Contacts of the helix formed by residues 161 - 174 (chain A) in PDB entry 1TQ6
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 LYS 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A GLU* 3.7 33.3 - - + +
78A THR 4.9 5.3 + - - -
156A SER* 4.4 3.1 - - - +
157A ALA* 5.6 4.7 - - - +
159A ARG* 3.3 37.2 + - - +
160A PHE* 1.3 75.2 - - - +
162A LYS* 1.3 65.8 - - - +
163A ASN* 4.2 4.9 - - - +
164A ASP* 3.2 31.6 + - - +
165A ILE* 3.1 24.3 + - - +
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Residues in contact with LYS 162 (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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160A PHE 3.8 2.2 + - - -
161A LYS* 1.3 71.8 - - - +
163A ASN* 1.3 68.6 + - - +
165A ILE* 3.2 15.7 + - + +
166A ASP* 3.0 47.6 + - - +
169A LYS* 3.6 22.2 - - - +
220A ASN* 3.8 15.8 - - - +
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Residues in contact with ASN 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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77A GLU* 3.6 16.1 - - + +
130A ILE* 3.2 24.7 + - + +
131A GLY* 3.0 34.2 - - - +
161A LYS* 3.2 4.0 - - - +
162A LYS* 1.3 82.2 + - - +
164A ASP* 1.3 64.3 + - - +
166A ASP* 2.9 21.9 + - - +
167A ILE* 3.0 15.2 + - - +
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Residues in contact with ASP 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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75A THR* 6.0 0.2 - - - +
76A GLY* 4.0 11.4 - - - -
77A GLU* 3.5 19.9 + - - +
154A ILE* 4.2 24.5 - - + +
155A ILE 4.0 6.0 - - - +
156A SER* 3.8 23.0 + - - -
160A PHE* 5.1 9.2 - - + -
161A LYS* 3.2 30.7 + - + +
163A ASN* 1.3 79.3 - - - +
165A ILE* 1.3 63.0 + - - +
167A ILE* 3.4 12.5 + - - +
168A ALA* 3.0 22.7 + - - +
180A PHE* 5.5 1.1 - - + -
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Residues in contact with ILE 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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160A PHE* 3.5 22.2 - - + -
161A LYS 3.1 17.0 + - - +
162A LYS* 3.4 24.9 - - + +
163A ASN 3.1 0.2 - - - -
164A ASP* 1.3 77.2 - - - +
166A ASP* 1.3 57.8 + - - +
168A ALA* 3.3 6.8 + - + +
169A LYS* 2.8 34.5 + - - +
216A THR* 3.3 34.8 - - + +
217A PHE* 5.1 7.2 - - + -
220A ASN* 3.6 32.1 - - + +
222A ILE* 4.6 2.9 - - + +
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Residues in contact with ASP 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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130A ILE* 6.0 0.9 - - + -
137A PRO* 3.8 24.3 - - + +
162A LYS* 3.0 40.6 + - - +
163A ASN* 2.9 11.7 + - - +
165A ILE* 1.3 75.9 - - - +
167A ILE* 1.3 53.5 + - + +
169A LYS* 3.1 26.6 + - - +
170A ALA* 2.7 34.3 + - - +
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Residues in contact with ILE 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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75A THR* 4.6 12.6 - - + +
76A GLY* 6.1 0.9 - - - +
77A GLU* 5.4 0.2 - - - +
130A ILE* 3.5 47.3 - - + +
137A PRO* 4.8 4.0 - - + -
140A TYR* 4.0 17.7 - - + -
141A LEU* 4.4 9.6 - - + -
152A PHE* 4.2 9.9 - - + -
154A ILE* 3.8 18.8 - - + -
163A ASN 3.0 15.9 + - - +
164A ASP* 3.6 13.9 - - - +
166A ASP* 1.3 70.8 - - - +
168A ALA* 1.3 61.1 + - - +
170A ALA* 3.1 7.8 + - - +
171A ILE* 2.9 47.8 + - + +
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Residues in contact with ALA 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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154A ILE* 4.1 7.4 - - + +
164A ASP 3.0 13.4 + - - +
165A ILE* 3.5 10.1 - - - +
167A ILE* 1.3 76.4 - - - +
169A LYS* 1.3 57.2 + - - +
171A ILE* 3.4 2.5 + - - +
172A SER* 2.9 32.4 + - - -
178A PHE* 3.7 33.6 - - + -
217A PHE* 4.2 16.2 - - + -
222A ILE* 3.9 9.5 - - + +
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Residues in contact with LYS 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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162A LYS* 3.6 23.4 - - - +
165A ILE* 2.8 26.7 + - - +
166A ASP* 3.1 22.6 + - - +
168A ALA* 1.3 77.6 - - - +
170A ALA* 1.3 56.9 + - - +
172A SER* 4.2 0.3 - - - -
173A ALA* 3.1 32.0 + - + +
220A ASN* 4.0 22.8 - - - +
221A GLY 5.7 0.4 - - - +
222A ILE* 3.2 19.5 - - + +
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Residues in contact with ALA 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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137A PRO* 3.8 21.8 - - + -
138A ASP* 4.2 14.9 - - - +
141A LEU* 3.8 18.6 - - + -
166A ASP 2.7 16.2 + - - +
167A ILE* 3.1 8.5 + - - +
169A LYS* 1.3 72.6 - - - +
171A ILE* 1.3 65.7 + - - +
173A ALA* 3.3 6.3 + - - +
174A MET* 3.0 24.8 + - - +
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Residues in contact with ILE 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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141A LEU* 4.1 15.5 - - + -
146A PHE* 3.8 13.2 - - + -
152A PHE* 3.2 41.5 - - + -
154A ILE* 4.3 2.2 - - + -
167A ILE* 2.9 21.9 + - + +
168A ALA 3.9 3.4 - - - +
170A ALA* 1.3 76.2 - - - +
172A SER* 1.3 63.2 - - - +
174A MET* 2.9 23.8 + - - +
176A LYS* 3.1 44.8 + - + +
177A GLU 3.9 6.1 - - - +
178A PHE* 3.8 20.4 - - + -
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Residues in contact with SER 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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168A ALA 2.9 19.2 + - - -
169A LYS 4.2 2.2 - - - -
171A ILE* 1.3 76.1 - - - +
173A ALA* 1.3 55.2 + - - +
174A MET 2.9 0.2 - - - -
175A LYS* 2.7 30.1 + - - +
176A LYS 4.2 9.2 + - - -
178A PHE* 4.9 3.7 - - - -
221A GLY 4.3 4.7 + - - -
222A ILE* 3.8 22.9 - - - -
223A ALA* 3.4 28.4 + - - +
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Residues in contact with ALA 173 (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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169A LYS* 3.1 20.5 + - + +
170A ALA* 3.7 5.6 - - - +
172A SER* 1.3 78.5 - - - +
174A MET* 1.3 57.5 - - - +
175A LYS* 3.2 8.8 + - - +
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Residues in contact with MET 174 (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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138A ASP* 5.1 7.9 - - - +
141A LEU* 4.3 22.4 - - - -
146A PHE* 3.2 43.3 - - + -
147A TYR* 3.1 32.9 + - + +
170A ALA 3.0 10.3 + - - +
171A ILE* 3.0 14.1 - - - +
172A SER 2.9 0.4 - - - -
173A ALA* 1.3 77.7 - - - +
175A LYS* 1.3 70.5 + - - +
176A LYS* 3.5 19.2 + - + -
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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