Contacts of the helix formed by residues 166 - 182 (chain A) in PDB entry 2J8X
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 GLY 166 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A VAL* 3.5 23.0 - - - +
163A ALA 5.1 0.6 + - - -
164A ASP* 3.5 2.6 - - - +
165A ILE* 1.3 80.3 - - - +
167A TRP* 1.3 66.0 + - - +
168A ALA 3.3 4.0 + - - +
169A TRP* 3.7 17.1 + - - +
170A PHE* 3.9 6.6 + - - +
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Residues in contact with TRP 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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48A LEU* 4.2 13.9 - - + -
51A VAL* 3.8 16.8 - - + -
52A ILE* 4.3 19.7 - - + -
55A VAL* 3.9 16.4 - - + +
71A CYS* 4.6 14.1 - - - -
72A MET* 5.0 4.3 - - - -
150A THR 3.7 14.5 - - - +
151A ILE* 3.9 19.7 - - + +
152A LEU* 3.6 45.8 - - + -
153A THR* 2.8 39.0 + - + +
162A HIS 4.8 0.4 - - - +
163A ALA 5.5 0.8 + - - -
165A ILE* 3.8 23.9 - - + +
166A GLY* 1.3 79.4 - - - +
168A ALA* 1.3 58.0 + - - +
170A PHE* 3.1 27.1 + + + +
171A THR* 3.0 28.4 + - - +
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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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150A THR* 4.2 4.7 + - - -
151A ILE* 4.3 15.0 - - + +
163A ALA 4.8 7.1 + - - +
166A GLY* 3.3 2.0 - - - +
167A TRP* 1.3 75.9 - - - +
169A TRP* 1.3 59.9 + - - +
171A THR* 3.8 7.6 - - - -
172A ASP* 2.9 43.7 + - - +
197A LYS* 5.3 6.1 - - - +
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Residues in contact with TRP 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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40A LEU* 5.5 1.8 - - + -
44A PHE* 3.4 67.9 - + + -
47A LYS* 3.5 42.7 - - + +
48A LEU* 3.8 13.0 - - + -
51A VAL* 5.3 1.8 - - + -
166A GLY* 3.7 14.8 + - - +
167A TRP 3.4 0.6 - - - -
168A ALA* 1.3 77.4 - - - +
170A PHE* 1.3 98.9 + + + +
172A ASP* 3.8 6.2 - - - +
173A HIS* 3.0 42.6 + + + +
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Residues in contact with PHE 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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30A LEU* 3.7 25.1 - - + -
38A LEU* 4.0 10.1 - - + -
40A LEU* 5.0 3.4 - - + -
48A LEU* 3.8 28.3 - - + -
51A VAL* 6.0 0.7 - - + -
72A MET* 2.8 38.4 - - + -
74A TRP* 3.9 7.9 - + - -
152A LEU* 4.2 0.7 - - + -
166A GLY 4.4 2.2 - - - +
167A TRP* 3.1 27.3 + + + +
169A TRP* 1.3 108.7 - + + +
171A THR* 1.3 66.0 + - + +
173A HIS* 3.1 9.9 + + + +
174A VAL* 2.9 47.1 + - + +
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Residues in contact with THR 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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148A LEU* 4.0 19.7 - - + -
149A ASN 3.5 15.7 - - - +
150A THR* 2.6 45.6 + - - +
152A LEU* 4.3 9.6 - - + -
167A TRP 3.0 12.5 + - - +
168A ALA* 3.7 5.5 + - - -
170A PHE* 1.3 83.7 - - + +
172A ASP* 1.3 62.5 + - - +
173A HIS 3.1 1.8 - - - -
174A VAL* 3.3 6.9 + - + +
175A ILE* 2.9 36.4 + - - +
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Residues in contact with ASP 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 27.7 + - - +
169A TRP* 3.8 6.3 - - - +
171A THR* 1.3 78.2 + - - +
173A HIS* 1.3 57.9 + - - +
175A ILE* 3.5 1.5 + - - +
176A SER* 2.9 33.0 + - - -
197A LYS* 2.9 39.8 + - - +
200A LEU* 3.5 26.4 - - + +
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Residues in contact with HIS 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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38A LEU* 4.3 12.7 + - + -
40A LEU* 3.7 30.2 - - + +
44A PHE* 3.5 32.3 - + - -
169A TRP* 3.0 35.1 + + + +
170A PHE* 3.3 11.9 - + - +
171A THR 3.1 0.2 - - - -
172A ASP* 1.3 76.3 - - - +
174A VAL* 1.3 60.4 + - - +
176A SER* 3.5 4.9 + - - -
177A LEU* 3.0 57.9 + - + +
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Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TRP* 3.7 20.6 - - + -
38A LEU* 4.3 17.7 - - + -
74A TRP* 4.3 11.2 - - + -
