Contacts of the helix formed by residues 149 - 165 (chain A) in PDB entry 1WDR
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 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A ASP 3.2 15.7 + - - -
141A ASN* 3.5 27.9 + - + +
142A GLU 3.2 17.5 - - - -
143A PRO* 3.7 10.3 - - + -
145A PHE* 4.0 2.2 - - - -
148A ARG* 1.3 76.2 - - - +
150A ALA* 1.3 63.7 + - - +
151A ILE* 4.1 1.6 - - - +
152A GLU* 2.9 36.5 + - - +
153A ILE* 3.0 22.2 + - - +
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Residues in contact with ALA 150 (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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135A LEU* 3.9 25.8 - - + -
139A VAL* 3.4 22.9 + - + +
140A ASP* 3.4 10.5 + - - +
145A PHE* 3.8 7.0 - - + -
149A THR* 1.3 73.9 - - - +
151A ILE* 1.3 62.7 + - - +
153A ILE* 3.1 14.9 + - - +
154A TYR* 3.1 40.0 + - + +
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Residues in contact with ILE 151 (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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140A ASP* 3.0 46.8 + - + +
141A ASN* 3.8 12.3 - - - +
149A THR* 4.3 2.0 - - - +
150A ALA* 1.3 77.5 - - - +
152A GLU* 1.3 56.8 + - + +
154A TYR* 3.2 7.4 + - + +
155A SER* 2.8 26.7 + - - -
276A GLN* 3.6 35.9 - - + +
277A ILE* 3.7 24.2 - - + -
280A GLU* 3.7 27.8 - - + -
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Residues in contact with GLU 152 (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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143A PRO* 5.4 0.2 - - - +
147A GLY 4.1 3.8 - - - +
148A ARG* 3.3 21.3 - - + +
149A THR* 2.9 43.3 + - - +
151A ILE* 1.3 72.2 - - + +
153A ILE* 1.3 66.6 + - - +
155A SER* 4.1 6.5 - - - -
156A ASP* 2.9 35.0 + - - +
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Residues in contact with ILE 153 (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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56A TRP* 3.5 44.9 - - + +
60A GLU* 3.9 7.8 - - - +
67A TYR* 4.8 0.3 + - - -
92A PHE* 5.4 0.2 - - + -
110A TRP* 3.9 13.7 - - + -
111A VAL* 4.9 0.2 - - + -
135A LEU* 4.8 2.2 - - + -
145A PHE* 3.7 35.7 - - + -
148A ARG* 3.7 31.9 + - + +
149A THR 3.0 17.7 + - - +
150A ALA* 3.1 12.1 + - - +
152A GLU* 1.3 75.9 - - - +
154A TYR* 1.3 68.6 + - + +
156A ASP* 3.9 1.7 - - - +
157A TYR* 3.1 22.5 + - - +
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Residues in contact with TYR 154 (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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56A TRP* 4.5 15.5 - + - -
92A PHE* 3.5 53.7 + + + -
134A TYR* 3.8 25.0 - + - -
135A LEU* 3.7 27.3 + - + +
140A ASP* 4.6 5.5 + - - -
150A ALA* 3.1 31.0 + - + +
151A ILE* 3.6 10.8 - - + +
153A ILE* 1.3 80.4 - - + +
155A SER* 1.3 62.6 + - - +
157A TYR* 3.3 2.8 + - - +
158A MET* 3.0 36.9 + - + +
277A ILE* 3.8 37.5 - - + -
280A GLU* 6.2 0.2 - - + -
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Residues in contact with SER 155 (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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151A ILE 2.8 16.2 + - - -
152A GLU* 3.6 8.5 - - - -
154A TYR* 1.3 73.8 - - - +
156A ASP* 1.3 68.6 + - - +
158A MET* 3.2 14.6 + - - +
159A LYS* 2.9 42.3 + - - +
280A GLU* 2.7 38.4 + - - +
284A ALA* 4.6 0.5 - - - +
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Residues in contact with ASP 156 (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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65A LYS* 3.2 19.0 + - - -
67A TYR* 3.3 17.5 + - + +
148A ARG* 2.9 37.6 + - - +
152A GLU* 2.9 22.7 + - - +
153A ILE 3.9 0.2 - - - +
155A SER* 1.3 75.9 + - - +
157A TYR* 1.3 57.5 + - - +
159A LYS* 3.4 14.9 + - - +
160A SER* 3.0 29.8 + - - -
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Residues in contact with TYR 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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54A VAL* 2.8 30.6 + - + +
55A TRP 3.3 3.8 - - - -
56A TRP* 3.3 43.2 + + + -
59A ILE* 3.4 28.9 - - + +
60A GLU* 4.3 1.3 - - - +
