Contacts of the helix formed by residues 140 - 158 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F VAL* 3.9 18.4 - - + +
137F ASN* 2.9 21.3 - - + +
139F GLN* 1.3 96.4 - - + +
141F LEU* 1.3 62.4 + - - +
142F ARG 3.4 2.5 - - - +
143F TYR* 3.2 45.1 - + + +
144F ALA* 3.0 21.7 + - - +
166F ARG* 4.5 20.0 - - - -
191F ASN* 6.4 0.2 - - - -
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Residues in contact with LEU 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F PRO* 3.5 38.4 - - + +
52F GLU* 3.8 24.7 - - + +
54F ILE* 3.5 15.9 - - + +
104F VAL* 5.0 4.9 - - + -
112F TYR* 4.0 16.2 - - + -
114F VAL* 3.7 28.0 - - + -
136F VAL* 3.9 12.3 - - + -
137F ASN 3.6 1.2 - - - -
138F LYS* 3.3 29.3 + - + +
139F GLN 3.6 0.8 - - - -
140F TRP* 1.3 73.8 - - - +
142F ARG* 1.4 67.3 + - + +
144F ALA* 3.1 2.6 + - - +
145F GLY 3.0 18.4 + - - -
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Residues in contact with ARG 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F GLU* 3.9 22.4 + - - +
57F ILE* 3.5 31.5 - - + +
139F GLN 5.0 3.0 + - - +
140F TRP* 3.4 0.6 - - - +
141F LEU* 1.4 74.8 - - + +
143F TYR* 1.3 58.5 + - - +
145F GLY* 3.0 2.4 + - - -
146F HIS* 2.8 50.6 + - + -
186F ASP* 4.6 1.7 + - - +
188F ASP* 2.8 24.5 + - - -
190F TYR* 3.5 43.8 - - - +
191F ASN* 4.2 17.3 - - - +
1431F SO4 2.7 44.6 + - - -
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Residues in contact with TYR 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F VAL* 5.1 6.7 - - + -
140F TRP* 3.2 53.2 + + + +
142F ARG* 1.3 79.6 - - - +
144F ALA* 1.3 63.1 + - - +
146F HIS* 3.4 9.6 + - - +
147F THR* 2.9 33.2 + - - -
164F ARG* 2.3 61.6 + - + -
430F LEU* 3.5 11.5 + - + -
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Residues in contact with ALA 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F VAL* 4.0 23.1 - - + +
134F TYR* 3.9 16.4 - - + -
136F VAL* 3.9 25.6 - - + -
140F TRP 3.0 13.0 + - - +
141F LEU 3.1 8.4 + - - +
143F TYR* 1.3 78.7 - - - +
145F GLY* 1.3 64.4 + - - +
147F THR* 3.1 17.5 + - - -
148F ALA* 3.1 11.1 + - - +
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Residues in contact with GLY 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F ILE* 4.0 27.7 - - - +
57F ILE* 4.2 11.2 - - - -
58F VAL* 3.9 3.1 - - - +
141F LEU 3.0 14.3 + - - -
142F ARG 3.0 2.6 + - - -
144F ALA* 1.3 79.4 - - - +
146F HIS* 1.3 56.0 + - - +
147F THR 3.2 0.2 + - - -
148F ALA* 3.2 5.7 + - - +
149F SER* 2.8 31.4 + - - -
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Residues in contact with HIS 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F ILE* 3.6 9.2 - - + +
61F ASP* 2.6 39.6 + - - -
142F ARG* 2.8 37.9 + - - +
143F TYR* 3.7 8.4 + - - +
145F GLY* 1.3 70.6 - - - +
147F THR* 1.3 55.9 + - - +
149F SER* 3.3 2.4 + - - -
150F ASP* 2.9 32.4 + - - +
163F PHE* 3.1 32.6 + - - +
164F ARG* 3.7 10.6 + - + -
186F ASP* 4.3 17.0 + - + -
187F TYR* 3.9 2.3 - + - -
188F ASP* 3.2 32.9 + - - -
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Residues in contact with THR 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F TYR* 3.4 33.4 - - + +
143F TYR* 2.9 29.0 + - - -
144F ALA* 3.4 10.8 - - - -
145F GLY 3.0 0.6 - - - -
146F HIS* 1.3 75.6 - - - +
148F ALA* 1.3 64.8 + - - +
150F ASP* 3.2 6.5 + - + +
151F GLU* 3.1 29.5 + - + +
164F ARG* 3.3 32.3 + - - +
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Residues in contact with ALA 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F PHE* 5.2 3.8 - - + -
54F ILE* 5.5 0.7 - - + -
58F VAL* 4.3 12.8 - - + -
100F VAL* 6.2 0.2 - - + -
114F VAL* 5.8 2.0 - - + -
116F TYR* 3.6 34.1 - - + -
134F TYR* 3.7 13.8 + - + -
144F ALA 3.1 11.0 + - - +
145F GLY* 3.5 9.9 - - - +
147F THR* 1.3 71.6 - - - +
149F SER* 1.3 68.4 + - - +
151F GLU* 3.2 2.6 + - - +
152F VAL* 2.9 29.2 + - + +
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Residues in contact with SER 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F VAL* 3.2 31.9 - - - +
