Contacts of the helix formed by residues 162 - 172 (chain A) in PDB entry 1OHT
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 GLY 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A HIS* 3.9 2.6 - - - -
117A TRP 3.7 1.6 - - - -
118A ARG* 3.5 28.9 - - - -
153A ARG* 3.5 5.2 - - - -
159A GLU 3.0 13.2 + - - -
160A CYS* 3.4 2.0 - - - +
161A PRO* 1.3 77.0 - - - +
163A GLY* 1.3 66.8 + - - -
164A ARG 3.4 2.2 - - - -
166A PHE* 2.9 24.9 + - - +
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Residues in contact with GLY 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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118A ARG* 3.4 13.7 + - - +
153A ARG* 3.3 21.6 - - - +
159A GLU* 5.1 1.4 + - - +
162A GLY* 1.3 71.0 - - - -
164A ARG* 1.3 57.3 + - - +
166A PHE* 3.2 3.3 + - - +
167A ALA* 2.9 29.3 + - - +
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Residues in contact with ARG 164 (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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117A TRP 3.5 5.8 - - - +
118A ARG 2.6 20.4 + - - +
119A THR* 3.2 27.4 - - - +
120A GLU 3.6 15.0 - - - +
121A LEU* 3.7 39.2 - - - +
163A GLY* 1.3 69.9 - - - +
165A LEU* 1.3 66.7 + - - +
167A ALA* 3.3 13.4 + - - +
168A GLU* 3.0 32.4 + - - +
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Residues in contact with LEU 165 (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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41A ILE* 3.9 11.2 - - + -
42A HIS 4.1 8.7 - - - +
43A HIS* 4.0 4.3 - - + -
113A LEU* 4.2 15.7 - - + -
117A TRP* 3.2 34.5 + - + +
120A GLU 4.9 0.2 + - - -
122A PRO* 4.0 17.9 - - + -
127A LEU* 5.5 2.2 - - + -
161A PRO* 3.2 38.6 - - + +
162A GLY 3.5 0.2 + - - -
163A GLY 3.4 0.2 - - - -
164A ARG* 1.3 78.0 - - - +
166A PHE* 1.3 57.0 + - - +
168A GLU* 3.2 10.2 + - + +
169A ILE* 2.8 44.7 + - + +
172A TRP* 5.7 0.7 - - + -
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Residues in contact with PHE 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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151A GLY* 4.1 3.8 - - - -
153A ARG* 3.8 42.6 - - + -
154A GLN* 3.6 37.5 - - + -
161A PRO* 4.2 11.1 - - + +
162A GLY 2.9 19.7 + - - +
163A GLY 3.5 5.4 - - - +
165A LEU* 1.3 75.5 - - - +
167A ALA* 1.3 69.6 + - - +
169A ILE* 3.3 16.1 + - + +
170A SER* 3.1 25.5 + - - -
175A PHE* 3.7 29.6 - + - -
177A HIS* 4.5 11.7 - + - -
1188A TLA 5.6 0.2 - - - -
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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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163A GLY 2.9 13.5 + - - +
164A ARG* 3.3 19.3 + - - +
166A PHE* 1.3 80.4 - - - +
168A GLU* 1.3 62.9 + - - +
170A SER* 2.7 23.7 + - - -
171A SER* 3.8 4.3 + - - -
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Residues in contact with GLU 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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121A LEU* 3.7 22.8 - - + +
127A LEU* 3.8 37.3 - - + +
131A LYS* 4.2 8.5 + - - -
164A ARG* 3.0 19.8 + - - +
165A LEU* 3.4 10.3 - - + +
166A PHE 3.1 0.2 - - - -
167A ALA* 1.3 77.6 - - - +
169A ILE* 1.3 66.4 + - + +
171A SER* 3.0 30.0 + - - -
172A TRP* 2.7 33.0 + - + +
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Residues in contact with ILE 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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41A ILE* 3.8 26.5 - - + -
149A LEU* 3.7 6.9 - - + +
150A LEU 4.0 2.7 - - - +
151A GLY* 3.7 34.8 - - - +
161A PRO* 4.4 4.0 - - + -
165A LEU* 2.8 38.2 + - + +
166A PHE* 3.4 23.8 - - + +
168A GLU* 1.3 73.0 - - - +
170A SER* 1.3 58.6 + - - +
171A SER 2.9 0.7 - - - -
172A TRP* 2.8 56.3 + - + +
175A PHE* 3.5 16.1 - - + +
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Residues in contact with SER 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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166A PHE* 3.1 16.1 + - - -
167A ALA* 2.7 23.4 + - - -
169A ILE* 1.3 77.6 - - - +
171A SER* 1.3 56.5 + - - +
172A TRP 3.3 1.6 + - - +
175A PHE* 3.4 44.4 - - - +
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Residues in contact with SER 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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167A ALA 4.6 3.6 - - - -
168A GLU* 3.0 23.2 + - - -
169A ILE 2.9 1.4 - - - -
170A SER* 1.3 78.7 + - - +
172A TRP* 1.3 68.2 + - - +
173A PRO* 3.9 1.9 - - - +
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Residues in contact with TRP 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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41A ILE* 4.6 9.0 - - + -
113A LEU* 5.5 4.7 - - + -
127A LEU* 3.7 37.5 - - + -
130A ALA* 3.8 30.3 - - + -
131A LYS* 3.8 27.5 - - + +
134A ILE* 4.3 19.3 - - + -
149A LEU* 3.4 22.7 - - + -
165A LEU* 5.7 0.2 - - + -
168A GLU* 2.7 35.6 + - + -
169A ILE* 2.8 36.1 + - + +
170A SER 4.5 0.3 - - - +
171A SER* 1.3 89.2 - - - +
173A PRO* 1.3 77.7 - - + +
174A HIS 3.4 0.2 + - - -
175A PHE* 3.1 17.5 + - - +
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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