Contacts of the helix formed by residues 165 - 176 (chain i) in PDB entry 5GJQ
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 ASN 165 (chain i).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163i GLY 3.5 0.4 + - - -
164i LYS* 1.3 81.6 - - - +
166i TYR* 1.3 65.5 + - - +
167i VAL* 3.2 7.7 + - - -
168i ASN* 3.4 22.3 + - + +
169i GLY* 3.1 18.9 + - - -
196i GLU 4.5 5.8 + - - +
197i SER* 3.7 28.5 + - - +
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Residues in contact with TYR 166 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29i ALA* 4.0 23.7 - - + +
161i ALA* 3.7 14.1 - - - +
162i MET* 3.6 26.0 - - + +
163i GLY 3.2 23.3 - - - +
164i LYS 3.2 2.4 - - - -
165i ASN* 1.3 77.9 - - - +
167i VAL* 1.3 81.2 + - + +
168i ASN 3.5 0.2 - - - -
169i GLY* 3.8 1.1 - - - +
170i LYS* 2.9 50.1 + - - +
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Residues in contact with VAL 167 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165i ASN* 4.2 3.1 - - - -
166i TYR* 1.3 110.8 - - + +
168i ASN* 1.3 79.8 + - - +
170i LYS* 3.1 10.1 + - - +
171i THR* 3.0 33.5 + - - +
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Residues in contact with ASN 168 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165i ASN* 3.4 23.1 + - + +
167i VAL* 1.3 86.7 - - - +
169i GLY* 1.3 60.8 - - - +
171i THR* 2.6 23.4 + - - +
172i PHE* 3.0 18.8 + - - +
196i GLU* 5.5 8.7 - - + +
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Residues in contact with GLY 169 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161i ALA* 4.3 9.4 - - - -
165i ASN 3.1 14.0 + - - -
166i TYR* 3.8 3.6 - - - -
168i ASN* 1.3 78.6 - - - +
170i LYS* 1.3 56.5 + - - +
172i PHE* 3.4 5.2 - - - +
173i LEU* 2.9 35.6 + - - +
193i THR* 3.7 16.9 + - - -
196i GLU* 5.7 4.7 - - - +
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Residues in contact with LYS 170 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147i GLN* 5.5 1.4 + - - +
157i TRP* 4.3 13.2 - - + -
160i THR* 2.7 31.9 + - - +
161i ALA* 3.4 14.7 + - + +
166i TYR* 2.9 37.5 + - - +
167i VAL* 3.1 9.6 + - + +
169i GLY* 1.3 78.9 - - - +
171i THR* 1.3 57.5 + - + +
173i LEU* 3.2 11.2 + - - +
174i GLU* 2.9 25.8 + - - +
53j HIS* 3.6 35.3 - - + +
55j LEU* 4.6 7.1 - - + +
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Residues in contact with THR 171 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167i VAL 3.0 15.3 + - - +
168i ASN* 2.6 31.0 + - - +
170i LYS* 1.3 73.1 - - + +
172i PHE* 1.3 59.5 + - - +
174i GLU* 2.9 31.5 + - - +
175i LYS* 3.0 15.0 + - - +
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Residues in contact with PHE 172 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160Q MET 5.6 2.5 - - - -
168i ASN 3.0 13.9 + - - +
169i GLY* 3.4 7.0 - - - +
171i THR* 1.3 81.5 + - - +
173i LEU* 1.3 59.1 + - + +
175i LYS* 4.0 3.8 - - - +
176i ARG* 2.8 46.9 + - + +
189i THR* 4.3 5.2 - - - -
192i LEU* 4.0 31.6 - - + -
193i THR* 3.6 36.1 - - - -
196i GLU* 3.2 39.9 - - + -
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Residues in contact with LEU 173 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35i VAL* 5.0 1.6 - - + -
36i GLY 4.7 1.6 - - - +
37i ILE* 4.1 19.1 - - + -
159i ALA* 4.1 6.5 - - + +
160i THR* 3.6 44.9 - - - +
161i ALA* 4.2 7.0 - - + +
169i GLY 2.9 19.4 + - - +
170i LYS* 3.4 9.6 - - - +
172i PHE* 1.3 76.6 - - + +
174i GLU* 1.3 63.6 + - - +
176i ARG 5.0 0.2 - - - -
177i TYR* 3.2 32.2 + - + +
189i THR* 4.2 9.2 - - - +
193i THR* 3.5 33.4 - - + +
55j LEU* 4.3 12.8 - - + +
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Residues in contact with GLU 174 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170i LYS 2.9 11.9 + - - +
171i THR* 2.9 20.3 + - - +
173i LEU* 1.3 76.2 - - - +
175i LYS* 1.3 61.3 + - - +
177i TYR 3.8 6.8 - - - +
178i ASN* 4.0 7.7 + - - +
53j HIS* 5.3 8.9 + - + +
54j LYS* 2.6 38.2 + - + +
55j LEU* 4.5 13.2 - - + +
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Residues in contact with LYS 175 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159Q LYS 3.1 18.6 - - - +
160Q MET* 5.4 0.3 - - - +
161Q ASP* 2.9 35.4 - - + +
171i THR 3.0 12.8 + - - +
172i PHE* 4.0 4.5 - - - +
174i GLU* 1.3 77.5 - - - +
176i ARG* 1.3 55.0 + - + +
177i TYR 2.8 17.2 + - - +
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Residues in contact with ARG 176 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124Q PHE* 5.0 6.5 - - + -
160Q MET* 3.5 39.2 - - + +
172i PHE* 2.8 44.3 + - + +
173i LEU 4.1 0.7 - - - -
175i LYS* 1.3 71.0 - - + +
177i TYR* 1.3 61.1 + - - +
181i LEU* 5.6 0.2 - - - +
189i THR* 3.6 14.8 + - - +
192i LEU* 5.4 6.1 - - + -
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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