Contacts of the helix formed by residues 161 - 182 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A MET* 1.3 82.3 - - - +
162A THR* 1.3 66.6 + - - +
163A GLN* 3.4 7.4 + - + +
164A LYS* 3.5 8.0 + - + +
165A ARG* 3.1 14.0 + - - +
5F G 5.6 0.4 + - - -
6F G 3.5 34.6 + - - +
7F T 2.8 37.6 + - - +
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Residues in contact with THR 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A LEU* 3.8 26.5 - - + -
161A LYS* 1.3 74.1 - - - +
163A GLN* 1.3 59.6 + - - +
165A ARG* 2.9 19.1 + - - +
166A ALA* 2.3 37.5 + - + +
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Residues in contact with GLN 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A LYS* 3.4 4.9 + - + +
162A THR* 1.3 85.3 - - - +
164A LYS* 1.3 58.6 + - + +
166A ALA* 2.8 30.5 + - - +
167A ALA* 2.8 17.9 + - + +
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Residues in contact with LYS 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A GLY 5.9 0.7 - - - +
145A LEU* 3.4 36.3 - - + +
146A ASN 6.0 0.6 - - - +
149A HIS* 5.5 2.5 - - + -
160A MET* 3.4 22.0 - - + -
161A LYS* 3.6 7.4 - - + +
163A GLN* 1.3 76.5 - - + +
165A ARG* 1.3 71.7 + - - +
167A ALA* 2.6 22.8 + - - +
168A LEU* 3.4 4.7 + - - +
7F T 3.5 41.1 + - - +
8F G 3.1 28.7 + - - -
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Residues in contact with ARG 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A MET 5.2 0.2 + - - -
114A LEU* 4.3 26.9 + - - +
116A GLU 4.6 1.0 + - - -
118A PRO* 3.6 28.9 - - - +
153A HIS* 3.7 24.7 - - - -
160A MET* 3.0 29.1 + - + +
161A LYS 3.1 10.3 - - - +
162A THR* 2.9 24.3 + - + +
164A LYS* 1.3 82.3 - - - +
166A ALA* 1.3 54.0 + - - +
167A ALA 2.4 0.3 + - - -
168A LEU* 2.2 37.8 + - - +
169A TYR* 2.7 44.6 + - + -
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Residues in contact with ALA 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A VAL* 4.2 6.6 - - + +
114A LEU* 3.7 19.1 - - + -
162A THR* 2.3 24.0 + - + +
163A GLN* 2.8 21.7 + - - +
165A ARG* 1.3 69.3 - - - +
167A ALA* 1.3 50.0 + - - +
168A LEU 2.9 1.0 + - - -
169A TYR* 3.6 11.3 - - - +
170A THR* 2.6 37.6 + - - +
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Residues in contact with ALA 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A THR* 3.3 30.0 - - - +
145A LEU* 4.7 8.3 - - + -
163A GLN* 2.8 11.5 + - + +
164A LYS* 3.0 14.6 - - - +
165A ARG 2.4 5.1 + - - -
166A ALA* 1.3 74.1 - - - +
168A LEU* 1.3 59.0 + - - +
170A THR* 3.0 13.6 + - - -
171A TRP* 4.0 1.7 + - - +
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Residues in contact with LEU 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ILE* 4.9 17.0 - - + -
129A MET* 6.1 1.1 - - - -
139A VAL* 4.0 26.9 - - + -
143A THR* 4.6 1.1 - - + -
145A LEU* 4.2 5.8 - - + -
150A LEU* 3.9 24.7 - - + -
153A HIS* 4.3 16.4 - - + +
154A LEU* 4.3 18.8 - - + -
160A MET* 4.9 5.6 - - - -
164A LYS 3.6 7.2 - - - +
165A ARG* 2.2 24.2 + - - +
167A ALA* 1.3 74.0 - - - +
169A TYR* 1.3 87.4 + - + +
170A THR 3.2 0.2 - - - -
171A TRP* 2.9 19.2 + - + +
172A TYR* 2.7 19.4 + - - +
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Residues in contact with TYR 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A VAL* 3.5 28.7 - - + -
113A MET* 3.5 38.9 + - + -
114A LEU* 4.7 9.4 - - + -
118A PRO* 4.3 8.7 + - - +
121A ALA* 3.8 30.8 - - + +
122A ALA 5.3 0.2 + - - -
125A ILE* 4.8 8.1 - - + -
153A HIS* 4.5 3.9 + - - -
165A ARG* 2.7 74.4 + - + -
166A ALA* 3.6 7.4 - - - -
168A LEU* 1.3 89.5 - - + +
170A THR* 1.4 51.9 + - - +
172A TYR* 2.4 30.0 + - - +
173A VAL* 2.7 16.0 + - - +
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Residues in contact with THR 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A GLN 6.5 0.4 - - - -
107A ARG* 6.3 3.8 - - + -
110A VAL* 3.2 20.5 - - + +
166A ALA 2.6 21.0 + - - +
167A ALA* 3.0 13.3 - - - -
169A TYR* 1.4 68.1 - - - +
171A TRP* 1.4 74.6 + - - -
172A TYR 2.9 0.5 + - - -
173A VAL* 3.2 3.3 - - - +
174A ARG* 2.6 50.2 + - - +
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Residues in contact with TRP 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ILE* 5.0 2.5 - - + -
128A TYR* 5.6 1.8 - + - -
129A MET* 4.6 14.6 - - + -
134A ILE* 4.0 25.1 - - + -
138A GLU* 3.9 17.6 + - + +
139A VAL* 3.8 29.6 - - + +
142A VAL* 3.9 40.8 - - + +
143A THR* 3.7 22.9 - - + -
167A ALA 4.0 1.5 + - - +
168A LEU* 2.9 21.5 + - + +
170A THR* 1.4 88.1 + - - +
