Contacts of the helix formed by residues 140 - 153 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A ARG 3.4 0.8 + - - -
139A PRO* 1.3 73.1 - - - +
141A ALA* 1.3 51.2 + - - +
142A ARG 3.3 3.1 - - - +
143A GLU* 3.2 9.6 + - + -
144A GLN* 2.8 35.8 + - - +
142D ARG* 5.9 0.2 - - - +
144D ALA* 3.8 11.4 - - + +
147D THR* 3.8 29.6 - - + +
148D GLN* 3.9 15.3 - - + +
151D GLU* 4.5 8.5 - - + +
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Residues in contact with ALA 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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112A THR* 4.9 5.2 + - - +
133A ALA* 5.0 1.8 - - - +
135A ASP* 3.7 26.7 - - + +
138A ARG* 3.1 37.3 + - + +
139A PRO 3.1 4.7 + - - -
140A ALA* 1.3 77.4 - - - +
142A ARG* 1.3 56.7 + - - +
144A GLN* 3.3 15.2 - - - +
145A LEU* 3.2 25.6 + - - +
187A ASP* 5.2 2.6 - - - +
1007A ALF 5.2 1.6 - - - -
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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
----------------------------------------------------------
133A ALA* 3.7 27.0 - - + +
135A ASP 3.9 16.0 + - - +
136A THR* 3.7 29.3 + - - +
140A ALA 3.3 0.2 - - - -
141A ALA* 1.3 74.3 - - - +
143A GLU* 1.3 63.2 + - - +
145A LEU* 3.6 2.1 + - - +
146A ARG* 3.1 24.5 + - - +
158A GLU* 3.4 30.8 - - + +
159A VAL 2.8 39.0 + - - +
160A MET* 4.0 0.8 - - - +
161A ASP* 3.0 39.1 + - - +
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Residues in contact with GLU 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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140A ALA* 3.2 14.8 + - + +
142A ARG* 1.3 77.1 - - - +
144A GLN* 1.3 56.1 + - - +
146A ARG* 3.5 34.5 + - - +
147A LEU* 2.9 54.9 + - + +
144D ALA* 4.5 2.1 - - + +
147D THR* 3.3 39.8 + - - +
165D GLU* 5.3 0.2 - - - +
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Residues in contact with GLN 144 (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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112A THR* 3.9 23.0 + - + +
113A THR* 4.6 4.0 + - - -
138A ARG* 3.6 23.6 + - - +
140A ALA 2.8 16.4 + - - +
141A ALA* 3.3 16.2 - - - +
142A ARG 3.3 0.2 - - - -
143A GLU* 1.3 74.5 - - - +
145A LEU* 1.3 58.6 + - - +
147A LEU* 3.5 2.9 + - - +
148A LEU* 3.1 35.2 + - + +
1001A GDP 3.1 24.1 + - - -
142D ARG* 3.4 28.2 + - - +
143D ALA* 3.6 20.2 - - + +
144D ALA* 3.9 11.2 - - + +
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Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A THR* 3.8 34.1 - - + +
115A ALA* 4.4 1.8 - - + -
116A ALA 4.6 1.6 - - - +
131A LEU* 4.0 35.0 - - + -
132A VAL 3.8 9.2 - - - +
133A ALA* 3.7 38.1 - - + +
141A ALA 3.2 11.9 + - - +
142A ARG 4.2 2.7 - - - +
144A GLN* 1.3 75.5 - - - +
146A ARG* 1.3 56.5 + - - +
148A LEU* 3.3 9.5 + - + -
149A GLY 2.7 30.8 + - - -
156A VAL* 3.5 10.0 - - + +
187A ASP* 4.0 15.0 - - + +
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Residues in contact with ARG 146 (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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142A ARG* 3.1 17.9 + - - +
143A GLU* 3.5 47.0 + - - +
145A LEU* 1.3 72.9 - - - +
147A LEU* 1.3 63.2 + - + +
149A GLY* 3.3 1.7 + - - -
150A GLU* 2.9 31.9 + - + +
156A VAL* 3.9 15.9 - - + +
158A GLU* 3.0 41.7 + - - +
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Residues in contact with LEU 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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143A GLU* 2.9 46.3 + - + +
144A GLN 3.7 4.5 - - - +
146A ARG* 1.3 77.1 - - + +
148A LEU* 1.3 62.8 + - - +
150A GLU* 3.4 21.5 + - - +
151A LYS* 3.1 22.3 + - - +
143D ALA* 4.1 8.1 - - + -
144D ALA 3.6 27.8 - - - +
165D GLU* 3.6 18.6 - - - +
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Residues in contact with LEU 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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112A THR* 4.1 27.4 - - + +
113A THR* 4.2 15.3 - - + +
116A ALA* 3.7 28.5 - - + -
144A GLN* 3.1 26.8 + - + +
145A LEU* 3.3 8.7 + - + +
147A LEU* 1.3 72.9 - - - +
149A GLY* 1.3 63.2 + - - +
151A LYS* 3.2 14.2 + - + +
152A VAL* 3.1 27.9 + - - +
274A GLU 6.0 2.2 - - - +
276A PRO* 4.8 16.4 - - + -
143D ALA* 4.1 16.4 - - + -
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Residues in contact with GLY 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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131A LEU* 3.9 12.9 - - - +
145A LEU 2.7 20.1 + - - -
146A ARG 3.6 2.0 - - - -
148A LEU* 1.3 71.3 - - - +
150A GLU* 1.3 55.9 + - - +
152A VAL* 3.4 2.9 + - - -
153A GLY 2.9 9.9 + - - -
154A VAL 2.9 43.8 + - - -
156A VAL* 3.7 9.4 - - - -
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Residues in contact with GLU 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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146A ARG* 2.9 17.4 + - + +
147A LEU* 3.6 26.7 - - - +
148A LEU 3.3 0.2 - - - -
149A GLY* 1.3 74.6 - - - +
151A LYS* 1.3 61.5 + - - +
153A GLY* 3.4 11.3 + - - -
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Residues in contact with LYS 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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147A LEU 3.1 12.6 + - - +
148A LEU* 3.2 19.3 + - + +
150A GLU* 1.3 78.8 - - - +
152A VAL* 1.3 60.7 + - + +
153A GLY 3.7 0.2 + - - -
275A LYS* 5.1 10.7 - - - +
276A PRO* 4.0 32.8 - - + +
277A GLU* 5.0 6.3 + - - -
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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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116A ALA* 4.1 17.3 - - + +
119A ALA* 4.3 5.8 - - + -
120A LEU* 3.9 30.3 - - + +
123A LYS* 3.3 25.4 + - - +
131A LEU* 4.7 2.0 - - + -
148A LEU 3.1 20.4 + - - +
149A GLY* 3.7 10.1 - - - +
151A LYS* 1.3 77.9 - - + +
153A GLY* 1.3 60.5 + - - +
154A VAL* 3.8 19.2 - - + +
276A PRO* 3.6 34.1 - - + -
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Residues in contact with GLY 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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123A LYS* 3.5 19.2 - - - -
149A GLY 2.9 5.2 + - - -
150A GLU* 3.4 9.0 + - - -
151A LYS 3.4 3.8 + - - -
152A VAL* 1.3 79.2 - - - +
154A VAL* 1.3 63.2 + - - +
155A PRO* 4.6 2.4 - - - +
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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