Contacts of the helix formed by residues 163 - 173 (chain J) in PDB entry 5A31
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 CYS 163 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130J SER* 5.8 2.2 - - - -
131J SER* 6.1 2.2 - - - -
134J LEU* 4.5 17.3 - - - -
156J ALA* 5.4 5.2 - - - -
157J LEU* 4.4 7.3 - - - +
160J ASP* 3.8 20.9 - - + +
161J VAL 3.2 9.0 + - - +
162J TYR* 1.3 71.4 - - - +
164J PHE* 1.3 60.7 + - - +
165J GLU* 4.0 4.3 - - - -
166J ALA* 3.8 31.0 + - - +
167J PHE 4.0 4.7 + - - -
13K TYR* 3.1 26.9 + - + +
18K GLN* 4.9 3.8 - - - +
21K SER* 3.7 7.2 - - - +
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Residues in contact with PHE 164 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162J TYR 3.2 7.4 + - - +
163J CYS* 1.3 72.4 - - - +
165J GLU* 1.3 60.3 + - - +
166J ALA 3.2 0.9 - - - -
167J PHE* 3.0 13.0 + + - -
168J ASP* 2.7 70.1 + - + -
205J PHE* 4.0 20.4 - + + -
208J LYS* 3.7 25.8 - - + -
20K GLN* 4.6 14.8 - - - -
21K SER* 3.7 5.3 + - - +
24K PHE* 3.5 70.4 - + + -
25K TRP* 4.4 1.3 - - + +
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Residues in contact with GLU 165 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134J LEU* 4.3 5.8 - - + -
138J LYS* 3.8 27.2 + - - -
163J CYS* 3.2 6.0 - - - -
164J PHE* 1.3 83.5 - - - +
166J ALA* 1.3 60.5 + - - +
168J ASP* 3.7 3.4 + - - +
169J LEU* 3.1 32.3 + - + +
18K GLN* 2.6 41.8 + - - +
19K TYR 4.5 2.1 + - - -
20K GLN* 3.2 34.3 + - + +
21K SER* 3.8 18.6 - - - +
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Residues in contact with ALA 166 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134J LEU* 4.2 15.4 - - + +
153J TYR* 4.2 27.0 - - + +
156J ALA* 4.3 7.0 - - + -
157J LEU* 3.8 18.5 - - + +
163J CYS* 3.8 19.8 - - - +
164J PHE 3.2 0.2 - - - -
165J GLU* 1.3 74.5 - - - +
167J PHE* 1.3 66.9 - - - +
169J LEU* 3.3 3.7 + - - +
170J LEU* 3.1 24.4 + - - +
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Residues in contact with PHE 167 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157J LEU* 3.6 23.4 - - + +
163J CYS 4.0 2.2 + - - +
164J PHE* 3.0 25.6 + + - +
166J ALA* 1.3 77.7 - - - +
168J ASP* 1.3 66.3 + - - +
170J LEU* 2.7 31.7 - - + +
171J THR* 3.0 38.5 + - + +
176J LEU* 6.4 0.2 - - + -
181J GLU* 5.5 5.8 - - + -
184J LEU* 5.1 11.4 - - + -
185J LEU* 5.3 6.5 - - + -
188J LEU* 5.5 4.5 - - + -
205J PHE* 4.0 41.5 - + + -
208J LYS* 4.2 15.9 - - + -
209J LEU* 4.1 26.2 - - + -
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Residues in contact with ASP 168 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164J PHE* 2.7 52.3 + - + +
165J GLU* 4.1 4.3 - - - +
167J PHE* 1.3 75.0 - - - +
169J LEU* 1.3 59.1 + - + +
171J THR* 3.6 13.8 - - - +
172J SER* 2.9 42.6 + - - -
208J LYS* 4.6 5.7 - - - +
20K GLN* 5.0 6.6 + - - +
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Residues in contact with LEU 169 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134J LEU* 5.4 0.7 - - + -
138J LYS* 5.0 12.8 - - + -
141J ASP* 4.0 7.6 - - + +
153J TYR* 2.9 46.9 - - + +
165J GLU* 3.1 30.1 + - + +
166J ALA 3.4 6.7 - - - +
167J PHE 3.2 0.4 - - - -
168J ASP* 1.3 78.2 - - + +
170J LEU* 1.3 62.5 + - - +
172J SER* 4.9 0.2 - - - -
173J HIS* 3.0 55.7 + - + +
175J MET* 4.1 2.3 - - + +
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Residues in contact with LEU 170 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150J THR* 4.8 2.9 - - - +
153J TYR* 4.3 18.6 - - + -
154J LYS* 4.2 16.6 - - + +
157J LEU* 4.2 7.2 - - + -
166J ALA 3.1 18.6 + - - +
167J PHE* 2.7 46.7 - - + +
169J LEU* 1.3 79.9 - - - +
171J THR* 1.3 65.9 + - - +
174J HIS* 3.3 2.4 + - - -
175J MET* 3.1 42.9 + - + -
176J LEU* 3.3 39.6 + - + -
181J GLU* 3.9 4.2 - - - +
184J LEU* 4.0 11.2 - - + -
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Residues in contact with THR 171 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167J PHE* 3.0 46.1 + - + +
168J ASP* 3.5 20.0 - - - +
170J LEU* 1.3 78.6 - - - +
172J SER* 1.3 67.7 + - - +
174J HIS* 3.4 16.3 + - - -
181J GLU* 3.3 25.3 + - - +
208J LYS* 3.1 26.2 + - + +
210J LYS* 4.5 7.4 + - - +
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Residues in contact with SER 172 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168J ASP* 2.9 29.7 + - - -
169J LEU* 4.9 0.2 - - - -
171J THR* 1.3 78.1 - - - +
173J HIS* 1.3 76.8 + - - +
174J HIS* 2.8 29.6 + - - -
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Residues in contact with HIS 173 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141J ASP* 5.5 2.2 - - - -
146J ARG* 6.4 0.2 - - - -
169J LEU* 3.0 45.3 + - + +
172J SER* 1.3 90.0 + - - +
174J HIS* 1.3 81.4 + - - +
175J MET* 3.3 32.1 + - + +
330J GLU* 4.1 14.1 + - + -
332J THR* 3.2 47.8 + - - +
363J LEU 4.7 3.1 - - - +
364J MET* 4.4 11.6 - - - +
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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