172A TYR* 1.3 93.0 + + + +
174A ARG* 3.1 7.4 + - + +
175A LYS* 2.9 48.1 + - + +
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Residues in contact with TYR 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A MET* 3.7 33.0 - - + -
124A MET* 4.0 22.9 - - + +
125A ILE* 3.8 27.4 - - + -
128A TYR* 3.3 40.4 - + + +
168A LEU 2.7 9.4 + - - +
169A TYR* 2.4 15.5 + - - +
171A TRP* 1.3 89.8 - + + +
173A VAL* 1.3 76.3 + - + +
175A LYS* 2.9 8.1 + - - +
176A GLN* 2.8 53.6 + - - +
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Residues in contact with VAL 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A GLN* 3.6 38.1 - - + +
109A GLU* 4.1 21.8 - - + -
110A VAL* 3.0 34.1 - - + +
113A MET* 4.7 6.5 - - - -
169A TYR 2.7 6.5 + - - +
170A THR* 3.2 11.2 - - - +
172A TYR* 1.3 86.7 - - + +
174A ARG* 1.3 68.6 + - + +
176A GLN* 2.8 24.1 + - - +
177A ARG* 3.7 11.9 + - - +
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Residues in contact with ARG 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU* 5.8 5.5 - - - +
106A GLN* 3.8 27.0 - - - +
107A ARG* 6.2 1.8 - - - +
170A THR* 2.6 39.2 + - - +
171A TRP* 3.5 10.7 - - + +
173A VAL* 1.3 71.9 - - + +
175A LYS* 1.3 56.6 + - - +
176A GLN 2.5 13.2 + - - -
177A ARG* 2.9 16.4 + - - +
178A GLU* 3.0 15.6 + - + -
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Residues in contact with LYS 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A TYR* 4.0 6.5 + - + -
134A ILE* 3.9 20.2 - - + +
138A GLU* 3.0 37.0 + - - +
171A TRP* 2.9 37.9 + - + +
172A TYR* 2.9 13.2 + - - +
174A ARG* 1.3 76.2 - - - +
176A GLN* 1.3 60.2 + - - +
178A GLU* 3.3 29.1 + - + +
179A ILE* 2.6 60.0 + - + +
182A GLN* 5.1 1.2 - - - +
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Residues in contact with GLN 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A TYR* 3.4 24.3 + - + +
172A TYR* 2.8 49.9 + - - -
173A VAL* 2.8 20.1 + - - +
174A ARG 2.5 5.1 + - - -
175A LYS* 1.3 83.9 - - - +
177A ARG* 1.4 63.4 + - - +
179A ILE* 3.2 3.5 + - - +
180A LEU* 3.0 39.1 + - + +
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Residues in contact with ARG 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A GLU* 2.8 39.4 + - - +
105A GLU* 3.2 31.1 + - - +
106A GLN* 3.3 51.9 + - - +
109A GLU* 6.0 2.4 - - - +
173A VAL* 4.0 16.0 + - - +
174A ARG* 2.9 10.3 + - - +
176A GLN* 1.4 76.6 - - - +
178A GLU* 1.3 73.8 + - - +
180A LEU* 2.6 34.9 + - + +
181A ARG* 3.1 25.1 + - - +
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Residues in contact with GLU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A GLU* 5.1 2.1 - - - +
174A ARG* 3.0 8.9 + - + +
175A LYS* 3.1 42.6 + - + +
177A ARG* 1.3 84.3 - - - +
179A ILE* 1.3 65.3 + - - +
180A LEU 2.7 0.2 + - - -
181A ARG* 2.9 20.5 + - - +
182A GLN* 3.4 26.7 + - - +
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Residues in contact with ILE 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A TYR* 3.9 8.7 - - - +
132A HIS* 3.6 44.4 - - + +
134A ILE* 5.0 4.7 - - + -
175A LYS* 2.6 53.4 + - + +
176A GLN 3.6 3.6 - - - +
178A GLU* 1.3 73.4 - - - +
180A LEU* 1.3 63.6 + - + +
182A GLN* 3.2 34.7 - - - +
183A PHE* 3.0 27.4 - - + +
276A ARG* 6.2 0.7 - - - +
285A GLY 5.4 2.7 - - - +
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Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A GLN* 3.0 22.9 + - + +
177A ARG* 2.6 64.1 + - + +
179A ILE* 1.3 78.5 - - + +
181A ARG* 1.3 62.9 + - - +
182A GLN 3.2 0.2 - - - -
183A PHE* 3.7 6.7 - - + -
184A ASN* 3.4 27.6 + - + +
185A GLN* 4.6 1.0 + - - +
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Residues in contact with ARG 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A GLU* 3.6 31.3 + - - -
177A ARG* 3.1 19.5 + - - +
178A GLU* 2.9 13.9 + - - +
180A LEU* 1.3 79.3 - - - +
182A GLN* 1.3 64.6 + - + +
183A PHE 2.5 12.7 + - - -
184A ASN 3.6 4.0 + - - -
185A GLN* 4.1 9.5 + - - +
186A THR* 3.2 25.0 + - - +
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Residues in contact with GLN 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A LYS* 5.1 1.8 - - - +
178A GLU* 3.4 25.9 + - - +
179A ILE* 3.2 46.2 - - - +
181A ARG* 1.3 81.8 - - + +
183A PHE* 1.3 66.9 + - + +
186A THR* 4.4 6.4 - - - +
282A LYS* 3.7 22.0 + - - -
285A GLY* 3.1 29.9 - - - +
287A GLY* 5.4 2.3 - - - -
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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