Contacts of the helix formed by residues 162 - 172 (chain A) in PDB entry 2KXH
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 VAL 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A CYS* 4.5 2.7 - - - -
136A GLY* 4.7 3.1 - - - -
137A PRO* 5.1 0.2 - - + -
160A TYR* 3.2 16.6 - - - +
161A GLU* 1.3 87.4 - - + +
163A PRO* 1.3 67.3 - - + +
164A GLU* 3.1 12.3 - - - +
165A ALA* 3.3 15.8 + - + +
166A ALA 3.7 0.9 + - - -
212A TYR* 3.4 26.5 - - + +
252A TYR* 3.6 35.9 - - + +
254A PHE* 4.2 13.5 - - + -
289A PRO* 5.8 2.5 - - + -
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Residues in contact with PRO 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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108A LEU* 3.8 12.8 - - + -
111A MET* 4.1 19.8 - - + +
112A CYS* 3.6 33.6 - - - -
161A GLU 4.5 1.1 - - - +
162A VAL* 1.3 82.2 - - + +
164A GLU* 1.3 70.2 + - - +
165A ALA 3.3 0.2 - - - -
166A ALA* 3.1 5.9 + - + +
167A GLN* 2.8 28.1 + - - +
286A VAL* 5.3 5.2 - - + +
287A THR* 3.3 32.8 - - + +
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Residues in contact with GLU 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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162A VAL* 3.1 9.5 - - + +
163A PRO* 1.3 98.7 - - - +
165A ALA* 1.3 60.2 + - - +
167A GLN* 3.2 9.3 + - - +
168A LEU* 3.0 27.9 + - - +
212A TYR* 3.6 28.2 - - + -
254A PHE* 4.0 18.1 - - + -
284A LYS 3.5 21.3 - - - +
285A ALA* 3.6 9.4 - - - -
286A VAL* 2.7 26.4 + - - +
287A THR* 2.8 23.1 + - - +
289A PRO* 5.2 1.0 - - - +
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Residues in contact with ALA 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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135A PHE* 3.4 18.7 - - + +
136A GLY* 3.3 36.1 - - - +
160A TYR* 3.8 11.7 - - + -
162A VAL* 3.3 13.5 + - + +
163A PRO 3.3 0.2 - - - -
164A GLU* 1.3 77.4 - - - +
166A ALA* 1.3 58.1 + - - +
168A LEU* 3.3 2.2 + - - -
169A ALA* 2.9 27.9 + - - +
212A TYR* 3.7 13.4 + - - +
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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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111A MET 3.1 28.3 - - - +
112A CYS 4.2 2.5 - - - -
114A VAL* 3.5 23.0 - - + +
160A TYR* 3.7 22.3 - - + -
162A VAL 3.7 1.0 + - - -
163A PRO* 3.1 11.5 + - + +
165A ALA* 1.3 77.5 - - - +
167A GLN* 1.3 57.8 + - - +
169A ALA* 3.3 3.3 + - - +
170A LEU* 3.0 26.5 + - - +
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Residues in contact with GLN 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 PRO 2.8 12.1 + - - +
164A GLU* 3.2 13.4 + - - +
166A ALA* 1.3 76.7 - - - +
168A LEU* 1.3 64.6 + - + +
170A LEU* 3.1 21.4 + - - +
171A GLU* 2.8 58.1 + - + +
284A LYS 5.4 3.8 - - - +
286A VAL* 4.1 27.5 - - + +
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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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135A PHE* 3.6 20.4 - - + -
164A GLU 3.0 16.7 + - - +
165A ALA* 3.8 3.1 - - - +
167A GLN* 1.3 84.2 - - + +
169A ALA* 1.3 57.5 + - - +
171A GLU* 5.4 2.0 - - + -
172A GLN* 2.9 59.3 + - - +
173A MET 3.6 0.2 + - - -
212A TYR* 3.5 30.5 - - + -
214A ALA* 3.6 19.1 - - + -
281A ARG* 3.9 16.2 - - + +
282A VAL 4.4 3.1 - - - -
283A GLY* 3.8 22.4 - - - -
284A LYS 4.9 2.5 - - - +
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Residues in contact with ALA 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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114A VAL* 4.4 9.4 - - + -
132A PHE* 3.7 16.4 - - + -
135A PHE* 3.5 10.7 - - + -
160A TYR* 3.5 21.8 - - - +
165A ALA 2.9 17.1 + - - +
166A ALA* 3.4 9.2 - - - +
167A GLN 3.2 0.2 - - - -
168A LEU* 1.3 78.4 - - - +
170A LEU* 1.3 59.7 + - - +
173A MET* 3.0 23.8 + - - +
185A VAL* 3.6 12.5 - - + +
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Residues in contact with LEU 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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114A VAL* 5.4 0.9 - - + -
166A ALA 3.0 12.4 + - - +
167A GLN* 3.4 23.3 - - - +
169A ALA* 1.3 76.7 - - - +
171A GLU* 1.3 75.4 + - - +
172A GLN 3.5 0.2 + - - -
174A ASN* 3.3 31.5 - - + +
175A SER* 4.6 0.5 + - - -
185A VAL* 3.2 38.3 - - + +
186A GLY* 5.1 1.8 - - - -
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Residues in contact with GLU 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 GLN* 2.8 51.1 + - + +
168A LEU* 5.4 1.6 - - + -
170A LEU* 1.3 81.6 - - + +
172A GLN* 1.3 71.9 + - - +
175A SER* 2.7 29.8 + - - -
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Residues in contact with GLN 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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135A PHE* 5.1 3.8 - - + -
168A LEU* 2.9 35.9 + - - +
171A GLU* 1.3 86.4 - - - +
173A MET* 1.3 59.2 + - - +
174A ASN 3.3 1.8 - - - -
175A SER* 3.0 3.2 + - - -
176A VAL* 2.9 41.6 + - + +
271A ASN* 4.6 10.5 - - - +
281A ARG* 3.7 39.1 - - + +
282A VAL 3.3 24.4 + - - -
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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