Contacts of the helix formed by residues 140 - 154 (chain A) in PDB entry 1CI1
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A GLU* 3.5 45.7 + - + +
134A GLU 3.7 2.2 + - - -
135A ARG* 3.6 30.7 + - - +
138A GLY* 3.6 2.8 - - - -
139A ARG* 1.3 78.0 - - - +
141A ALA* 1.3 65.5 + - - +
143A VAL* 3.0 9.2 + - - +
144A VAL* 3.0 25.3 + - + +
186A GLU* 6.1 0.7 - - - +
187A VAL* 4.3 16.2 - - + -
190A LEU* 5.8 1.1 - - + -
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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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138A GLY 5.5 0.4 + - - -
139A ARG 3.4 0.6 - - - -
140A THR* 1.3 79.0 - - - +
142A ALA* 1.3 64.5 + - - +
145A LEU* 3.2 33.5 + - + +
190A LEU* 3.8 33.7 - - + -
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Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ARG* 3.1 45.3 + - + +
141A ALA* 1.3 77.4 - - - +
143A VAL* 1.3 61.8 + - + +
145A LEU* 4.1 2.2 - - - +
146A THR* 2.7 35.3 + - - +
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Residues in contact with VAL 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLY 4.1 12.1 - - - +
130A GLU* 4.0 11.9 - - + -
134A GLU* 3.7 45.8 - - + +
139A ARG* 2.9 24.2 + - + +
140A THR 3.0 7.3 + - - +
142A ALA* 1.3 76.6 - - + +
144A VAL* 1.3 63.6 + - - +
146A THR* 3.2 7.2 + - - -
147A GLN* 3.0 34.1 + - + +
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Residues in contact with VAL 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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128A VAL* 4.5 8.8 - - + +
129A GLY* 4.0 33.0 - - - +
130A GLU* 4.3 5.6 - - - +
140A THR* 3.0 20.3 + - + +
141A ALA* 3.6 6.3 - - - +
143A VAL* 1.3 76.9 - - + +
145A LEU* 1.3 61.3 + - - +
147A GLN* 3.3 10.0 + - - +
148A LEU* 3.0 28.9 + - - +
167A TYR* 4.3 15.9 - - + -
187A VAL* 4.6 6.7 - - + -
190A LEU* 4.0 20.9 - - + -
191A LEU* 4.2 17.7 - - + +
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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
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141A ALA* 3.2 24.3 + - + +
142A ALA* 4.1 2.9 - - - +
144A VAL* 1.3 76.0 - - - +
146A THR* 1.3 56.4 + - - +
148A LEU* 3.8 5.2 - - + +
149A ALA* 2.8 36.3 + - - +
190A LEU* 4.2 26.5 - - + +
191A LEU* 4.0 21.8 - - + -
194A TRP* 3.6 50.7 - - + +
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Residues in contact with THR 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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107A ASN* 4.0 14.7 - - - +
142A ALA* 2.7 24.3 + - - +
143A VAL* 3.6 6.3 - - - -
145A LEU* 1.3 76.6 - - - +
147A GLN* 1.3 61.5 + - - +
149A ALA* 3.8 5.9 - - - +
150A ALA* 3.2 23.3 + - + +
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Residues in contact with GLN 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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100A ARG* 3.7 31.4 + - - +
107A ASN* 3.4 30.0 + - - +
128A VAL* 3.3 18.9 - - + +
129A GLY 2.8 43.9 + - - +
143A VAL* 3.0 25.0 + - + +
144A VAL* 3.5 12.9 - - - +
146A THR* 1.3 78.6 - - - +
148A LEU* 1.3 61.0 + - - +
150A ALA* 3.7 7.4 + - - +
151A VAL* 3.6 18.0 + - - +
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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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126A VAL* 6.1 1.1 - - + -
128A VAL* 4.5 11.6 - - + +
144A VAL 3.0 16.2 + - - +
145A LEU* 3.8 5.6 - - + +
147A GLN* 1.3 75.6 - - - +
149A ALA* 1.3 65.7 + - - +
151A VAL* 3.0 14.0 + - + +
152A ALA* 2.9 21.2 + - - +
160A TRP* 4.0 16.2 - - + -
165A ILE* 3.6 33.7 - - + -
191A LEU* 4.1 27.4 - - + +
194A TRP* 3.8 32.1 - - + -
195A VAL* 4.1 13.7 - - + -
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Residues in contact with ALA 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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145A LEU 2.8 23.5 + - - +
146A THR* 3.8 7.4 - - - +
148A LEU* 1.3 73.6 - - - +
150A ALA* 1.3 62.8 + - - +
153A GLN* 3.0 36.8 + - + +
194A TRP* 4.0 28.2 - - + +
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Residues in contact with ALA 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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107A ASN* 3.9 31.9 - - + +
108A GLU* 4.5 8.7 - - + +
111A ALA* 3.3 16.1 - - + +
146A THR* 3.2 16.1 + - + +
147A GLN 3.8 6.3 - - - +
148A LEU 3.2 0.2 - - - -
149A ALA* 1.3 78.6 - - - +
151A VAL* 1.3 60.7 + - - +
153A GLN* 3.8 15.2 + - - +
154A LYS* 4.0 5.0 - - - +
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Residues in contact with VAL 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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100A ARG* 5.5 0.7 - - - +
107A ASN 5.3 1.1 - - - +
110A VAL* 4.5 9.6 - - + -
111A ALA* 3.9 20.8 - - + +
114A VAL* 4.0 20.6 - - + -
126A VAL* 4.1 27.6 - - + -
147A GLN 3.6 14.6 + - - +
148A LEU* 3.0 14.3 + - + +
150A ALA* 1.3 76.5 - - + +
152A ALA* 1.3 64.8 + - - +
154A LYS* 3.3 14.0 + - - +
155A LEU* 3.4 29.5 - - + +
160A TRP* 5.3 6.5 - - + -
163A VAL* 5.6 2.2 - - + -
165A ILE* 6.4 0.7 - - + -
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Residues in contact with ALA 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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148A LEU 2.9 14.3 + - - +
149A ALA 3.9 3.8 - - - +
151A VAL* 1.3 76.6 - - - +
153A GLN* 1.3 67.5 + - - +
155A LEU* 3.0 23.0 + - - +
160A TRP* 3.5 32.5 + - + +
194A TRP* 4.0 23.3 - - + -
199A LEU* 5.3 3.4 - - + -
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Residues in contact with GLN 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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149A ALA* 3.0 37.9 + - + +
150A ALA* 3.8 10.1 - - - +
151A VAL 3.2 0.6 - - - -
152A ALA* 1.3 85.3 - - - +
154A LYS* 1.3 63.3 + - + +
155A LEU 3.5 1.8 - - - +
194A TRP* 4.6 8.1 - - - -
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Residues in contact with LYS 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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108A GLU 5.2 0.9 - - - +
111A ALA* 3.8 26.0 - - + +
112A GLU* 3.2 37.4 + - - +
115A ALA* 4.1 24.1 - - + +
150A ALA 4.0 10.8 - - - +
151A VAL 3.3 7.0 + - - +
152A ALA 3.1 1.0 - - - -
153A GLN* 1.3 81.1 - - + +
155A LEU* 1.3 65.3 + - - +
156A SER 4.2 0.7 + - - -
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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