Contacts of the helix formed by residues 152 - 166 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94D PHE* 3.8 18.6 - + + -
98D CYS* 3.5 23.6 - - + -
101D PHE* 3.7 36.3 - + + -
114D ALA* 3.4 25.8 - - - -
117D ILE* 3.3 32.5 - - + -
118D PHE* 4.1 7.4 - - + -
122D ILE* 4.3 4.7 - - + -
140D THR* 3.8 26.2 - - + -
144D LEU* 5.1 1.1 - - + -
149D ALA 4.7 1.2 + - - -
150D THR 3.3 0.6 - - - -
151D CYS* 1.3 92.3 - - + +
153D ASP* 1.3 60.7 + - - +
154D ALA 3.4 2.0 - - - -
155D ALA* 3.3 5.8 + - - +
156D GLN* 2.8 31.4 + - - +
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Residues in contact with ASP 153 (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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102D LYS* 3.6 27.2 + - - -
149D ALA 3.7 5.4 - - - +
150D THR* 3.2 41.7 + - - +
151D CYS 3.5 0.4 - - - -
152D PHE* 1.3 77.5 + - - +
154D ALA* 1.3 63.3 + - - +
156D GLN* 4.1 6.1 - - - +
157D GLY* 3.2 19.8 + - - -
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Residues in contact with ALA 154 (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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136D THR* 3.9 9.8 + - + +
139D LEU* 3.5 33.7 - - + -
140D THR* 5.6 2.0 - - - +
143D ASN* 5.6 4.4 - - - +
150D THR 5.0 0.2 + - - -
151D CYS 5.1 1.5 + - - +
152D PHE 3.4 0.4 - - - -
153D ASP* 1.3 78.3 - - - +
155D ALA* 1.3 61.1 + - - +
157D GLY* 3.7 1.2 + - - -
158D LYS* 3.4 26.3 + - - +
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Residues in contact with ALA 155 (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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94D PHE* 3.6 21.5 - - + -
122D ILE* 4.3 2.5 - - + -
132D ILE* 4.3 12.0 - - + +
136D THR* 3.4 22.9 - - + +
140D THR* 3.6 18.2 + - - +
152D PHE* 3.3 8.0 + - - +
154D ALA* 1.3 76.3 - - - +
156D GLN* 1.3 60.2 + - - +
158D LYS* 3.4 2.5 + - - +
159D THR* 3.0 31.5 + - - -
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Residues in contact with GLN 156 (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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94D PHE* 3.7 9.6 - - - -
95D TRP* 3.3 52.8 + - + +
98D CYS* 3.7 22.7 - - + +
99D GLU* 3.3 21.4 + - - -
102D LYS* 3.1 25.5 + - - -
152D PHE 2.8 20.4 + - - +
153D ASP* 4.1 7.4 - - - +
155D ALA* 1.3 72.5 - - - +
157D GLY* 1.3 53.0 + - - +
159D THR* 3.3 2.4 + - - -
160D ARG* 2.8 34.6 + - + +
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Residues in contact with GLY 157 (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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153D ASP 3.2 15.0 + - - -
154D ALA 4.1 2.0 - - - -
155D ALA 3.3 0.2 - - - -
156D GLN* 1.3 78.4 - - - +
158D LYS* 1.3 55.6 + - - +
160D ARG* 3.3 8.3 - - - +
161D THR* 3.0 31.0 + - - -
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Residues in contact with LYS 158 (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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86C ARG* 6.3 1.6 - - - +
131D ASN 5.6 2.6 - - - +
132D ILE* 4.6 15.7 - - + -
133D ASP* 4.6 12.3 - - - +
136D THR* 3.6 23.8 - - - +
154D ALA 3.4 15.5 + - - +
155D ALA* 3.4 7.5 + - - +
156D GLN 3.3 0.4 - - - -
157D GLY* 1.3 73.0 - - - +
159D THR* 1.3 61.8 + - - +
161D THR* 3.5 9.7 + - + +
162D LEU* 3.0 29.5 + - - +
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Residues in contact with THR 159 (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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91D ASN* 3.1 50.6 + - + +
94D PHE* 3.3 24.3 - - + -
95D TRP* 4.9 2.7 - - + +
