Contacts of the helix formed by residues 163 - 174 (chain N) in PDB entry 5A0Q
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 THR 163 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161N SER* 3.1 6.7 + - - -
162N GLN* 1.3 88.6 + - - +
164N GLU* 1.3 63.7 + - - +
166N ARG* 3.3 17.0 + - - +
167N ASP* 3.0 48.9 + - - +
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Residues in contact with GLU 164 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153N VAL* 4.4 8.6 - - + +
157N GLN* 2.8 44.2 + - - +
160N LEU* 3.7 21.3 - - + +
161N SER* 3.0 33.7 + - - +
163N THR* 1.3 79.5 - - - +
165N ALA* 1.3 57.8 + - - +
167N ASP* 4.0 3.3 - - - +
168N LEU* 3.0 28.0 + - - +
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Residues in contact with ALA 165 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14N VAL* 4.0 13.2 - - + -
15N LYS 3.1 22.7 - - - +
16N PHE* 2.1 43.2 - - + -
160N LEU* 4.1 13.6 - - + +
161N SER 3.4 0.6 + - - -
164N GLU* 1.3 73.8 - - - +
166N ARG* 1.4 53.7 + - - +
168N LEU* 3.4 7.7 - - - +
169N VAL* 3.1 32.7 + - - +
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Residues in contact with ARG 166 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16N PHE* 1.7 32.3 - - + -
21N VAL* 4.4 9.0 - - + +
162N GLN* 3.0 59.2 + - - +
163N THR* 3.3 20.8 + - - +
165N ALA* 1.4 66.3 - - - +
167N ASP* 1.3 63.4 + - - +
169N VAL* 3.4 2.9 + - - +
170N GLU* 3.0 51.0 + - - +
189N ILE* 6.2 0.2 - - - +
191N THR* 5.8 5.6 - - - +
200N GLU* 5.1 8.7 + - - -
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Residues in contact with ASP 167 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163N THR* 3.0 37.1 + - - +
164N GLU* 4.2 3.1 - - - +
166N ARG* 1.3 80.7 - - - +
168N LEU* 1.3 65.9 + - - +
170N GLU* 3.1 23.1 - - - +
171N ARG* 3.1 33.0 + - + +
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Residues in contact with LEU 168 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14N VAL* 5.4 0.7 - - + -
149N LEU* 3.9 16.2 - - + +
150N LEU* 3.6 41.5 - - + +
153N VAL* 3.7 37.0 - - + -
160N LEU* 4.1 20.6 - - + -
164N GLU 3.0 17.5 + - - +
165N ALA* 3.4 7.9 - - - +
166N ARG 3.2 0.4 - - - -
167N ASP* 1.3 76.5 - - - +
169N VAL* 1.4 53.6 + - + +
171N ARG* 3.8 4.4 - - - +
172N CYS* 2.8 47.0 + - + +
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Residues in contact with VAL 169 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N LEU* 4.4 17.3 - - + -
13N GLY* 5.4 0.4 - - - -
14N VAL* 3.4 26.7 - - + +
21N VAL* 3.5 19.1 - - + -
23N ALA* 3.3 35.0 - - + +
150N LEU* 5.1 3.1 - - + -
165N ALA 3.1 16.6 + - - +
166N ARG 3.9 1.8 - - - +
168N LEU* 1.4 74.4 - - + +
170N GLU* 1.3 65.6 + - + +
172N CYS* 4.1 6.3 - - - -
173N MET* 3.0 30.4 + - + +
189N ILE* 5.2 4.7 - - + -
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Residues in contact with GLU 170 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166N ARG* 3.0 46.1 + - - +
167N ASP* 3.1 22.8 + - - +
169N VAL* 1.3 77.1 - - + +
171N ARG* 1.3 61.1 + - + +
174N ARG* 4.1 12.0 + - - +
187N PHE* 4.3 15.2 - - + -
189N ILE* 4.2 24.4 - - + +
200N GLU* 5.6 2.3 - - - +
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Residues in contact with ARG 171 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167N ASP* 3.1 22.7 + - + +
168N LEU* 3.9 3.4 - - - +
170N GLU* 1.3 79.1 - - + +
172N CYS* 1.3 60.3 + - - +
173N MET 3.2 0.2 - - - -
174N ARG* 3.0 43.3 + - - +
175N VAL* 3.1 14.1 + - + +
140W ASP* 3.2 48.4 + - - +
141W LYS* 4.7 11.7 - - - +
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Residues in contact with CYS 172 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N LEU* 4.1 10.4 - - + +
145N LEU* 5.1 2.0 - - - +
146N ALA* 3.4 46.8 - - - +
149N LEU* 4.0 18.2 - - + -
150N LEU* 5.1 0.9 - - - -
168N LEU* 2.8 30.5 + - + +
169N VAL* 3.3 6.7 + - - +
171N ARG* 1.3 76.4 - - - +
173N MET* 1.3 60.4 + - - +
175N VAL* 3.1 26.5 + - - +
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Residues in contact with MET 173 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10N SER* 4.0 15.0 - - - +
12N LEU* 3.6 29.4 - - + -
23N ALA* 4.0 21.3 - - + +
24N ALA 4.1 1.1 - - - -
25N ASP* 3.6 36.3 - - + +
169N VAL* 3.0 22.7 + - + +
170N GLU 4.6 0.2 - - - +
172N CYS* 1.3 75.4 - - - +
174N ARG* 1.3 61.6 + - - +
175N VAL 4.3 3.1 - - - -
183N SER* 6.0 1.8 - - - -
185N ASN* 6.0 1.4 - - - +
187N PHE* 2.9 49.7 - - + -
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Residues in contact with ARG 174 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170N GLU 4.1 7.1 + - - +
171N ARG* 3.0 37.3 + - - +
173N MET* 1.3 75.4 - - - +
175N VAL* 1.3 69.7 + - - +
185N ASN* 5.0 17.0 - - - +
187N PHE* 4.4 1.2 - - + -
139W GLU* 4.6 3.1 - - - +
140W ASP* 5.6 2.0 + - - -
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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