61F ASP* 2.7 33.2 + - - +
62F LEU* 4.1 3.3 - - - +
145F GLY 2.8 14.2 + - - -
146F HIS 3.3 6.7 - - - -
148F ALA* 1.3 76.0 - - - +
150F ASP* 1.3 56.6 + - - +
152F VAL* 3.8 2.8 - - - +
153F PHE* 2.9 32.6 + - - +
163F PHE* 3.4 14.3 - - - -
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Residues in contact with ASP 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146F HIS 2.9 16.1 + - - -
147F THR* 3.2 10.0 + - + +
149F SER* 1.3 73.6 - - - +
151F GLU* 1.3 60.8 + - + +
153F PHE* 3.5 0.9 + - - +
154F GLU* 2.9 33.0 + - - +
160F LYS* 5.8 1.4 + - - -
161F GLY* 3.1 29.6 + - - +
162F ALA* 3.2 0.5 + - - -
163F PHE* 2.7 37.0 + - - +
164F ARG* 3.7 31.9 + - - +
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Residues in contact with GLU 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F TYR* 2.8 32.9 + - + +
130F ALA* 5.1 2.9 - - + +
131F GLN 4.3 1.4 - - - -
132F ASN* 2.8 30.3 + - - +
134F TYR* 2.7 27.0 + - - -
147F THR* 3.1 17.4 + - + +
148F ALA 3.2 4.5 + - - +
150F ASP* 1.3 76.0 - - + +
152F VAL* 1.3 67.2 + - - +
154F GLU* 4.0 3.9 - - - +
155F LYS* 3.0 26.0 + - - +
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Residues in contact with VAL 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F ILE* 4.3 0.2 - - + -
58F VAL* 5.1 2.7 - - + -
62F LEU* 4.0 25.1 - - + -
68F PHE* 5.5 0.2 - - + -
100F VAL* 4.0 21.5 - - + -
116F TYR* 3.9 27.1 - - + -
118F LEU* 4.0 31.0 - - + -
148F ALA* 2.9 20.7 + - + +
149F SER* 3.8 4.7 - - - +
151F GLU* 1.3 76.1 - - - +
153F PHE* 1.3 65.9 + - - +
155F LYS* 3.2 1.0 + - - +
156F LEU* 3.0 35.6 + - + +
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Residues in contact with PHE 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F LEU* 3.9 7.4 - - + -
65F SER* 3.6 26.9 - - - -
67F LYS* 3.9 24.2 - - + -
68F PHE* 3.8 20.2 - + - -
149F SER 2.9 17.9 + - - +
150F ASP 3.8 2.5 - - - +
152F VAL* 1.3 77.5 - - - +
154F GLU* 1.3 53.2 + - - +
156F LEU* 3.8 0.2 - - - -
157F THR* 2.7 49.1 + - + +
159F ILE* 3.3 32.8 - - + -
160F LYS 3.7 12.3 - - - -
161F GLY* 3.7 13.0 - - - -
163F PHE* 3.6 24.7 - + + -
385F ASN* 4.0 10.5 - - - -
387F THR* 4.8 4.5 - - + -
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Residues in contact with GLU 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F ASP 2.9 22.2 + - - +
151F GLU* 4.1 3.9 - - - +
153F PHE* 1.3 72.6 - - - +
155F LYS* 1.3 62.9 - - - +
157F THR* 4.1 0.2 - - - -
158F GLY* 2.8 31.5 + - - +
159F ILE 3.1 22.0 - - - +
160F LYS* 3.8 31.9 + - - +
161F GLY 4.5 0.7 + - - -
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Residues in contact with LYS 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F LEU* 4.0 21.8 - - + -
129F LEU* 3.4 39.8 + - + +
130F ALA* 4.5 8.3 - - + -
151F GLU 3.0 18.7 + - - +
152F VAL 3.7 3.4 - - - +
154F GLU* 1.3 79.7 - - - +
156F LEU* 1.3 65.7 + - + +
158F GLY 4.5 1.0 + - - -
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Residues in contact with LEU 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F ARG* 3.4 41.5 + - - +
37F ILE* 3.7 20.0 - - + -
68F PHE* 3.6 35.0 - - + -
98F ALA* 4.1 14.1 - - + -
118F LEU* 4.0 19.7 - - + -
129F LEU* 4.2 16.6 - - + -
152F VAL* 3.0 24.0 + - + +
155F LYS* 1.3 83.6 - - + +
157F THR* 1.3 60.3 + - - +
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Residues in contact with THR 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F ARG* 6.1 0.4 - - - +
67F LYS* 4.4 12.8 - - + -
68F PHE* 3.8 27.1 - - + -
153F PHE* 2.7 35.7 + - + +
156F LEU* 1.3 80.7 - - - +
158F GLY* 1.3 63.9 + - - +
159F ILE* 3.1 38.4 + - - +
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Residues in contact with GLY 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154F GLU* 2.8 24.6 + - - +
155F LYS 4.5 1.3 + - - -
156F LEU 3.7 0.6 - - - -
157F THR* 1.3 79.3 - - - +
159F ILE* 1.3 60.7 + - - +
160F LYS 4.3 0.3 + - - -
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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