130D VAL* 4.1 12.5 - - + +
131D ASN 5.9 0.4 - - - -
132D ILE* 4.1 6.8 - - - +
155D ALA 3.0 18.6 + - - -
156D GLN 3.7 3.1 - - - -
158D LYS* 1.3 75.0 - - - +
160D ARG* 1.3 63.4 + - - +
162D LEU* 3.6 7.6 - - - +
163D MET* 3.3 25.1 + - + +
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Residues in contact with ARG 160 (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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66D PHE* 4.1 7.1 - - + -
70D LEU* 5.8 2.2 - - + -
95D TRP* 4.5 13.5 - - - +
156D GLN 2.8 15.1 + - - +
157D GLY* 3.3 12.8 - - - +
159D THR* 1.3 72.1 - - - +
161D THR* 1.3 68.8 + - - +
162D LEU 3.0 1.1 - - - -
163D MET* 2.9 26.4 + - + +
164D GLU* 2.9 16.1 + - - +
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Residues in contact with THR 161 (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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157D GLY 3.0 13.9 + - - -
158D LYS* 3.9 10.1 - - + +
160D ARG* 1.3 77.6 - - - +
162D LEU* 1.3 63.4 + - - +
164D GLU* 4.4 6.7 - - - -
165D LYS* 3.0 38.9 + - + +
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Residues in contact with LEU 162 (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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180C LYS* 3.6 51.4 - - + +
182C THR* 3.9 14.4 - - + -
91D ASN* 3.7 30.7 - - - +
131D ASN* 3.8 31.4 - - + +
158D LYS 3.0 19.1 + - - +
159D THR* 3.6 7.9 - - - +
160D ARG 2.9 0.2 + - - -
161D THR* 1.3 78.1 - - - +
163D MET* 1.3 60.8 + - - +
165D LYS* 4.4 1.5 - - - +
166D ASP* 3.2 28.9 + - - +
167D SER* 4.2 0.7 + - - -
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Residues in contact with MET 163 (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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66D PHE* 3.9 16.2 - - + -
70D LEU* 5.2 2.7 - - + -
79D PHE* 4.1 22.9 - - + -
83D LEU* 4.6 3.1 - - + -
91D ASN* 3.7 28.5 - - + +
92D LEU* 3.8 29.8 - - + -
95D TRP* 4.1 21.5 - - + -
159D THR 3.3 22.2 + - - +
160D ARG* 2.9 15.1 + - - +
162D LEU* 1.3 75.1 - - - +
164D GLU* 1.3 64.5 + - - +
165D LYS 3.1 1.2 + - - -
167D SER* 3.2 18.7 + - - +
168D TYR* 2.9 29.5 + - - -
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Residues in contact with GLU 164 (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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66D PHE* 3.3 35.0 - - + -
160D ARG 2.9 12.6 + - - +
161D THR* 3.9 8.5 - - - +
163D MET* 1.3 77.1 - - - +
165D LYS* 1.3 61.0 + - + +
168D TYR* 3.6 13.8 - - + -
169D PRO* 3.5 17.5 - - - +
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Residues in contact with LYS 165 (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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72C VAL* 5.7 7.5 - - + +
75C SER* 5.7 4.9 - - - +
179C VAL* 3.4 26.9 - - + +
180C LYS 6.1 0.4 - - - +
161D THR* 3.0 33.8 + - + +
162D LEU* 4.4 1.6 - - - +
164D GLU* 1.3 82.6 - - + +
166D ASP* 1.3 60.0 + - - +
169D PRO* 3.7 12.5 - - - +
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Residues in contact with ASP 166 (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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179C VAL* 3.5 15.3 - - + +
180C LYS 3.2 22.9 - - - +
181C THR* 3.3 10.9 + - - +
182C THR* 2.9 30.7 + - + +
162D LEU 3.2 14.6 + - - +
165D LYS* 1.3 79.7 - - + +
167D SER* 1.3 66.2 + - - +
168D TYR 3.6 0.4 - - - -
169D PRO* 3.4 10.7 - - - +
170D ARG* 3.1 50.8 + - - +
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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