.1 - - - -
25A PRO* 3.8 35.7 - - + +
176A SER* 2.9 38.9 + - - +
177A THR* 3.9 4.4 - - - +
179A GLY* 1.3 73.9 - - - +
181A ALA* 1.3 56.6 + - - +
182A PHE 3.1 0.2 - - - -
183A GLU* 3.1 30.3 + - - +
184A LEU* 3.5 17.2 + - + +
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Residues in contact with ALA 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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29A VAL* 3.7 15.4 - - + +
110A VAL* 3.8 13.0 - - + -
111A SER 3.7 15.3 - - - +
113A SER* 2.8 34.9 + - - -
114A SER 4.5 1.5 + - - +
177A THR 3.0 21.6 + - - +
178A ILE* 3.2 6.0 + - - +
180A GLN* 1.3 74.4 - - - +
182A PHE* 1.3 58.9 + - + +
184A LEU* 3.9 12.0 - - - +
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Residues in contact with PHE 182 (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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113A SER* 3.3 12.4 + - - -
115A LEU* 4.5 9.9 - - + -
131A MET* 4.2 9.0 - - + -
134A ILE* 3.7 49.8 - - + -
135A SER 4.0 14.8 - - - -
136A PHE* 3.9 30.5 - - - -
137A ALA 4.3 1.3 - - - -
150A TYR* 4.5 15.0 - + + -
178A ILE* 3.1 44.0 + - + -
179A GLY* 3.3 12.3 - - - +
180A GLN 3.1 0.6 - - - -
181A ALA* 1.3 77.8 - - + +
183A GLU* 1.3 57.5 + - - +
184A LEU 3.1 9.5 + - - -
185A ARG 3.9 2.8 + - - -
186A PHE* 4.1 14.4 + - - +
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Residues in contact with GLU 183 (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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179A GLY 3.6 6.1 + - - +
180A GLN* 3.1 19.6 + - - +
182A PHE* 1.3 75.8 - - + +
184A LEU* 1.3 64.6 + - + +
185A ARG* 3.7 0.4 - - - -
186A PHE 5.5 1.1 - - - -
190A LEU* 5.6 5.8 - - + +
193A PRO* 4.5 9.7 - - - +
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Residues in contact with LEU 184 (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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25A PRO 5.7 0.7 - - - +
29A VAL* 4.0 9.9 - - + +
30A MET* 4.1 25.4 - - + +
112A THR* 3.7 36.3 - - + -
113A SER* 3.7 6.7 - - - +
180A GLN* 3.5 12.3 - - + +
181A ALA* 3.9 19.3 - - - +
182A PHE 3.1 1.2 + - - -
183A GLU* 1.3 77.8 - - - +
185A ARG* 1.3 65.3 + - - +
193A PRO* 3.1 23.0 - - - +
197A VAL* 3.7 31.0 - - + +
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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