Contacts of the helix formed by residues 140 - 153 (chain B) in PDB entry 2W8I
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 140 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B GLU* 3.8 27.8 + - + +
85B TYR 4.0 16.6 - - - +
86B ARG* 3.4 30.5 - - - +
87B ILE* 4.4 0.2 - - - -
139B LYS* 1.3 74.8 - - - +
141B VAL* 1.3 70.7 + - - +
142B SER* 3.8 6.4 + - - -
143B GLN* 2.8 33.1 + - - +
144B VAL* 2.8 23.4 + - - +
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Residues in contact with VAL 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B TYR* 4.8 4.7 + - + +
87B ILE* 4.4 6.2 - - + +
139B LYS 4.4 0.2 + - - -
140B THR* 1.3 72.4 - - - +
142B SER* 1.3 59.8 + - - +
144B VAL* 3.5 8.1 + - - +
145B ARG* 2.7 38.5 + - - +
163B VAL* 3.6 33.3 - - + +
164B SER* 3.8 9.0 - - - -
165B ILE* 3.7 33.7 - - + -
189B ASN* 6.5 0.9 - - + -
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Residues in contact with SER 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B THR* 3.0 6.8 - - - -
141B VAL* 1.3 82.0 - - - +
143B GLN* 1.3 65.2 + - - +
145B ARG* 2.9 33.8 + - - +
146B GLN* 2.9 38.8 + - - +
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Residues in contact with GLN 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ARG* 3.4 21.6 + - - +
139B LYS* 3.3 24.9 - - + +
140B THR* 2.8 42.4 + - - +
142B SER* 1.3 74.7 - - - +
144B VAL* 1.3 65.5 + - - +
146B GLN* 3.2 13.3 + - - +
147B ASP* 2.9 23.5 + - - +
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Residues in contact with VAL 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE* 3.3 32.1 - - + -
93B LEU* 4.6 11.2 - - + -
134B VAL* 5.2 2.9 - - + -
135B GLN 5.0 0.9 - - - +
136B VAL* 3.8 23.3 - - + -
139B LYS* 3.9 13.0 - - + +
140B THR 2.8 14.6 + - - +
141B VAL* 3.6 9.0 - - - +
143B GLN* 1.3 72.0 - - - +
145B ARG* 1.3 65.1 + - - +
147B ASP* 3.0 9.1 + - - +
148B ILE* 2.8 44.3 + - + +
163B VAL* 4.3 13.0 - - + -
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Residues in contact with ARG 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B VAL* 2.7 25.1 + - - +
142B SER* 2.9 38.8 + - - +
144B VAL* 1.3 74.4 - - - +
146B GLN* 1.3 64.9 + - + +
148B ILE* 3.3 2.6 + - - +
149B THR* 2.8 28.4 + - - +
161B VAL* 3.1 32.5 - - - +
162B ASP* 2.6 38.8 + - - +
163B VAL* 4.0 23.0 + - + -
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Residues in contact with GLN 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B SER* 2.9 28.2 + - - +
143B GLN* 3.7 11.2 + - - +
145B ARG* 1.3 79.3 - - + +
147B ASP* 1.3 64.2 + - - +
149B THR* 3.2 8.3 + - - -
150B SER* 3.0 26.5 + - - -
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Residues in contact with ASP 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B VAL* 3.6 21.6 - - + +
135B GLN 3.8 1.2 + - - +
139B LYS* 2.9 27.7 + - - +
143B GLN 2.9 14.1 + - - +
144B VAL* 3.3 13.7 - - - +
146B GLN* 1.3 78.9 - - - +
148B ILE* 1.3 62.0 + - - +
150B SER* 3.3 7.8 + - - -
151B ARG* 3.2 36.3 + - - +
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Residues in contact with ILE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B VAL* 4.0 33.9 - - + -
126B ILE* 4.5 13.0 - - + -
128B TYR* 4.6 6.3 - - + -
131B ILE* 4.0 23.5 - - + +
134B VAL* 4.4 11.9 - - + -
144B VAL* 2.8 40.8 + - + +
145B ARG 4.0 2.9 - - - +
147B ASP* 1.3 71.0 - - - +
149B THR* 1.3 62.3 + - - +
151B ARG* 3.9 1.3 - - - +
152B LEU* 2.8 53.3 + - + +
161B VAL* 4.1 12.3 - - + -
163B VAL* 4.2 4.5 - - + -
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Residues in contact with THR 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B ARG* 2.8 21.3 + - - +
146B GLN* 3.2 10.9 + - - -
148B ILE* 1.3 77.9 - - - +
150B SER* 1.3 66.1 + - - +
152B LEU* 2.9 16.5 + - - +
153B THR* 3.1 14.6 + - - +
159B PRO* 3.5 32.6 - - + +
161B VAL* 3.5 24.1 + - - +
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Residues in contact with SER 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B GLN 3.0 11.3 + - - -
147B ASP* 3.3 11.6 + - - -
149B THR* 1.3 81.0 - - - +
151B ARG* 1.3 80.2 + - - +
153B THR* 3.1 25.2 + - - -
154B THR* 4.4 1.9 + - - +
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Residues in contact with ARG 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ILE* 2.6 56.8 + - + +
132B GLY 4.3 0.2 - - - -
133B LYS 3.0 25.7 + - - +
134B VAL* 3.4 27.9 - - - +
135B GLN 4.7 1.0 - - - +
147B ASP* 3.2 33.2 + - - +
148B ILE 4.1 0.2 - - - +
149B THR 3.2 0.4 - - - -
150B SER* 1.3 88.1 + - - +
152B LEU* 1.3 58.2 + - - +
153B THR 2.9 5.9 + - - -
154B THR* 3.1 24.5 - - - +
155B TYR* 4.1 0.7 - - - -
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Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B VAL* 4.7 7.4 - - + -
103B LEU* 5.0 3.1 - - + -
128B TYR* 4.2 17.0 - - + -
129B PRO 4.6 2.5 - - - +
130B TYR* 4.5 18.4 - - + -
131B ILE* 3.8 17.9 - - + -
148B ILE* 2.8 39.4 + - + +
149B THR* 2.9 8.2 + - - +
151B ARG* 1.3 75.9 - - - +
153B THR* 1.3 58.3 + - - +
154B THR 3.3 0.9 - - - -
155B TYR* 3.1 19.5 + - + -
156B ILE* 3.2 35.2 + - + +
159B PRO* 3.9 7.0 - - + -
161B VAL* 4.0 17.5 - - + -
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Residues in contact with THR 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B THR* 3.1 15.1 + - - +
150B SER* 3.1 17.2 + - - -
151B ARG 2.9 0.8 + - - -
152B LEU* 1.3 75.4 - - - +
154B THR* 1.3 67.0 + - - +
155B TYR 3.0 3.1 + - - -
156B ILE 3.3 15.3 + - - +
157B GLU* 5.1 1.7 - - - -
158B SER 5.5 1.6 - - - +
159B PRO* 3.7 20.0 - - + +
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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