Contacts of the helix formed by residues 163 - 180 (chain A) in PDB entry 1WMA
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 THR 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A THR 3.9 8.5 - - - +
162A ILE* 1.3 80.9 - - - +
164A GLU* 1.4 64.4 + - - +
165A GLU* 3.6 13.6 + - - +
166A GLU* 3.0 37.5 + - - +
167A LEU 3.0 18.2 + - - -
206A ILE* 3.7 4.3 - - - +
209A ARG* 4.3 0.2 - - - +
303A SO4 3.4 32.3 - - - +
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Residues in contact with GLU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A PHE* 5.8 0.2 - - + -
118A ARG* 2.7 43.6 + - - +
122A THR* 4.2 8.0 + - - -
163A THR* 1.4 73.6 - - - +
165A GLU* 1.3 71.0 + - - +
167A LEU* 3.2 4.0 + - - +
168A VAL* 2.9 28.0 + - + +
203A LEU* 4.0 14.4 - - + -
206A ILE* 3.9 25.4 - - + +
207A HIS* 2.8 31.7 + - - -
210A LYS* 4.7 11.3 + - - +
303A SO4 4.5 1.8 + - - -
311A P33 4.3 8.1 - - - +
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Residues in contact with GLU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ARG* 5.2 9.3 + - - +
163A THR* 3.7 12.0 - - - +
164A GLU* 1.3 93.6 + - - +
166A GLU* 1.3 65.6 + - - +
168A VAL* 3.5 9.1 + - - +
169A GLY* 3.1 19.1 + - - -
210A LYS* 5.2 6.4 + - - -
303A SO4 4.9 1.9 + - - -
311A P33 4.9 12.5 - - - +
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Residues in contact with GLU 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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161A THR 4.2 1.7 - - - +
162A ILE* 3.5 18.5 - - + +
163A THR* 3.0 43.1 + - - +
165A GLU* 1.3 77.7 - - + +
167A LEU* 1.3 62.3 + - - +
169A GLY* 3.2 2.8 + - - -
170A LEU* 3.1 29.7 + - + +
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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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114A PHE* 3.7 18.2 - - + -
157A PHE* 3.9 28.0 - - + -
162A ILE* 4.2 9.3 - - + +
163A THR 3.0 11.4 + - - +
164A GLU 3.2 7.4 + - - +
166A GLU* 1.3 74.0 - - - +
168A VAL* 1.3 59.3 + - - +
170A LEU* 3.1 3.7 + - - +
171A MET* 2.9 40.0 + - + +
199A GLY* 3.7 12.6 - - - +
202A VAL* 3.9 15.0 - - + -
203A LEU* 3.5 36.8 - - + +
206A ILE* 3.9 13.9 - - + -
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Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A PHE* 4.0 15.7 - - + -
115A PHE* 3.8 15.2 - - + -
118A ARG* 3.4 41.5 - - - +
164A GLU* 2.9 21.8 + - + +
165A GLU* 3.7 8.5 - - - +
166A GLU 3.3 0.2 - - - -
167A LEU* 1.3 73.6 - - - +
169A GLY* 1.3 65.3 + - - +
171A MET* 3.3 1.9 + - - +
172A ASN* 3.0 32.3 + - - +
304A SO4 3.8 19.3 - - - +
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Residues in contact with GLY 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 GLU 3.1 14.5 + - - -
166A GLU 3.2 3.6 + - - -
167A LEU 3.2 0.4 - - - -
168A VAL* 1.3 80.1 - - - +
170A LEU* 1.3 56.2 + - - +
172A ASN* 3.6 4.8 + - - +
173A LYS* 2.9 27.9 + - - +
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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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153A LEU* 4.1 21.5 - - + -
156A LYS* 4.1 32.1 - - + -
157A PHE* 4.0 25.6 - - + -
162A ILE* 4.4 12.8 - - + -
166A GLU* 3.1 19.9 + - + +
167A LEU* 3.1 6.9 + - - +
169A GLY* 1.3 74.0 - - - +
171A MET* 1.3 60.3 + - - +
173A LYS* 3.2 17.4 + - + -
174A PHE 2.9 23.9 + - - -
188A TRP* 3.2 20.0 - - + -
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Residues in contact with MET 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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110A MET* 3.6 31.4 - - - +
114A PHE* 3.8 31.9 - - + -
115A PHE* 4.4 2.2 - - + -
157A PHE* 3.6 36.6 - - + -
167A LEU* 2.9 25.0 + - + +
168A VAL 3.3 3.6 + - - +
170A LEU* 1.3 78.6 - - - +
172A ASN* 1.3 61.9 + - - +
174A PHE* 3.3 5.2 + - - +
175A VAL* 3.3 25.1 + - - +
188A TRP* 4.3 1.1 - - + -
195A VAL* 3.7 26.5 - - + +
198A ILE* 4.7 0.7 - - + -
