Contacts of the helix formed by residues 161 - 182 (chain B) in PDB entry 2H8R
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 LYS 161 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159B PRO 4.1 1.2 + - - -
160B MET* 1.3 70.2 - - - +
162B THR* 1.3 72.7 + - - +
163B GLN* 2.7 9.5 + - + +
164B LYS* 2.6 23.0 + - + +
165B ARG* 3.3 0.4 + - - -
4E G 5.4 0.8 + - - -
5E G 3.6 36.4 + - - +
6E T 3.0 35.2 + - - +
21F A 6.2 2.2 - - - -
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Residues in contact with THR 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LEU* 3.8 21.3 - - + -
160B MET 3.3 3.2 + - - -
161B LYS* 1.3 76.7 - - - +
163B GLN* 1.3 70.9 + - - +
165B ARG* 2.8 22.4 + - - +
166B ALA* 2.7 25.0 + - + +
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Residues in contact with GLN 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LYS* 2.7 11.5 + - + +
162B THR* 1.3 83.0 - - - +
164B LYS* 1.3 71.6 + - + +
166B ALA* 3.0 7.9 - - - +
167B ALA* 3.0 18.2 + - - +
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Residues in contact with LYS 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B GLY 6.1 0.4 - - - -
145B LEU* 3.4 27.4 - - + +
149B HIS* 4.8 1.7 - - + -
160B MET* 3.4 22.4 - - + +
161B LYS 2.6 17.2 + - - +
163B GLN* 1.3 81.4 - - + +
165B ARG* 1.3 68.9 + - - +
166B ALA 2.8 1.8 - - - -
167B ALA* 2.8 8.6 + - - +
168B LEU* 2.8 18.4 + - - +
6E T 2.9 52.3 + - - +
7E T 4.6 16.5 + - - -
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Residues in contact with ARG 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B MET 4.0 4.4 + - - -
114B LEU* 3.6 29.3 + - + +
116B GLU 3.9 7.1 + - - -
118B PRO* 3.9 26.8 - - - +
153B HIS* 3.7 13.1 + - - -
160B MET* 3.1 57.8 + - + +
161B LYS 3.6 1.8 - - - +
162B THR* 3.2 25.8 + - - +
164B LYS* 1.3 76.2 - - - +
166B ALA* 1.3 56.9 - - - +
168B LEU* 2.7 4.9 + - - +
169B TYR* 2.3 75.1 + - + -
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Residues in contact with ALA 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B VAL* 4.4 5.5 - - + +
114B LEU* 4.1 17.7 - - + -
162B THR* 2.7 8.7 + - + +
163B GLN* 3.0 18.6 - - - +
165B ARG* 1.3 84.9 - - - +
167B ALA* 1.4 66.6 + - - +
169B TYR* 3.0 11.0 + - - +
170B THR* 2.7 27.1 + - - -
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Residues in contact with ALA 167 (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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143B THR* 4.4 16.0 - - + +
145B LEU* 4.5 11.2 - - + -
163B GLN 3.0 6.8 + - - +
164B LYS* 2.8 13.1 + - - +
166B ALA* 1.4 78.6 - - - +
168B LEU* 1.3 70.5 + - - +
170B THR* 2.7 23.9 + - - +
171B TRP* 3.0 4.5 + - - +
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Residues in contact with LEU 168 (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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125B ILE* 4.0 31.6 - - + -
129B MET* 5.9 0.7 - - - -
139B VAL* 4.2 24.0 - - + -
143B THR* 4.0 9.4 - - - -
145B LEU* 3.8 15.5 - - + -
150B LEU* 4.4 16.2 - - + -
153B HIS* 4.3 24.2 - - + -
154B LEU* 4.5 9.0 - - + -
160B MET* 4.3 4.9 - - + -
164B LYS 2.8 7.5 + - - +
165B ARG 2.7 11.1 + - - +
167B ALA* 1.3 73.8 - - - +
169B TYR* 1.4 73.9 + - + +
171B TRP* 2.8 28.4 + - + +
