Contacts of the helix formed by residues 140 - 154 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139B PHE* 1.3 74.6 - - - +
141B LEU* 1.3 56.3 + - - +
142B ASP* 3.8 5.0 + - - +
143B LYS* 3.2 36.3 + - - +
144B THR* 2.7 33.8 + - - -
166B ASN* 5.4 2.9 - - - +
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Residues in contact with LEU 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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139B PHE 3.9 0.4 + - - -
140B SER* 1.3 72.5 - - - +
142B ASP* 1.3 65.1 + - - +
144B THR* 3.3 0.5 + - - -
145B ARG* 2.8 50.2 + - - +
166B ASN* 4.4 16.9 - - - +
168B ASP* 3.8 43.7 - - + +
169B PHE* 4.1 14.4 - - + -
171B HIS* 5.7 2.7 - - + +
172B LEU* 3.8 31.0 - - + -
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Residues in contact with ASP 142 (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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117B LEU* 4.8 2.0 - - + +
140B SER* 3.3 5.9 + - - +
141B LEU* 1.3 85.5 - - - +
143B LYS* 1.3 60.6 + - + +
145B ARG* 2.9 30.2 + - - +
146B ALA* 2.9 31.3 + - - +
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Residues in contact with LYS 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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112B ALA 3.1 22.8 + - - -
113B ASP* 3.4 16.0 + - - +
114B THR 4.6 0.2 - - - -
115B PHE 2.5 30.3 + - - -
116B SER* 4.9 2.9 - - - +
117B LEU* 4.1 25.1 - - + +
120B MSE 4.5 8.5 - - - -
139B PHE* 4.1 20.5 - - + -
140B SER* 3.2 25.3 + - - +
142B ASP* 1.3 74.9 - - + +
144B THR* 1.3 65.6 + - - +
146B ALA* 3.3 1.6 + - - +
147B LEU* 2.9 33.3 + - + +
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Residues in contact with THR 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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135B GLN* 3.0 40.1 + - - +
136B GLN 4.6 3.8 + - - +
139B PHE* 3.3 21.9 + - - +
140B SER 2.7 21.8 + - - -
141B LEU 3.7 3.4 - - - -
143B LYS* 1.3 77.0 - - - +
145B ARG* 1.3 62.8 + - - +
147B LEU* 4.6 0.2 - - - -
148B PHE* 3.1 28.4 + - + -
160B PHE* 4.0 23.1 - - + -
169B PHE* 4.1 10.5 - - + -
172B LEU* 4.0 7.2 - - + -
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Residues in contact with ARG 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 LEU* 2.8 39.7 + - - +
142B ASP* 2.9 32.4 + - - +
144B THR* 1.3 76.6 - - - +
146B ALA* 1.3 58.4 + - - +
148B PHE* 3.2 5.2 + - - +
149B GLN* 2.9 56.9 + - - +
171B HIS* 5.9 3.2 - - - +
172B LEU* 4.1 26.9 - - + +
175B LEU* 4.0 15.3 - - + -
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Residues in contact with ALA 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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117B LEU* 3.5 30.7 - - + -
121B ILE* 5.1 5.4 - - + +
142B ASP 2.9 19.0 + - - +
143B LYS 3.7 2.0 - - - +
145B ARG* 1.3 76.0 - - - +
147B LEU* 1.3 58.3 + - - +
149B GLN* 3.4 14.5 + - - +
150B TYR* 3.0 28.2 + - - +
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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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6B THR* 3.8 18.4 - - + +
117B LEU* 3.9 18.6 - - + -
120B MSE 4.0 35.2 - - + -
121B ILE* 4.4 16.6 - - + +
124B MSE 5.0 10.0 - - - +
133B LEU* 3.4 14.9 - - + +
135B GLN* 3.1 34.5 - - - +
139B PHE* 4.3 5.4 - - + -
143B LYS* 2.9 23.5 + - + +
146B ALA* 1.3 74.5 - - - +
148B PHE* 1.3 64.0 + - - +
150B TYR* 3.3 5.0 + - + +
151B ALA 3.0 17.7 + - - -
