Contacts of the helix formed by residues 152 - 166 (chain B) in PDB entry 2IK8
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 PHE 152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94B PHE* 3.7 17.5 - + + -
98B CYS* 3.5 24.0 - - + -
101B PHE* 4.2 17.5 - + + -
114B ALA* 3.7 25.8 - - + -
117B ILE* 3.5 39.7 - - + -
118B PHE* 3.8 6.5 - - + -
122B ILE* 3.8 14.6 - - + -
140B THR* 3.4 28.9 - - + -
144B LEU* 4.7 0.9 - - + -
149B ALA 4.8 1.4 + - - -
150B THR 2.7 4.8 + - - -
151B CYS* 1.3 93.3 - - + +
153B ASP* 1.3 53.3 + - - +
154B ALA 3.1 3.9 + - - -
155B ALA* 3.1 6.5 + - + +
156B GLN* 2.7 36.1 + - - +
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Residues in contact with ASP 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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102B LYS* 3.9 22.9 + - - -
149B ALA 4.9 1.2 - - - +
150B THR* 2.8 51.6 + - - +
151B CYS 3.6 0.2 - - - -
152B PHE* 1.3 71.0 - - - +
154B ALA* 1.3 62.3 + - - +
156B GLN* 3.4 9.4 + - - +
157B GLY* 3.0 20.6 + - - -
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Residues in contact with ALA 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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136B THR* 3.8 11.2 - - + -
139B LEU* 3.7 30.1 - - + -
140B THR* 4.8 3.1 - - - +
143B ASN* 5.7 3.8 - - - +
150B THR 4.8 0.2 + - - -
151B CYS 5.2 1.0 + - - +
152B PHE 3.2 0.6 - - - -
153B ASP* 1.3 78.1 - - - +
155B ALA* 1.3 64.2 + - - +
157B GLY* 3.1 11.6 + - - -
158B LYS* 3.1 17.2 + - + +
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Residues in contact with ALA 155 (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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94B PHE* 3.8 22.0 - - + -
122B ILE* 4.2 12.1 - - + -
132B ILE* 4.4 8.7 - - + +
136B THR* 3.6 15.1 - - + +
140B THR* 3.7 18.5 + - - +
152B PHE* 3.1 9.4 + - + +
154B ALA* 1.3 79.4 - - - +
156B GLN* 1.3 59.8 + - - +
158B LYS* 3.5 3.4 + - - +
159B THR* 3.1 29.6 + - - -
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Residues in contact with GLN 156 (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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94B PHE* 4.1 7.6 - - - -
95B TRP* 3.0 38.3 - - + +
98B CYS* 3.6 31.1 - - + +
99B GLU* 3.2 23.2 + - - +
102B LYS* 3.3 20.9 + - - +
152B PHE 2.7 20.2 + - - +
153B ASP* 3.8 13.7 + - - +
155B ALA* 1.3 72.7 - - - +
157B GLY* 1.3 59.9 + - - +
159B THR* 3.7 2.7 + - - -
160B ARG* 3.0 27.9 + - - +
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Residues in contact with GLY 157 (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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153B ASP 3.0 15.2 + - - -
154B ALA 3.1 3.3 + - - -
156B GLN* 1.3 75.5 - - - +
158B LYS* 1.3 65.7 + - - +
160B ARG* 3.4 8.1 + - - +
161B THR* 3.0 30.5 + - - -
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Residues in contact with LYS 158 (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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131B ASN 5.4 1.6 - - - +
132B ILE* 4.1 18.6 - - + -
133B ASP* 3.6 15.0 - - - +
136B THR* 3.5 31.6 - - + +
154B ALA 3.1 14.0 + - - +
155B ALA 3.8 7.0 - - - +
157B GLY* 1.3 75.1 - - - +
159B THR* 1.3 58.5 + - - +
161B THR* 3.4 6.3 + - - -
162B LEU* 3.0 27.0 + - - +
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Residues in contact with THR 159 (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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91B ASN* 3.4 44.6 + - + +