172B TYR 3.1 2.6 + - - -
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Residues in contact with TYR 169 (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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110B VAL* 3.6 13.4 - - + +
113B MET* 3.8 51.1 - - + -
114B LEU* 4.0 13.9 - - + -
118B PRO* 3.7 18.2 + - - +
121B ALA* 3.9 19.7 - - + +
122B ALA 5.2 0.7 - - - -
125B ILE* 3.9 19.7 - - + -
153B HIS* 4.4 3.9 + + - -
165B ARG* 2.3 83.7 + - + +
166B ALA* 3.7 7.6 - - - +
168B LEU* 1.4 74.4 - - + +
170B THR* 1.3 67.2 + - - +
172B TYR* 2.8 9.0 + - - +
173B VAL* 2.7 22.2 + - - +
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Residues in contact with THR 170 (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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110B VAL* 3.3 23.7 - - - +
166B ALA 2.7 17.5 + - - -
167B ALA* 2.7 14.9 + - - +
169B TYR* 1.3 75.2 - - - +
171B TRP* 1.4 71.3 + - - +
173B VAL* 2.9 4.1 + - + +
174B ARG* 2.8 53.1 + - - +
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Residues in contact with TRP 171 (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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125B ILE* 4.5 5.8 - - + -
128B TYR* 5.4 4.9 - + - -
129B MET* 4.3 22.0 - - + -
134B ILE* 4.4 10.8 - - + -
138B GLU* 3.9 28.5 + - - -
139B VAL* 3.5 31.9 - - + -
142B VAL* 3.9 31.2 - - + +
143B THR* 3.9 22.2 - - + -
167B ALA 3.0 1.8 + - - -
168B LEU* 2.8 25.5 + - + +
170B THR* 1.4 82.0 - - - +
172B TYR* 1.3 101.6 + + + +
174B ARG* 2.9 8.0 - - + +
175B LYS* 2.9 46.2 + - + +
178B GLU* 5.7 0.6 + - - -
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Residues in contact with TYR 172 (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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109B GLU* 6.3 0.9 - - - -
113B MET* 3.8 30.7 - - + -
124B MET* 3.4 26.8 - - + +
125B ILE* 4.0 24.5 - - + -
128B TYR* 3.2 42.2 - + + -
168B LEU 3.7 4.5 - - - +
169B TYR* 2.8 11.4 + - - +
171B TRP* 1.3 103.9 - + + +
173B VAL* 1.4 76.7 + - + +
175B LYS* 2.7 15.0 + - + +
176B GLN* 2.7 46.5 + - - +
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Residues in contact with VAL 173 (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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106B GLN* 3.9 31.4 - - + +
109B GLU* 3.2 42.0 - - + +
110B VAL* 3.9 17.9 - - + -
113B MET* 4.8 2.5 - - - -
169B TYR 2.7 16.0 + - - +
170B THR* 3.2 16.4 - - + +
172B TYR* 1.4 84.9 - - + +
174B ARG* 1.3 74.5 + - + +
176B GLN* 3.3 19.7 + - - +
177B ARG* 3.6 14.8 + - - +
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Residues in contact with ARG 174 (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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103B ALA* 5.8 0.8 + - - +
106B GLN* 3.5 38.9 - - - +
107B ARG* 6.2 1.8 - - - +
170B THR* 2.8 32.5 + - - +
171B TRP* 2.9 13.9 - - + +
173B VAL* 1.3 76.9 - - - +
175B LYS* 1.3 56.3 + - - +
176B GLN 2.4 16.0 + - - -
177B ARG* 2.4 21.6 + - + +
178B GLU* 3.3 10.7 + - + +
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Residues in contact with LYS 175 (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 TYR* 5.2 9.4 - - + -
134B ILE* 4.0 19.8 - - + +
138B GLU* 2.5 42.5 + - - +
