Contacts of the helix formed by residues 140 - 152 (chain D) in PDB entry 3IKH
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 SER 140 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113D ASP* 5.8 1.8 + - - -
139D PHE* 1.3 74.0 - - - +
141D LEU* 1.3 64.9 + - - +
142D ASP* 3.8 7.5 + - - +
143D LYS* 3.2 25.6 + - - +
144D THR* 2.8 26.7 + - - -
166D ASN* 5.0 4.5 - - - +
169D PHE* 4.5 0.2 - - - -
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Residues in contact with LEU 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D SER* 1.3 73.1 - - - +
142D ASP* 1.3 63.2 + - - +
144D THR* 3.4 0.9 + - - -
145D ARG* 2.9 60.6 + - - +
166D ASN* 4.4 8.9 - - - +
168D ASP* 3.6 45.5 - - + +
169D PHE* 4.2 11.4 - - + -
171D HIS* 5.1 9.0 - - + +
172D LEU* 3.2 29.4 - - + -
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Residues in contact with ASP 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D SER* 3.3 7.1 + - - +
141D LEU* 1.3 82.7 - - - +
143D LYS* 1.3 57.0 + - - +
145D ARG* 3.6 24.0 + - - +
146D ALA* 3.0 31.0 + - - +
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Residues in contact with LYS 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D ALA 2.8 30.3 + - - -
113D ASP* 4.3 8.2 + - - +
116D SER* 3.6 12.0 - - - +
117D LEU* 4.0 31.0 - - + +
120D MSE 3.5 32.1 - - - +
139D PHE* 3.7 29.7 - - + -
140D SER* 3.2 19.0 + - - +
142D ASP* 1.3 75.5 - - - +
144D THR* 1.3 65.1 + - - +
146D ALA* 3.5 5.7 + - - +
147D LEU* 3.1 31.3 + - + +
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Residues in contact with THR 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D GLN* 3.2 25.4 + - - +
136D GLN 4.8 2.5 + - - +
139D PHE* 3.5 20.7 + - - +
140D SER 2.8 21.8 + - - -
141D LEU 3.7 2.7 - - - -
143D LYS* 1.3 74.0 - - - +
145D ARG* 1.3 66.2 + - - +
147D LEU 3.3 1.6 + - - -
148D PHE* 3.1 44.3 + - + -
160D PHE* 3.9 13.9 - - + -
169D PHE* 3.9 9.8 - - + -
172D LEU* 3.7 15.9 - - + -
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Residues in contact with ARG 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D LEU* 2.9 51.3 + - - +
142D ASP* 3.6 21.9 + - - +
144D THR* 1.3 77.7 - - - +
146D ALA* 1.3 57.1 + - - +
148D PHE* 3.2 9.2 + - - +
149D GLN* 2.8 56.1 + - - +
171D HIS* 5.6 5.8 - - - +
172D LEU* 4.0 15.2 - - + +
175D LEU* 3.8 19.5 - - + -
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Residues in contact with ALA 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D LEU* 3.3 37.9 - - + -
121D ILE* 5.8 0.5 - - - +
142D ASP 3.0 20.3 + - - +
143D LYS 3.6 1.6 - - - +
145D ARG* 1.3 76.3 - - - +
147D LEU* 1.3 63.2 + - - +
149D GLN* 3.2 17.2 + - - +
150D TYR* 2.9 23.6 + - - +
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Residues in contact with LEU 147 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6D THR* 3.5 23.8 - - + +
117D LEU* 3.4 21.1 - - + -
120D MSE 4.0 24.5 - - + -
121D ILE* 4.5 11.4 - - + +
124D MSE 5.2 7.4 - - - +
133D LEU* 3.4 13.9 - - + +
135D GLN* 3.2 34.1 - - - +
139D PHE* 3.9 16.6 - - + -
143D LYS* 3.1 20.1 + - + +
144D THR 3.3 0.2 + - - -
146D ALA* 1.3 76.4 - - - +
148D PHE* 1.3 59.4 + - - +
150D TYR* 3.3 8.5 + - + +
151D ALA 3.0 22.0 + - - -
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Residues in contact with PHE 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D LEU* 3.8 10.8 - - + -
135D GLN* 3.4 33.2 - - + -
144D THR* 3.1 32.9 + - + -
145D ARG* 3.2 7.6 + - - +
147D LEU* 1.3 75.1 - - - +
149D GLN* 1.3 60.2 + - - +
151D ALA* 3.1 4.5 + - - +
152D ARG* 2.9 32.4 + - - +
158D THR* 3.6 30.4 - - + +
159D VAL 3.7 12.6 - - - -
160D PHE* 3.6 34.3 - + + -
172D LEU* 4.6 7.2 - - + -
175D LEU* 4.1 18.2 - - + -
176D ILE* 3.4 20.6 - - + -
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Residues in contact with GLN 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D ARG* 2.8 40.2 + - - +
146D ALA* 3.2 16.9 + - - +
148D PHE* 1.3 76.9 - - - +
150D TYR* 1.3 52.6 + - - +
152D ARG* 2.5 34.3 - - - +
153D SER* 3.6 5.7 + - - -
175D LEU* 3.9 21.0 - - + +
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Residues in contact with TYR 150 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121D ILE* 3.5 47.7 + - + +
124D MSE 4.1 37.2 + - + -
125D ALA* 4.6 3.3 - - - -
146D ALA 2.9 13.8 + - - +
147D LEU* 3.4 11.0 - - + +
148D PHE 3.2 0.2 - - - -
149D GLN* 1.3 71.4 - - - +
151D ALA* 1.3 58.1 + - - +
152D ARG 2.4 21.4 - - - +
153D SER* 3.0 11.2 + - - -
154D ARG* 2.4 65.2 + - + +
156D MSE 5.0 0.4 - - - -
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Residues in contact with ALA 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D LEU* 3.7 27.4 - - + -
147D LEU 3.0 13.8 + - - +
148D PHE 3.1 9.4 + - - +
150D TYR* 1.3 74.3 - - - +
152D ARG* 1.3 65.8 + - - +
154D ARG* 3.1 9.9 + - - +
156D MSE 3.0 42.7 + - + -
158D THR* 3.8 16.8 - - + -
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Residues in contact with ARG 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D PHE 2.9 15.8 + - - +
149D GLN* 2.5 14.7 - - - +
150D TYR 2.4 28.4 - - - +
151D ALA* 1.3 78.2 - - - +
153D SER* 1.3 62.9 + - - +
155D GLY* 4.4 2.9 - - - +
156D MSE 4.4 10.0 + - - -
158D THR* 3.8 8.1 + - + +
174D PRO 3.4 19.2 + - - -
175D LEU* 3.1 52.2 + - + +
176D ILE 3.7 4.2 + - - +
177D ASP* 3.2 28.6 + - - -
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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