Contacts of the helix formed by residues 140 - 154 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130B GLU* 2.8 42.6 + - - +
134B GLU 4.0 1.6 + - - -
135B ARG* 3.8 19.0 + - - +
138B GLY 3.5 3.8 + - - -
139B ARG* 1.3 76.0 - - - +
141B ALA* 1.3 65.1 + - - +
143B VAL* 3.7 1.4 - - - +
144B VAL* 3.1 33.4 + - + +
187B VAL* 4.3 16.8 - - + -
190B LEU* 5.0 0.9 - - + -
261B HEX 3.5 36.1 - - + +
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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
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138B GLY 5.3 0.6 + - - -
139B ARG 3.3 0.4 - - - -
140B THR* 1.3 76.7 - - - +
142B ALA* 1.3 67.5 + - - +
144B VAL* 4.0 7.4 - - - -
145B LEU* 3.0 36.0 + - + +
190B LEU* 3.9 27.4 - - + -
261B HEX 4.9 7.5 - - + +
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Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ARG* 3.2 35.0 + - + +
141B ALA* 1.3 78.0 - - - +
143B VAL* 1.3 57.1 + - - +
145B LEU* 4.4 2.1 - - - +
146B THR* 2.6 38.4 + - - +
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Residues in contact with VAL 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLY 4.1 0.4 - - - +
130B GLU* 3.8 13.9 - - + -
134B GLU* 3.5 48.7 - - + +
139B ARG* 2.9 39.9 + - + +
140B THR 3.7 2.9 - - - +
142B ALA* 1.3 76.2 - - - +
144B VAL* 1.3 60.7 + - - +
146B THR* 3.3 4.4 + - - -
147B GLN* 3.0 49.0 + - + +
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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
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128B VAL* 4.6 6.2 - - + +
129B GLY* 4.0 31.2 - - - +
130B GLU* 4.3 5.4 - - - +
140B THR* 3.1 19.8 + - + +
141B ALA 3.7 4.3 - - - +
143B VAL* 1.3 75.4 - - + +
145B LEU* 1.3 61.7 + - + +
147B GLN* 3.2 10.4 + - - +
148B LEU* 2.9 28.3 + - - +
167B TYR* 4.2 18.4 - - + -
187B VAL* 4.6 4.0 - - + -
190B LEU* 3.8 26.0 - - + -
191B LEU* 4.1 18.1 - - + +
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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
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141B ALA* 3.0 24.7 + - + +
142B ALA* 4.4 2.0 - - - +
144B VAL* 1.3 76.0 - - + +
146B THR* 1.3 55.8 + - - +
148B LEU* 3.8 5.1 - - + +
149B ALA* 2.7 35.7 + - - +
190B LEU* 3.4 33.9 - - + +
191B LEU* 4.1 19.7 - - + -
194B TRP* 3.6 50.9 - - + +
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Residues in contact with THR 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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107B ASN* 3.8 16.8 + - - +
142B ALA* 2.6 26.0 + - - +
143B VAL* 3.6 5.6 - - - -
145B LEU* 1.3 75.3 - - - +
147B GLN* 1.3 66.1 + - - +
149B ALA* 3.9 6.1 - - + +
150B ALA* 3.1 23.7 + - - +
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Residues in contact with GLN 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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100B ARG* 3.9 26.3 + - - +
107B ASN* 3.4 30.4 - - - +
128B VAL* 3.3 19.3 - - + +
129B GLY 2.8 45.7 + - - +
134B GLU* 5.4 0.2 + - - -
143B VAL* 3.0 27.4 + - + +
144B VAL* 3.5 11.8 - - - +
146B THR* 1.3 79.0 - - - +
148B LEU* 1.3 59.6 + - - +
150B ALA* 3.6 7.1 - - - +
151B VAL* 3.4 20.3 - - - +
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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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126B VAL* 6.3 0.7 - - + -
128B VAL* 4.5 8.0 - - + +
144B VAL 2.9 16.2 + - - +
145B LEU* 3.8 8.1 - - + +
147B GLN* 1.3 73.7 - - - +
149B ALA* 1.3 64.9 + - - +
150B ALA 3.1 2.8 + - - -
151B VAL* 3.2 10.2 + - + +
152B ALA* 3.0 22.4 + - - +
160B TRP* 3.9 17.7 - - + -
165B ILE* 3.6 33.9 - - + -
191B LEU* 3.7 31.6 - - + +
194B TRP* 4.3 18.6 - - + -
195B VAL* 4.3 20.4 - - + -
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Residues in contact with ALA 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 LEU 2.7 23.8 + - - +
146B THR* 3.9 6.7 - - - +
148B LEU* 1.3 72.9 - - - +
150B ALA* 1.3 62.5 + - - +
152B ALA* 3.6 8.9 - - - +
153B GLN* 3.1 25.3 + - - +
194B TRP* 4.1 19.4 - - + +
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Residues in contact with ALA 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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107B ASN* 4.0 32.8 - - + +
108B GLU* 5.6 0.9 - - - -
111B ALA* 3.6 12.1 - - + +
146B THR* 3.1 17.7 + - + +
147B GLN 3.6 7.4 - - - +
148B LEU 3.1 0.4 - - - -
149B ALA* 1.3 78.7 - - - +
151B VAL* 1.3 63.2 + - + +
153B GLN* 3.8 15.7 + - - +
154B LYS* 3.9 6.4 + - - +
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Residues in contact with VAL 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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100B ARG* 5.7 1.6 - - - +
107B ASN 5.4 0.7 - - - +
110B VAL* 5.1 3.6 - - + -
111B ALA* 3.8 26.0 - - + +
114B VAL* 4.7 13.7 - - + -
126B VAL* 4.3 27.4 - - + -
128B VAL* 6.1 1.3 - - + -
147B GLN 3.4 17.7 - - - +
148B LEU* 3.2 13.8 + - + +
150B ALA* 1.3 73.6 - - + +
152B ALA* 1.3 72.2 + - - +
154B LYS* 3.0 13.4 + - - +
155B LEU* 3.3 26.1 + - + +
160B TRP* 4.3 16.8 - - + -
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Residues in contact with ALA 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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148B LEU 3.0 16.3 + - - +
149B ALA 3.6 5.4 - - - +
150B ALA 3.4 0.2 - - - -
151B VAL* 1.3 78.3 - - - +
153B GLN* 1.3 63.2 + - - +
155B LEU* 3.1 22.7 + - - +
160B TRP* 3.8 27.1 + - + -
194B TRP* 3.8 25.6 - - + -
199B LEU* 4.4 9.4 - - + +
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Residues in contact with GLN 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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149B ALA 3.1 16.9 + - - +
150B ALA* 3.9 9.4 - - - +
151B VAL 3.3 0.2 - - - -
152B ALA* 1.3 75.7 - - - +
154B LYS* 1.3 61.8 + - + +
155B LEU 3.8 2.1 + - - +
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Residues in contact with LYS 154 (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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108B GLU* 4.3 9.4 - - - +
111B ALA* 3.4 41.1 - - + +
112B GLU* 2.5 33.7 + - - +
115B ALA* 3.9 19.2 - - + +
150B ALA 3.9 4.5 + - - +
151B VAL 3.0 10.9 + - - +
153B GLN* 1.3 82.0 - - + +
155B LEU* 1.3 65.3 + - + +
156B SER 4.1 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