171B TRP* 2.9 38.3 + - + +
172B TYR* 2.7 9.5 + - + +
174B ARG* 1.3 76.3 - - + +
176B GLN* 1.3 53.5 + - - +
177B ARG 3.1 0.2 - - - -
178B GLU* 3.6 36.8 + - - +
179B ILE* 2.6 64.8 + - + +
182B GLN* 5.3 0.4 + - - -
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Residues in contact with GLN 176 (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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109B GLU* 4.0 19.0 + - - -
128B TYR* 3.7 25.0 - - + +
172B TYR* 2.7 58.0 + - - +
173B VAL* 3.3 18.3 + - - +
174B ARG 2.4 1.6 + - - -
175B LYS* 1.3 82.6 - - - +
177B ARG* 1.3 60.0 + - + +
179B ILE* 3.7 5.0 - - - +
180B LEU* 3.3 16.8 + - - +
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Residues in contact with ARG 177 (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 GLU* 3.3 40.6 + - - +
105B GLU* 3.7 34.9 + - - +
106B GLN* 2.2 56.5 + - - +
109B GLU* 5.2 8.9 + - - +
173B VAL* 3.9 10.5 + - - +
174B ARG* 2.4 26.0 + - + +
176B GLN* 1.3 68.5 - - - +
178B GLU* 1.3 61.2 + - - +
179B ILE 2.6 1.6 - - - -
180B LEU* 2.2 33.7 + - + +
181B ARG* 3.0 27.6 + - - +
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Residues in contact with GLU 178 (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 GLU* 5.4 0.9 - - - +
171B TRP* 5.7 1.0 + - - -
174B ARG* 3.3 5.5 + - + +
175B LYS* 3.5 51.5 + - - +
177B ARG* 1.3 80.4 - - - +
179B ILE* 1.3 60.1 + - - +
181B ARG* 4.2 12.2 + - - +
182B GLN* 3.5 27.1 + - - +
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Residues in contact with ILE 179 (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 TYR* 3.6 22.4 - - + +
132B HIS* 4.4 25.6 - - + +
134B ILE* 5.4 5.4 - - + -
175B LYS* 2.6 53.5 + - + +
176B GLN 3.7 4.0 - - - +
177B ARG 2.5 1.4 + - - -
178B GLU* 1.3 76.9 - - - +
180B LEU* 1.3 72.5 - - + +
182B GLN* 3.2 35.2 + - - +
183B PHE* 3.9 16.5 - - + +
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Residues in contact with LEU 180 (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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176B GLN 3.5 12.1 - - - +
177B ARG* 2.2 32.9 + - + +
179B ILE* 1.3 74.2 - - + +
181B ARG* 1.3 64.7 + - - +
182B GLN 2.9 3.6 - - - -
183B PHE* 2.8 18.0 + - + +
184B ASN* 3.4 39.0 + - + +
185B GLN* 5.7 5.2 - - - +
278B VAL* 6.4 1.8 - - + -
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Residues in contact with ARG 181 (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 GLU* 3.7 30.3 + - - -
177B ARG* 3.0 28.5 + - - +
178B GLU* 4.3 10.2 - - - +
180B LEU* 1.3 71.7 - - - +
182B GLN* 1.3 60.6 + - + +
183B PHE* 2.4 18.3 + - - -
185B GLN* 3.1 64.5 + - + +
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Residues in contact with GLN 182 (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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175B LYS* 5.3 0.3 + - - -
178B GLU* 3.5 21.6 - - - +
179B ILE* 3.2 34.0 - - - +
180B LEU 2.8 1.8 + - - -
181B ARG* 1.3 84.5 - - + +
183B PHE* 1.3 64.0 + - + +
185B GLN 4.9 1.7 - - - +
284B HIS* 3.9 17.8 + - - -
285B GLY* 2.7 38.3 + - - -
286B LEU 4.9 0.4 + - - -
287B GLY* 4.8 5.7 - - - +
288B SER 5.7 0.2 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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