Contacts of the helix formed by residues 140 - 158 (chain A) in PDB entry 2W8B
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 TRP 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A VAL* 3.9 18.2 - - + +
137A ASN* 2.8 31.9 + - - +
139A GLN* 1.3 93.4 - - + +
141A LEU* 1.3 64.0 + - - +
142A ARG 3.3 2.5 - - - +
143A TYR* 3.2 44.0 - + + +
144A ALA* 3.0 21.5 + - - +
166A ARG* 4.4 20.6 - - - -
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Residues in contact with LEU 141 (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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51A PRO* 3.6 36.1 - - + +
52A GLU* 3.6 26.5 - - + +
54A ILE* 3.4 14.4 - - + +
104A VAL* 5.0 3.8 - - + -
112A TYR* 4.0 15.5 - - + -
114A VAL* 3.8 20.0 - - + -
136A VAL* 3.8 19.1 - - + -
137A ASN 3.5 5.5 + - - +
138A LYS* 3.2 26.7 + - + +
139A GLN 3.6 0.6 - - - -
140A TRP* 1.3 78.2 - - - +
142A ARG* 1.3 57.6 + - - +
144A ALA* 3.2 2.8 + - - +
145A GLY 2.9 24.1 + - - -
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Residues in contact with ARG 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLU* 3.9 25.0 + - - +
57A ILE* 3.7 41.8 - - + +
60A ALA* 6.2 1.6 - - - +
139A GLN 5.2 2.2 + - - +
140A TRP* 3.3 1.0 - - - +
141A LEU* 1.3 74.3 - - + +
143A TYR* 1.3 59.6 + - - +
145A GLY* 3.1 2.9 + - - -
146A HIS* 2.8 50.9 + - + -
186A ASP* 4.6 1.1 + - - +
188A ASP* 2.8 27.1 + - - -
190A TYR* 3.4 59.2 + - - +
191A ASN* 4.1 17.9 - - - +
1434A GOL 5.6 0.7 - - - -
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Residues in contact with TYR 143 (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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136A VAL* 5.1 6.7 - - + -
140A TRP* 3.2 51.4 + + + +
142A ARG* 1.3 80.5 - - - +
144A ALA* 1.3 59.6 + - - +
146A HIS* 3.3 10.5 + - - +
147A THR* 2.9 32.0 + - - -
164A ARG* 3.0 64.6 + - + -
430A LEU* 4.0 13.0 - - + -
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Residues in contact with ALA 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A VAL* 4.0 29.8 - - + -
134A TYR* 3.8 16.8 - - + -
136A VAL* 4.1 17.9 - - + -
140A TRP 3.0 13.4 + - - +
141A LEU 3.2 8.0 + - - +
143A TYR* 1.3 75.1 - - - +
145A GLY* 1.3 68.6 + - - +
147A THR* 3.0 10.0 + - - -
148A ALA* 3.0 19.4 + - - +
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Residues in contact with GLY 145 (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 ILE* 3.8 29.0 - - - +
57A ILE* 4.0 15.3 - - - -
58A VAL* 3.7 3.7 - - - +
141A LEU 2.9 13.9 + - - -
142A ARG 3.1 4.2 + - - -
144A ALA* 1.3 75.6 - - - +
146A HIS* 1.3 55.3 + - - +
148A ALA* 3.2 5.9 + - - +
149A SER* 2.9 28.9 + - - -
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Residues in contact with HIS 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ILE* 3.6 12.0 - - + +
61A ASP* 2.7 38.9 + - - -
142A ARG* 2.8 36.9 + - - +
143A TYR* 3.6 9.1 + - - +
144A ALA 3.1 0.2 - - - -
145A GLY* 1.3 73.6 - - - +
147A THR* 1.3 60.9 + - - +
149A SER* 3.3 2.6 + - - -
150A ASP* 2.9 32.4 + - - +
163A PHE* 3.2 26.8 + - - +
164A ARG* 3.7 15.2 - - + -
186A ASP* 4.4 13.2 + - + -
187A TYR* 4.1 1.3 - + - -
188A ASP* 3.2 34.2 + - - -
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Residues in contact with THR 147 (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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134A TYR* 3.5 34.0 - - + +
143A TYR* 2.9 21.1 + - - -
144A ALA* 3.0 10.4 + - - -
146A HIS* 1.3 75.6 - - - +
148A ALA* 1.3 64.1 - - - +
150A ASP* 3.2 8.2 + - + +
151A GLU* 3.1 30.5 + - + +
164A ARG* 2.9 37.6 + - - +
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Residues in contact with ALA 148 (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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42A PHE* 5.4 0.4 - - + -
54A ILE* 5.2 4.7 - - + -
58A VAL* 4.1 13.2 - - + -
114A VAL* 5.6 2.2 - - + -
116A TYR* 3.6 33.2 - - + -
134A TYR* 3.6 13.3 + - + -
144A ALA 3.0 11.5 + - - +
145A GLY* 3.5 10.1 - - - +
147A THR* 1.3 76.5 - - - +
149A SER* 1.3 63.0 + - - +
151A GLU* 3.2 2.6 + - - +
152A VAL* 3.1 28.8 + - + +
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Residues in contact with SER 149 (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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58A VAL* 3.3 29.0 - - - +
61A ASP* 2.6 36.0 + - - -
62A LEU* 4.2 3.6 - - - +
