Contacts of the helix formed by residues 162 - 174 (chain D) in PDB entry 2ZJQ
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 162 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124D GLY 4.7 1.8 - - - -
126D GLY* 3.9 3.4 - - - -
160D ALA* 3.6 6.9 - - - +
161D LYS* 1.3 96.7 - - + +
163D ASP* 1.3 60.0 + - - +
164D GLU* 3.6 12.0 - - - +
165D GLU* 3.1 42.6 + - - +
166D ALA 2.9 21.0 + - - -
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Residues in contact with ASP 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ALA* 3.7 33.7 - - + +
122D PHE 4.4 1.7 + - - +
123D ASP 2.8 23.8 - - - +
124D GLY* 3.0 28.0 + - - +
126D GLY* 3.1 10.6 + - - -
127D ASN 4.3 2.1 - - - +
162D THR* 1.3 70.0 - - - +
164D GLU* 1.3 72.6 + - - +
166D ALA* 3.3 7.8 - - - +
167D ARG* 3.0 23.1 + - - +
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Residues in contact with GLU 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D PHE* 4.0 23.3 - - + -
162D THR* 3.6 12.8 - - - +
163D ASP* 1.3 83.4 - - - +
165D GLU* 1.3 64.6 + - - +
167D ARG* 3.2 12.7 + - - +
168D ALA* 3.4 9.2 + - - +
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Residues in contact with GLU 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU* 5.1 0.9 - - - +
20D PHE* 3.5 24.6 - - + -
22D TYR* 2.8 34.5 + - - +
27D ALA 5.0 0.9 - - - +
29D PRO* 3.0 27.2 - - + +
160D ALA* 4.6 0.2 - - + -
161D LYS* 4.4 10.3 + - - +
162D THR* 3.1 36.2 + - - +
163D ASP 3.3 0.2 - - - -
164D GLU* 1.3 80.5 - - - +
166D ALA* 1.3 69.1 + - - +
168D ALA* 3.1 15.1 - - - +
169D LEU* 3.1 8.1 + - - +
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Residues in contact with ALA 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D GLY 3.1 28.3 - - - +
128D TYR* 6.0 0.2 - - + -
158D THR* 4.7 2.0 - - - +
160D ALA* 3.6 10.9 - - + +
162D THR 2.9 13.5 + - - +
163D ASP* 3.1 13.2 + - + +
165D GLU* 1.3 73.7 - - - +
167D ARG* 1.3 56.5 + - - +
168D ALA 2.8 1.4 + - - -
169D LEU* 2.9 8.0 + - - +
170D LEU* 2.5 50.5 + - + +
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Residues in contact with ARG 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D PRO* 3.1 31.1 + - - +
120D ASN* 3.0 25.7 - - - +
121D ALA* 3.4 19.8 - - - +
128D TYR* 5.3 4.0 - - - -
163D ASP 3.0 7.9 + - - +
164D GLU* 3.5 10.5 - - - +
166D ALA* 1.3 77.2 - - - +
168D ALA* 1.3 68.9 + - - +
170D LEU* 3.1 15.1 - - + +
171D GLN* 2.8 21.2 + - + +
177D PHE* 3.4 29.4 - - + -
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Residues in contact with ALA 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU* 4.2 4.5 - - + -
19D GLN* 4.1 11.7 - - - +
20D PHE* 3.6 28.0 - - + -
164D GLU 3.4 4.8 + - - +
165D GLU 3.1 12.8 + - - +
166D ALA 2.8 0.4 + - - -
167D ARG* 1.3 84.7 - - - +
169D LEU* 1.3 70.5 + - - +
171D GLN* 4.1 1.0 - - - +
172D SER* 2.8 23.3 + - - -
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Residues in contact with LEU 169 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D TYR* 3.9 12.3 - - + -
12D VAL* 3.2 39.0 - - + -
16D LEU* 4.8 4.9 - - + +
29D PRO* 3.2 15.5 - - + +
30D ARG* 3.2 46.4 - - - +
31D ILE* 4.1 11.2 - - + +
158D THR* 4.9 6.1 - - + -
160D ALA* 5.4 0.9 - - + -
165D GLU 3.1 6.9 + - - +
166D ALA* 2.9 8.3 + - - +
168D ALA* 1.3 74.5 - - - +
170D LEU* 1.3 75.6 + - + +
172D SER* 2.5 23.3 + - - -
173D MET* 2.8 15.7 + - + +
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Residues in contact with LEU 170 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31D ILE* 6.3 3.1 - - + -
128D TYR* 3.3 39.7 - - + -
156D ILE* 3.7 37.0 - - + -
158D THR* 4.4 10.3 - - + -
166D ALA* 2.5 29.1 + - + +
167D ARG* 3.1 31.2 - - + +
168D ALA 2.8 0.4 + - - -
169D LEU* 1.3 79.6 - - + +
171D GLN* 1.3 62.8 + - - +
173D MET* 3.4 5.4 - - - +
174D GLY 3.2 17.7 + - - +
175D LEU* 3.3 17.9 - - + -
177D PHE* 4.9 0.9 - - + -
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Residues in contact with GLN 171 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167D ARG* 2.8 14.3 + - + +
168D ALA* 2.9 0.6 + - - -
170D LEU* 1.3 77.0 - - - +
172D SER* 1.3 68.9 + - - +
174D GLY* 2.7 14.7 + - - -
175D LEU* 2.9 40.7 + - + +
177D PHE* 3.9 32.4 - - + +
179D LYS* 4.5 15.7 + - - +
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Residues in contact with SER 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D GLN* 4.1 23.9 + - - +
12D VAL* 3.1 29.5 - - - +
16D LEU* 5.5 4.7 - - - -
168D ALA* 2.8 19.7 + - - -
169D LEU* 2.5 16.5 + - - -
171D GLN* 1.3 73.1 + - - +
173D MET* 1.3 76.9 + - - +
174D GLY* 2.7 3.3 + - - -
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Residues in contact with MET 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 3.2 41.0 - - + +
7D LYS 4.8 0.7 - - - +
8D TYR* 3.1 52.0 - - + -
11D GLN* 4.9 6.6 - - - +
12D VAL* 3.3 11.9 - - + -
31D ILE* 4.1 24.5 - - + -
97D TYR* 4.6 4.0 - - + -
100D LEU* 4.8 9.6 - - + -
104D ILE* 4.1 13.1 - - + +
169D LEU* 2.8 15.2 + - + +
170D LEU* 3.4 4.9 - - - +
172D SER* 1.3 81.4 + - - +
174D GLY* 1.3 59.3 + - - +
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Residues in contact with GLY 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D LEU* 6.0 1.0 - - - +
104D ILE* 3.0 26.7 - - - +
170D LEU 3.2 5.7 - - - +
171D GLN 2.7 10.3 + - - -
172D SER 3.6 1.3 - - - -
173D MET* 1.3 82.7 - - - +
175D LEU* 1.3 69.3 + - - +
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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