67A TYR* 3.6 26.0 + + + -
69A TRP* 3.8 16.2 - + - -
90A MET* 4.1 22.0 - - - -
92A PHE* 3.4 26.5 - + + -
153A ILE 3.1 17.4 + - - +
154A TYR 3.5 3.6 - - - +
155A SER 3.2 0.2 - - - -
156A ASP* 1.3 76.2 - - - +
158A MET* 1.3 60.5 + - - +
160A SER* 3.3 2.4 + - - -
161A PHE* 2.9 28.2 + - - +
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Residues in contact with MET 158 (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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90A MET* 3.9 32.8 - - + -
92A PHE* 4.3 6.3 - - + -
154A TYR* 3.0 30.4 + - + +
155A SER* 3.8 4.7 - - - +
157A TYR* 1.3 75.4 - - - +
159A LYS* 1.3 60.2 + - - +
161A PHE* 3.3 7.4 + - - +
162A ARG* 2.9 28.9 + - - +
179A VAL* 4.3 11.0 - - + -
277A ILE* 4.1 18.4 - - + +
280A GLU* 4.1 5.6 - - + -
281A ALA* 3.7 42.6 - - + +
284A ALA* 3.7 15.0 - - + -
285A PHE* 3.9 13.2 - - + -
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Residues in contact with LYS 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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155A SER* 2.9 37.5 + - - +
156A ASP* 3.8 13.5 - - - +
158A MET* 1.3 77.1 - - - +
160A SER* 1.3 56.3 + - - +
162A ARG* 3.2 5.2 + - - +
163A GLU* 3.0 43.0 + - - +
280A GLU* 5.0 1.3 - - - -
283A LYS* 3.8 35.2 + - - +
284A ALA* 3.7 17.7 - - + +
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Residues in contact with SER 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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67A TYR* 3.2 28.5 - - - -
69A TRP* 2.8 26.5 + - - -
156A ASP 3.0 17.8 + - - -
157A TYR 3.3 4.9 + - - -
159A LYS* 1.3 72.8 - - - +
161A PHE* 1.3 61.2 + - - +
163A GLU* 4.5 7.0 - - - +
164A ASN* 2.9 46.4 + - - +
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Residues in contact with PHE 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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54A VAL* 4.2 14.8 - - + -
69A TRP* 3.5 33.1 - + + -
72A TYR* 6.0 0.2 - - + -
76A LEU* 4.7 6.7 - - + -
86A LEU* 5.7 0.2 - - + -
88A ALA* 4.0 13.7 - - + -
90A MET* 4.0 19.5 - - + -
157A TYR 2.9 16.9 + - - +
158A MET* 3.5 7.4 - - - +
160A SER* 1.3 77.6 - - - +
162A ARG* 1.3 64.8 + - - +
165A MET* 2.9 62.6 + - + +
169A LEU* 4.8 1.6 - - + -
174A ILE* 4.0 28.3 - - + -
177A ILE* 4.0 15.7 - - + -
285A PHE* 3.8 18.2 - + - -
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Residues in contact with ARG 162 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A MET 2.9 13.3 + - - +
159A LYS* 3.5 7.4 - - - +
161A PHE* 1.3 77.6 - - - +
163A GLU* 1.3 74.4 + - - +
166A SER* 3.2 24.2 + - - -
169A LEU* 3.6 13.7 - - + +
283A LYS 4.4 2.4 + - - -
284A ALA 2.9 43.8 + - - +
285A PHE* 3.5 12.7 - - + -
286A LEU* 2.9 35.1 + - - +
287A GLY* 5.0 1.0 - - - -
288A CME 3.5 46.8 + - - +
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Residues in contact with GLU 163 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A LYS* 3.0 26.5 + - + +
160A SER* 4.0 7.3 - - - +
162A ARG* 1.3 88.3 - - - +
164A ASN* 1.3 68.1 + - - +
166A SER* 3.1 23.6 + - - -
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Residues in contact with ASN 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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69A TRP* 3.4 32.9 - - + +
73A ARG* 2.9 26.7 + - - -
160A SER* 2.9 43.4 + - - +
161A PHE 4.4 0.9 - - - +
163A GLU* 1.3 82.4 + - - +
165A MET* 1.3 58.9 + - - +
166A SER 3.4 1.2 + - - -
167A ASP* 4.2 0.3 - - - +
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Residues in contact with MET 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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69A TRP* 3.9 23.8 - - + +
72A TYR* 3.9 17.0 - - + -
73A ARG* 3.5 48.7 - - + +
76A LEU* 4.1 22.2 - - + -
161A PHE* 2.9 53.7 + - + +
162A ARG 3.7 2.2 - - - -
164A ASN* 1.3 76.4 - - + +
166A SER* 1.4 63.7 + - - +
167A ASP* 3.2 8.1 - - - -
168A PHE* 3.1 6.7 + - + +
169A LEU* 2.9 25.6 + - + +
174A ILE* 4.9 0.2 - - + -
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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