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Residues in contact with PHE 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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133B LEU* 3.8 11.7 - - + -
135B GLN* 3.3 34.1 - - + -
144B THR* 3.1 23.9 + - + -
145B ARG* 3.7 6.5 - - - +
147B LEU* 1.3 73.6 - - - +
149B GLN* 1.3 60.3 + - - +
151B ALA* 3.3 2.9 + - - +
152B ARG* 2.9 29.9 + - - +
158B THR* 3.7 28.4 - - + +
159B VAL 3.6 13.2 - - - -
160B PHE* 3.5 38.6 - + + -
172B LEU* 4.7 9.2 - - + -
175B LEU* 4.3 19.3 - - + -
176B ILE* 3.5 28.7 - - + -
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Residues in contact with GLN 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 ARG* 2.9 46.3 + - + +
146B ALA* 3.6 15.5 + - - +
148B PHE* 1.3 76.6 - - - +
150B TYR* 1.3 62.5 + - - +
152B ARG* 3.2 10.2 + - - +
153B SER* 3.0 21.3 + - - -
175B LEU* 4.3 18.9 - - + +
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Residues in contact with TYR 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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267A ARG* 6.3 0.4 - - - -
268A ARG 5.9 0.4 - - - -
272A SER* 2.6 47.3 + - - -
121B ILE* 3.8 37.0 + - + +
124B MSE 4.0 37.2 + - + -
125B ALA* 4.7 2.9 - - - -
146B ALA 3.0 16.5 + - - +
147B LEU* 3.7 6.1 - - - +
149B GLN* 1.3 77.6 - - - +
151B ALA* 1.3 64.8 + - - +
153B SER* 2.5 34.2 + - - -
154B ARG* 3.0 44.6 + - + +
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Residues in contact with ALA 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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124B MSE 4.0 2.2 - - + -
133B LEU* 3.6 39.5 - - + -
147B LEU 3.0 5.5 + - - -
148B PHE 3.3 8.3 + - - +
150B TYR* 1.3 76.1 - - - +
152B ARG* 1.3 61.3 + - - +
154B ARG* 3.0 7.6 + - - -
156B MSE 2.9 48.1 + - + +
158B THR* 4.0 11.2 - - + -
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Residues in contact with ARG 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 PHE 2.9 11.6 + - - +
149B GLN* 3.3 13.5 - - - +
151B ALA* 1.3 76.3 - - - +
153B SER* 1.3 57.5 + - - +
155B GLY* 3.0 18.0 + - - -
156B MSE 3.3 15.5 + - - -
157B THR* 4.5 0.2 - - - +
158B THR* 3.7 9.5 + - - -
174B PRO 4.2 7.7 + - - -
175B LEU* 3.5 46.1 + - + +
176B ILE 4.3 2.6 + - - -
177B ASP* 2.8 43.4 + - - -
195B LYS* 4.5 3.8 - - - +
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Residues in contact with SER 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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266A SER 6.2 0.2 - - - -
267A ARG* 3.8 27.9 + - - +
149B GLN 3.0 10.2 + - - -
150B TYR* 2.5 40.3 + - - -
152B ARG* 1.3 75.2 - - - +
154B ARG* 1.3 60.4 + - - +
155B GLY 3.2 1.1 + - - -
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Residues in contact with ARG 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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49A ARG* 5.5 0.2 - - - +
267A ARG* 3.6 42.3 + - - +
271A LEU 5.3 0.8 + - - -
272A SER 3.8 7.3 + - - -
274A PHE 4.2 5.5 + - - -
276A GLY 4.1 1.8 - - - +
279A GLU* 3.5 14.8 + - - +
124B MSE 3.8 8.2 + - - -
125B ALA* 2.9 30.2 + - - +
127B ALA* 2.8 33.2 + - + +
128B VAL* 4.1 1.4 - - - -
129B ALA* 3.4 21.7 + - - +
150B TYR* 3.0 57.8 + - + +
151B ALA 3.0 9.0 + - - +
153B SER* 1.3 77.4 - - - +
155B GLY* 1.3 62.5 + - - +
156B MSE 3.5 19.2 + - + -
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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