Contacts of the helix formed by residues 166 - 181 (chain A) in PDB entry 2WMH
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 GLN 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A ARG* 3.5 34.5 - - + +
134A ASN* 5.9 0.5 + - - -
164A ASN* 2.8 20.9 + - - +
165A ASN* 1.3 85.7 + - - +
167A LEU* 1.3 57.5 + - + +
168A ALA 3.4 1.1 - - - -
169A PRO* 3.4 5.3 - - - +
170A HIS* 2.9 65.0 + - + +
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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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128A MET* 3.6 17.7 - - + +
131A GLY* 3.7 32.5 - - - +
132A GLU 4.0 11.4 - - - +
133A ARG* 5.5 0.2 - - - -
156A ASN* 5.1 0.7 - - - +
159A ASN* 3.5 36.6 - - + +
163A TYR* 4.2 12.8 - - + -
164A ASN* 3.6 37.0 - - - +
165A ASN 3.5 0.8 - - - -
166A GLN* 1.3 78.3 - - + +
168A ALA* 1.3 57.9 + - - +
170A HIS* 5.9 0.4 - - - +
171A SER* 2.9 35.4 + - - -
187A TRP* 4.3 12.3 - - + -
194A PHE* 5.2 0.7 - - + -
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Residues in contact with ALA 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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163A TYR* 5.0 6.0 + - - +
164A ASN 4.9 0.6 + - - -
165A ASN 4.7 1.2 + - - -
167A LEU* 1.3 78.1 - - - +
169A PRO* 1.3 71.0 - - + +
171A SER 3.2 1.4 + - - -
172A ALA* 2.9 19.8 + - - +
187A TRP* 4.0 16.7 - - + -
198A ILE* 4.2 13.6 - - + +
201A ASP* 3.6 28.5 - - + +
204A PHE* 3.5 20.8 - - + -
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Residues in contact with PRO 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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165A ASN 3.2 25.6 - - - +
166A GLN* 3.4 10.5 - - - +
168A ALA* 1.3 94.8 - - + +
170A HIS* 1.3 64.8 + - + +
172A ALA* 3.2 3.5 + - - +
173A LYS* 3.1 27.9 + - - +
201A ASP* 3.9 12.7 - - - +
203A THR* 4.0 27.8 - - + +
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Residues in contact with HIS 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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128A MET* 3.9 16.1 - - + +
132A GLU 4.9 2.6 + - - -
133A ARG* 3.1 31.9 + - - -
135A THR* 4.6 7.1 + - - -
166A GLN* 2.9 52.7 + - + +
167A LEU* 5.9 0.2 - - - +
169A PRO* 1.3 82.3 - - + +
171A SER* 1.3 62.7 + - - +
173A LYS* 3.2 10.7 + - + +
174A TYR* 3.1 33.3 + + + -
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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
----------------------------------------------------------
128A MET* 3.5 7.3 - - - +
156A ASN* 3.0 27.0 + - - -
167A LEU 2.9 23.1 + - - -
168A ALA 3.2 2.0 + - - -
170A HIS* 1.3 76.6 - - - +
172A ALA* 1.3 56.3 + - - +
174A TYR* 3.3 2.6 + - - +
175A LEU* 2.8 30.3 + - - +
185A PHE* 3.5 24.8 - - - -
187A TRP* 3.5 20.7 - - - -
204A PHE* 3.8 4.0 - - - -
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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 ALA 2.9 14.5 + - - +
169A PRO 3.2 9.6 + - - +
171A SER* 1.3 75.5 - - - +
173A LYS* 1.3 63.7 + - + +
175A LEU* 3.2 4.9 + - - +
176A GLU* 3.0 22.3 + - - +
203A THR* 3.7 24.5 - - + +
204A PHE* 3.7 11.5 - - + -
207A ALA* 3.6 28.4 - - + +
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Residues in contact with LYS 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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138A PRO* 4.4 18.8 - - + -
169A PRO* 3.1 15.7 + - + +
170A HIS* 3.2 11.9 + - + +
172A ALA* 1.3 77.4 - - + +
174A TYR* 1.3 63.2 + - - +
176A GLU* 3.3 22.6 + - - +
177A VAL* 3.2 25.6 + - - +
203A THR* 5.7 8.5 - - + +
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Residues in contact with TYR 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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127A ILE* 3.6 28.7 - - + -