146A LEU* 4.5 0.2 - - + -
148A LEU* 4.1 15.5 - - + -
170A PHE* 2.9 49.6 + - + +
171A THR* 3.3 10.3 + - + +
173A HIS* 1.3 73.0 - - + +
175A ILE* 1.3 67.3 + - - +
177A LEU* 3.4 1.0 + - - +
178A LEU* 2.9 41.9 + - + +
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Residues in contact with ILE 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL* 5.3 4.5 - - + -
88A LEU* 3.9 38.6 - - + -
148A LEU* 4.3 9.2 - - + -
150A THR* 4.5 7.4 - - + -
171A THR 2.9 26.2 + - - +
172A ASP* 3.6 9.2 - - - +
174A VAL* 1.3 76.9 - - - +
176A SER* 1.3 55.9 + - - +
178A LEU* 3.4 8.6 + - + +
179A SER* 3.0 27.4 + - - -
187A PHE* 4.3 6.8 - - + -
197A LYS* 4.3 16.2 - - + +
200A LEU* 3.8 24.0 - - + -
201A ILE* 3.9 22.9 - - + -
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Residues in contact with SER 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ASP 2.9 22.3 + - - -
173A HIS* 3.8 7.4 - - - -
175A ILE* 1.3 77.4 - - - +
177A LEU* 1.3 59.8 + - - +
179A SER* 3.5 2.6 + - - -
180A GLU* 2.9 46.1 + - - +
200A LEU* 3.7 35.6 + - - +
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Residues in contact with LEU 177 (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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37A PHE* 4.3 8.3 - - + +
38A LEU* 4.2 27.8 - - + +
39A GLN* 5.9 1.1 - - + -
173A HIS* 3.0 53.8 + - + +
174A VAL 3.9 2.7 - - - +
176A SER* 1.3 77.4 - - - +
178A LEU* 1.3 56.9 + - - +
180A GLU* 3.9 21.3 - - - +
181A ARG* 2.8 71.6 + - + +
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Residues in contact with LEU 178 (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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34A TRP* 4.0 15.3 - - + -
37A PHE* 3.6 26.0 - - + -
80A PRO 4.5 6.1 - - - +
83A ILE* 4.6 3.8 - - + -
86A VAL* 4.0 17.3 - - + -
146A LEU* 3.4 31.6 - - + -
148A LEU* 5.3 0.9 - - + -
174A VAL* 2.9 30.5 + - + +
175A ILE* 3.4 8.7 - - - +
177A LEU* 1.3 73.8 - - - +
179A SER* 1.3 64.7 + - - +
182A LEU* 3.1 49.4 + - + +
187A PHE* 4.3 9.6 - - + -
206A HIS* 4.4 0.2 - - - -
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Residues in contact with SER 179 (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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175A ILE 3.0 13.8 + - - -
176A SER 3.6 8.5 - - - -
178A LEU* 1.3 78.0 - - - +
180A GLU* 1.3 58.8 - - - +
182A LEU 3.5 0.5 - - - +
187A PHE* 4.0 8.2 - - - -
200A LEU 3.9 13.4 + - - -
201A ILE* 3.6 5.0 - - - -
202A ASN* 2.9 33.0 + - - +
205A LYS* 2.8 14.0 + - - +
206A HIS* 2.7 35.6 + - - -
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Residues in contact with GLU 180 (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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176A SER* 2.9 35.0 + - - +
177A LEU* 3.3 24.3 + - - +
179A SER* 1.3 77.9 - - - +
181A ARG* 1.3 63.7 + - + +
205A LYS* 2.8 20.1 + - - +
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Residues in contact with ARG 181 (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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36A ASP 4.4 4.8 + - - -
37A PHE* 2.4 67.6 + - + +
39A GLN* 4.0 16.1 - - - +
177A LEU* 2.8 44.6 + - + +
180A GLU* 1.3 77.1 - - + +
182A LEU* 1.3 66.1 + - - +
183A LYS* 3.8 8.7 + - - +
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Residues in contact with LEU 182 (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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37A PHE* 4.1 11.2 - - + -
80A PRO 3.9 16.2 - - - +
81A SER* 4.0 21.3 - - - +
83A ILE* 3.6 33.0 - - + +
178A LEU* 3.1 33.4 + - + +
181A ARG* 1.3 82.9 - - - +
183A LYS* 1.3 61.3 + - - +
184A ALA 4.3 2.9 - - - +
185A CYS* 3.8 24.5 - - + -
205A LYS* 2.9 25.6 + - - -
206A HIS* 3.1 12.6 - - + -
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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
------------------------------------------------------------
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