94B PHE* 3.7 20.9 - - + -
95B TRP* 4.7 7.6 - - + -
130B VAL* 4.0 6.3 - - + +
131B ASN 5.2 0.5 + - - -
132B ILE* 4.0 13.0 - - - +
155B ALA 3.1 17.1 + - - -
156B GLN* 3.9 3.8 - - - -
158B LYS* 1.3 76.3 - - - +
160B ARG* 1.3 66.0 + - - +
162B LEU* 3.2 10.4 + - - +
163B MET* 3.1 23.4 + - + +
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Residues in contact with ARG 160 (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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66B PHE* 3.8 19.0 - - + +
67B ASP* 3.8 34.8 - - - +
70B LEU* 4.4 9.0 - - + +
95B TRP* 4.3 20.7 - - + +
156B GLN* 3.0 20.4 + - - +
157B GLY* 3.4 8.5 + - - +
159B THR* 1.3 74.7 - - - +
161B THR* 1.3 52.7 + - - +
163B MET* 3.2 15.2 + - - +
164B GLU* 2.8 63.6 + - - +
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Residues in contact with THR 161 (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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157B GLY 3.0 18.1 + - - -
158B LYS* 3.5 6.9 - - - -
160B ARG* 1.3 74.5 - - - +
162B LEU* 1.3 61.0 + - - +
164B GLU* 4.2 11.1 + - - +
165B LYS* 2.8 48.3 + - + +
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Residues in contact with LEU 162 (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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180A LYS* 3.6 47.3 - - + +
182A THR* 3.8 26.4 - - + +
91B ASN* 3.8 27.4 - - - +
131B ASN* 3.8 29.4 - - + +
158B LYS 3.0 14.5 + - - +
159B THR* 3.2 13.0 + - - +
161B THR* 1.3 76.6 - - - +
163B MET* 1.3 61.0 + - - +
165B LYS* 5.3 0.7 - - - -
166B ASP* 3.2 30.1 + - - +
167B SER* 4.0 1.2 + - - -
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Residues in contact with MET 163 (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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66B PHE* 3.7 25.8 - - + -
70B LEU* 4.3 14.1 - - + -
79B PHE* 4.1 17.3 - - + -
83B LEU* 4.6 2.2 - - + -
91B ASN* 3.8 19.7 - - + +
92B LEU* 3.6 35.9 - - + -
95B TRP* 4.3 17.0 - - + -
159B THR 3.1 10.8 + - - +
160B ARG* 3.6 19.1 - - - +
162B LEU* 1.3 76.4 - - - +
164B GLU* 1.3 61.7 + - - +
167B SER* 3.4 13.0 + - - +
168B TYR* 2.8 32.4 + - - +
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Residues in contact with GLU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B PHE* 3.6 32.5 - - + +
160B ARG* 2.8 43.3 + - - +
161B THR* 3.9 11.0 + - - +
163B MET* 1.3 75.3 - - - +
165B LYS* 1.3 67.5 + - + +
168B TYR* 3.5 24.0 - - + +
169B PRO* 3.6 5.9 - - - +
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Residues in contact with LYS 165 (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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72A VAL* 5.7 8.7 - - + +
75A SER* 5.9 3.6 - - - +
179A VAL* 3.9 28.3 - - + +
161B THR* 2.8 39.0 + - + +
162B LEU* 4.7 1.1 - - - +
164B GLU* 1.3 81.4 - - + +
166B ASP* 1.3 57.8 + - - +
169B PRO* 3.3 18.9 - - - +
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Residues in contact with ASP 166 (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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179A VAL* 3.6 13.5 - - + +
180A LYS 3.2 24.2 - - - +
181A THR* 3.5 7.2 - - - +
182A THR* 2.9 33.9 + - + +
162B LEU 3.2 16.9 + - - +
165B LYS* 1.3 79.2 - - - +
167B SER* 1.3 61.4 + - - +
169B PRO* 3.3 13.0 - - - +
170B ARG* 2.8 40.4 + - - +
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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