Contacts of the helix formed by residues 140 - 153 (chain B) in PDB entry 2CNW
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 ALA 140 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B ARG 3.3 0.8 + - - -
139B PRO* 1.3 73.2 - - - +
141B ALA* 1.3 57.3 + - - +
142B ARG 3.3 2.9 - - - +
143B GLU* 3.6 9.4 + - + +
144B GLN* 2.9 29.7 + - - +
144E ALA* 3.8 10.7 - - + +
147E THR* 3.6 31.4 - - + +
148E GLN* 3.8 14.8 - - + +
151E GLU* 4.7 8.3 - - + +
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Residues in contact with ALA 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B THR* 4.8 5.9 + - - +
133B ALA* 4.8 1.5 - - - +
135B ASP* 3.5 37.0 - - + +
138B ARG* 3.1 29.6 + - + +
139B PRO 3.1 1.7 + - - -
140B ALA* 1.3 77.9 - - - +
142B ARG* 1.3 63.3 + - - +
144B GLN* 3.4 14.3 - - - +
145B LEU* 3.3 21.5 + - - +
187B ASP* 5.2 2.0 - - - +
1007B ALF 5.4 1.3 - - - -
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Residues in contact with ARG 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ALA* 3.9 24.9 - - + +
135B ASP 3.9 15.4 + - - +
136B THR* 3.6 25.9 + - - +
140B ALA 3.3 0.4 - - - -
141B ALA* 1.3 76.2 - - - +
143B GLU* 1.3 60.3 + - - +
145B LEU* 3.4 4.2 + - - +
146B ARG* 3.0 28.6 + - - +
158B GLU* 3.6 32.3 - - + +
159B VAL 2.8 38.6 + - - -
160B MET* 4.0 0.8 - - - +
161B ASP* 2.8 40.6 + - - +
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Residues in contact with GLU 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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140B ALA* 3.6 13.3 + - + +
142B ARG* 1.3 74.4 - - - +
144B GLN* 1.3 59.2 + - - +
146B ARG* 3.3 37.2 + - - +
147B LEU* 2.8 56.6 + - + +
144E ALA* 4.4 3.0 - - + +
147E THR* 3.4 39.0 + - - +
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Residues in contact with GLN 144 (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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112B THR* 3.8 24.0 + - + +
113B THR* 4.6 3.6 + - - -
138B ARG* 3.7 21.8 + - - -
140B ALA 2.9 18.3 + - - +
141B ALA* 3.4 11.9 - - - +
142B ARG 3.2 0.4 - - - -
143B GLU* 1.3 76.9 - - - +
145B LEU* 1.3 62.3 + - - +
147B LEU* 3.2 3.6 + - - +
148B LEU* 3.1 27.8 + - + +
1001B GDP 3.2 24.9 + - - -
142E ARG* 3.3 26.8 + - - +
143E ALA* 3.4 24.3 - - + +
144E ALA* 3.8 10.7 - - + +
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Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B THR* 3.8 32.5 - - + +
115B ALA* 4.5 2.7 - - + -
116B ALA 4.6 1.3 - - - +
131B LEU* 4.0 35.0 - - + -
132B VAL 3.7 13.0 - - - +
133B ALA* 3.7 34.3 - - + +
141B ALA 3.3 10.3 + - - +
142B ARG 4.0 4.9 - - - +
144B GLN* 1.3 76.3 - - - +
146B ARG* 1.3 60.8 + - - +
148B LEU* 3.2 10.5 + - + +
149B GLY 2.8 26.0 + - - -
156B VAL* 3.6 10.3 - - + +
187B ASP* 4.0 15.0 - - + +
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Residues in contact with ARG 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 ARG 3.0 18.5 + - - +
143B GLU* 3.5 46.0 + - - +
145B LEU* 1.3 73.6 - - - +
147B LEU* 1.3 70.6 + - + +
149B GLY* 3.3 1.0 + - - -
150B GLU* 3.0 24.0 + - + +
156B VAL* 3.9 15.6 - - + +
158B GLU* 2.8 49.7 + - - +
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Residues in contact with LEU 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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143B GLU* 2.8 49.9 + - + +
144B GLN 3.6 3.8 - - - +
146B ARG* 1.3 78.3 - - + +
148B LEU* 1.3 61.5 + - - +
150B GLU* 3.5 20.7 + - - +
151B LYS* 3.2 22.0 + - - +
143E ALA* 4.2 10.5 - - + -
144E ALA* 3.7 25.4 - - - +
165E GLU* 5.2 5.8 - - - +
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Residues in contact with LEU 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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112B THR* 3.9 37.7 - - + +
113B THR* 4.2 14.4 - - + +
116B ALA* 3.7 21.5 - - + -
144B GLN* 3.1 20.7 + - + +
145B LEU* 3.5 8.5 - - + +
146B ARG 3.2 0.4 - - - -
147B LEU* 1.3 75.0 - - - +
149B GLY* 1.3 63.4 + - - +
151B LYS* 3.3 14.1 + - + +
152B VAL* 3.1 29.1 + - - +
274B GLU 5.8 4.5 - - - +
276B PRO* 5.0 14.8 - - + -
143E ALA* 4.1 18.2 - - + -
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Residues in contact with GLY 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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131B LEU* 3.8 16.3 - - - +
145B LEU 2.8 18.9 + - - -
146B ARG 3.3 2.0 + - - -
148B LEU* 1.3 73.4 - - - +
150B GLU* 1.3 54.9 + - - +
152B VAL* 3.3 3.1 + - - +
153B GLY 2.9 9.5 + - - -
154B VAL 2.8 44.6 + - - -
156B VAL* 3.9 4.0 - - - -
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Residues in contact with GLU 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 ARG* 3.0 16.3 + - + +
147B LEU* 3.7 21.7 - - - +
149B GLY* 1.3 73.0 - - - +
151B LYS* 1.3 64.3 + - - +
153B GLY* 3.2 12.9 + - - -
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Residues in contact with LYS 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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147B LEU 3.2 10.8 + - - +
148B LEU* 3.3 17.2 + - + +
150B GLU* 1.3 80.2 - - - +
152B VAL* 1.3 59.9 + - + +
275B LYS* 5.8 2.8 - - - +
276B PRO* 4.0 32.7 - - + +
277B GLU* 4.5 10.9 + - - -
165E GLU* 6.0 2.7 - - - +
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Residues in contact with VAL 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ALA* 4.0 15.0 - - + +
119B ALA* 4.5 5.2 - - + -
120B LEU* 3.7 31.5 - - + +
123B LYS* 3.4 22.7 - - - +
131B LEU* 4.9 1.8 - - + -
148B LEU 3.1 18.3 + - - +
149B GLY* 3.6 10.3 - - - +
151B LYS* 1.3 78.9 - - - +
153B GLY* 1.3 60.7 + - - +
154B VAL* 3.9 19.7 - - + -
276B PRO* 3.6 34.1 - - + -
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Residues in contact with GLY 153 (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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123B LYS* 3.0 26.4 + - - -
149B GLY 2.9 4.5 + - - -
150B GLU* 3.2 12.1 + - - -
151B LYS 3.4 0.6 + - - -
152B VAL* 1.3 76.7 - - - +
154B VAL* 1.3 57.6 + - - +
155B PRO* 4.6 1.8 - - - +
181B ARG* 5.4 1.6 + - - -
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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