128A MET* 3.5 38.1 - - + -
135A THR* 2.7 24.9 + - - -
136A VAL* 2.3 35.3 + - + +
137A PRO 4.3 1.6 - - - -
138A PRO* 4.0 27.1 - - + +
141A LEU* 3.9 14.4 - - + +
170A HIS* 3.1 25.1 + - + -
171A SER 3.7 0.7 - - - +
173A LYS* 1.3 79.5 - - - +
175A LEU* 1.3 57.3 + - - +
177A VAL* 3.1 7.8 + - + +
178A CYS* 2.9 30.7 + - - -
185A PHE* 3.6 22.0 - + + -
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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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171A SER 2.8 17.0 + - - +
172A ALA 3.2 4.7 + - - +
174A TYR* 1.3 78.6 - - - +
176A GLU* 1.3 56.8 + - - +
178A CYS* 3.1 4.5 + - + +
179A ALA* 2.8 27.9 + - - +
185A PHE* 3.9 21.9 - - + -
204A PHE* 4.5 8.1 - - + -
207A ALA* 3.8 36.1 - - + +
208A SER 4.3 0.4 - - - +
211A TYR* 3.7 26.0 - - + +
214A ASN* 3.8 27.4 - - + +
215A LEU* 4.0 26.2 - - + -
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Residues in contact with GLU 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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172A ALA 3.0 12.1 + - - +
173A LYS* 3.5 29.4 + - - +
174A TYR 3.3 0.2 - - - -
175A LEU* 1.3 74.9 - - - +
177A VAL* 1.3 62.8 + - + +
179A ALA* 3.2 3.9 + - - +
180A LYS* 3.0 21.3 + - - +
210A LYS* 5.7 3.0 + - - -
211A TYR* 3.6 39.9 + - + +
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Residues in contact with VAL 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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138A PRO* 3.9 28.3 - - + +
141A LEU* 4.1 7.0 - - + -
142A ASP* 3.8 31.6 - - + +
145A PHE* 3.8 24.0 - - + -
173A LYS 3.2 14.9 + - - +
174A TYR* 3.1 10.4 + - - +
176A GLU* 1.3 73.0 - - + +
178A CYS* 1.3 67.2 + - - +
180A LYS* 3.1 20.7 + - - +
181A TYR* 3.4 11.1 - - + -
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Residues in contact with CYS 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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141A LEU* 4.9 0.2 - - - -
145A PHE* 3.8 21.8 - - - -
154A VAL* 4.1 13.7 - - - -
174A TYR 2.9 18.0 + - - +
175A LEU* 3.1 10.7 + - - +
177A VAL* 1.3 77.1 - - - +
179A ALA* 1.3 61.6 + - - +
181A TYR 3.1 6.8 + - - -
183A ALA* 2.9 46.0 + - - +
184A HIS 3.8 26.0 - - - -
185A PHE* 4.0 10.8 - - + +
214A ASN* 4.7 2.5 - - + -
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Residues in contact with ALA 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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35A VAL* 3.9 9.4 - - - +
175A LEU 2.8 14.2 + - - +
176A GLU 3.5 8.3 - - - +
178A CYS* 1.3 73.1 - - - +
180A LYS* 1.3 63.7 + - - +
181A TYR 3.2 0.7 + - - -
182A GLY* 3.4 7.8 + - - -
211A TYR* 3.3 36.8 - - + -
214A ASN* 3.4 26.2 + - - +
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Residues in contact with LYS 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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35A VAL* 3.8 16.1 - - - +
142A ASP* 2.7 33.6 + - - +
146A GLN* 5.5 0.4 - - - +
176A GLU 3.0 11.7 + - - +
177A VAL* 3.1 15.0 + - + +
179A ALA* 1.3 77.5 - - - +
181A TYR* 1.3 81.2 + - + +
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Residues in contact with TYR 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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35A VAL* 4.0 13.5 - - + +
36A GLN 4.3 0.5 - - - +
38A ARG* 2.8 53.5 + - - +
142A ASP* 2.5 50.3 + - - -
145A PHE* 3.4 27.4 - + + -
146A GLN* 3.0 34.1 + - + +
177A VAL* 3.4 20.0 - - + +
178A CYS 3.1 4.4 + - - +
180A LYS* 1.3 101.8 + - + +
182A GLY* 1.3 60.4 + - - +
183A ALA 3.2 0.9 - - - +
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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