145A GLY 2.9 15.1 + - - -
146A HIS 3.3 4.2 + - - -
148A ALA* 1.3 72.2 - - - +
150A ASP* 1.3 51.7 + - - +
152A VAL* 3.8 2.4 - - - +
153A PHE* 2.7 38.3 + - - +
163A PHE* 3.3 16.8 - - - -
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Residues in contact with ASP 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A HIS 2.9 16.9 + - - -
147A THR* 3.2 11.1 + - + +
149A SER* 1.3 72.0 - - - +
151A GLU* 1.3 59.8 + - + +
153A PHE* 3.7 1.2 - - - +
154A GLU* 2.9 32.0 + - - +
161A GLY* 3.3 18.6 + - - +
163A PHE* 2.8 36.5 + - - +
164A ARG* 3.5 11.3 + - - +
1435A ACT 2.4 33.6 + - - +
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Residues in contact with GLU 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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116A TYR* 2.7 31.9 + - + +
130A ALA* 5.0 2.8 - - + +
131A GLN 4.1 2.6 - - - +
132A ASN* 2.7 29.3 + - - +
134A TYR* 2.6 27.6 + - - -
147A THR* 3.1 18.2 + - + +
148A ALA 3.2 6.0 + - - +
150A ASP* 1.3 77.7 - - + +
152A VAL* 1.3 67.1 + - - +
154A GLU* 3.4 4.5 + - - +
155A LYS* 3.0 27.3 + - - +
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Residues in contact with VAL 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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37A ILE* 4.3 0.2 - - + -
58A VAL* 5.2 2.5 - - + -
62A LEU* 4.1 17.9 - - + -
100A VAL* 4.1 32.1 - - + -
116A TYR* 3.8 28.0 - - + -
118A LEU* 4.2 15.3 - - + -
130A ALA* 5.8 0.2 - - - -
148A ALA* 3.1 18.8 + - + +
149A SER* 3.8 5.4 - - - +
151A GLU* 1.3 75.4 - - - +
153A PHE* 1.3 64.7 + - - +
155A LYS* 3.3 1.1 + - - +
156A LEU* 2.9 43.6 + - + +
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Residues in contact with PHE 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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62A LEU* 4.0 8.3 - - + -
65A SER* 3.6 26.9 - - - -
67A LYS* 3.8 31.2 - - + -
68A PHE* 3.7 22.0 - + - -
149A SER 2.7 20.5 + - - +
150A ASP* 3.7 2.9 - - - +
152A VAL* 1.3 77.8 - - - +
154A GLU* 1.3 56.2 + - - +
157A THR* 2.8 44.5 + - + +
159A ILE* 3.2 40.8 - - + -
160A LYS 3.8 8.1 - - - -
161A GLY* 3.8 12.3 - - - -
163A PHE* 3.7 24.2 - + + -
385A ASN* 4.2 7.6 - - - -
387A THR* 5.2 3.4 - - + -
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Residues in contact with GLU 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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150A ASP 2.9 21.8 + - - +
151A GLU* 4.2 4.5 - - - +
153A PHE* 1.3 71.3 - - - +
155A LYS* 1.3 61.1 + - - +
158A GLY* 2.8 37.2 + - - +
159A ILE 3.2 24.0 + - - +
160A LYS* 3.9 30.6 + - - +
161A GLY 4.7 0.9 + - - -
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Residues in contact with LYS 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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118A LEU* 3.8 22.4 - - + -
129A LEU* 3.6 42.3 + - + +
130A ALA* 4.3 7.4 - - + -
151A GLU 3.0 19.1 + - - +
152A VAL 3.6 3.8 - - - +
154A GLU* 1.3 78.5 - - - +
156A LEU* 1.3 65.2 + - + +
158A GLY 4.4 1.0 + - - -
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Residues in contact with LEU 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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35A ARG* 3.2 45.9 + - - +
37A ILE* 3.7 30.3 - - + -
68A PHE* 3.9 20.6 - - + -
98A ALA* 4.0 12.8 - - + -
118A LEU* 3.7 21.8 - - + -
129A LEU* 4.2 15.7 - - + -
152A VAL* 2.9 26.7 + - + +
155A LYS* 1.3 82.8 - - + +
157A THR* 1.3 59.2 + - - +
365D THR* 5.6 6.2 - - - +
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Residues in contact with THR 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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35A ARG* 5.4 1.6 - - - +
67A LYS* 4.4 9.6 - - + -
68A PHE* 3.6 34.3 - - + -
153A PHE* 2.8 32.8 + - + +
156A LEU* 1.3 78.0 - - - +
158A GLY* 1.3 60.3 + - - +
159A ILE* 3.1 39.5 + - - +
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Residues in contact with GLY 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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154A GLU* 2.8 26.5 + - - +
155A LYS 4.4 1.2 + - - -
156A LEU 3.7 0.6 - - - -
157A THR* 1.3 75.2 - - - +
159A ILE* 1.3 60.5 + - - +
160A LYS 4.1 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
------------------------------------------------------------
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