199A GLY* 3.7 21.3 - - - +
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Residues in contact with ASN 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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115A PHE* 3.2 36.9 - - - -
168A VAL* 3.0 23.2 + - - +
169A GLY* 4.0 4.4 - - - +
171A MET* 1.3 73.1 - - - +
173A LYS* 1.3 61.3 + - - +
175A VAL* 3.3 10.4 + - - +
176A GLU* 2.9 41.7 + - + +
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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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153A LEU* 6.2 0.7 - - + -
169A GLY 2.9 19.1 + - - +
170A LEU* 3.2 19.7 + - + +
172A ASN* 1.3 73.2 - - - +
174A PHE* 1.3 60.6 + - - +
176A GLU* 3.7 7.5 - - - +
177A ASP* 2.7 67.2 + - - +
186A GLU* 2.8 32.7 + - - +
188A TRP* 4.3 10.6 - - + +
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Residues in contact with PHE 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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102A PHE* 4.5 4.7 - + - -
106A ALA* 3.9 16.6 - - + -
110A MET* 3.8 19.3 - - + -
170A LEU 2.9 8.0 + - - +
171A MET 3.6 7.2 - - - +
172A ASN 3.3 0.2 - - - -
173A LYS* 1.3 75.3 - - - +
175A VAL* 1.3 66.8 + - + +
177A ASP* 3.1 2.4 + - - +
178A THR* 2.9 46.0 + - + +
183A HIS* 4.1 4.7 - + + -
188A TRP* 3.5 61.5 - + + +
189A PRO 3.9 11.2 - - - -
191A SER 4.5 0.4 - - - -
192A ALA* 3.7 37.0 - - + -
195A VAL* 3.8 19.1 - - + -
196A THR* 5.8 0.2 - - + -
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Residues in contact with VAL 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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103A HIS* 4.6 2.6 - - - +
106A ALA* 3.8 9.6 - - - +
107A GLU* 3.6 39.7 - - + +
110A MET* 3.7 35.0 - - + -
171A MET 3.6 12.3 - - - +
172A ASN* 3.3 14.3 + - - +
173A LYS 3.3 0.6 - - - -
174A PHE* 1.3 79.8 - - + +
176A GLU* 1.3 65.5 + - + +
178A THR* 2.7 25.3 + - - -
179A LYS* 3.2 7.4 + - + +
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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 ASN* 2.9 28.9 + - + +
173A LYS* 3.9 7.0 - - - +
175A VAL* 1.3 78.8 - - + +
177A ASP* 1.3 64.8 + - - +
179A LYS* 3.1 9.7 + - - +
180A LYS* 3.1 43.3 + - - +
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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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173A LYS* 2.7 60.9 + - - +
174A PHE 3.6 3.6 - - - +
176A GLU* 1.3 69.2 - - - +
178A THR* 1.3 65.2 + - - +
180A LYS* 3.2 19.9 + - - +
181A GLY 3.1 4.3 + - - -
182A VAL* 3.0 33.0 + - + +
183A HIS* 3.7 20.6 - - + -
186A GLU* 3.4 12.6 - - - +
188A TRP* 3.0 17.7 + - - +
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Residues in contact with THR 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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102A PHE* 3.7 20.8 - - + -
103A HIS* 3.3 29.6 + - - +
106A ALA* 3.6 11.8 - - + +
174A PHE* 2.9 51.5 + - + +
175A VAL 2.7 16.1 + - - -
177A ASP* 1.3 76.6 - - - +
179A LYS* 1.3 60.9 + - - +
181A GLY* 3.1 12.3 + - - -
183A HIS* 3.6 16.5 + - + -
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Residues in contact with LYS 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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103A HIS* 3.6 41.8 + - + +
104A ILE* 5.9 2.0 - - - +
107A GLU* 5.2 8.8 + - - +
175A VAL* 3.2 6.9 + - + +
176A GLU* 3.1 12.8 + - - +
178A THR* 1.3 82.3 + - - +
180A LYS* 1.3 62.4 + - + +
181A GLY 3.5 0.3 + - - -
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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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176A GLU* 3.1 29.9 + - - +
177A ASP* 3.2 28.1 + - - +
179A LYS* 1.3 78.6 - - + +
181A GLY* 1.3 62.6 + - - +
182A VAL* 3.3 15.4 + - + +
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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