Contacts of the helix formed by residues 160 - 180 (chain A) in PDB entry 2JBO
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 GLU 160 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A THR* 1.3 70.5 - - - +
161A ARG* 1.3 56.9 + - - +
163A ALA* 3.0 7.8 + - - +
164A SER 3.0 21.8 + - - -
257A LEU* 4.4 7.6 - - + -
293A GLU 4.6 7.3 - - - +
294A VAL* 4.8 9.5 - - - +
295A SER* 3.7 25.3 + - - -
298A VAL* 3.8 4.5 - - - +
324A TRP* 3.2 37.9 + - + +
331A VAL* 3.9 2.7 - - + -
332A PRO* 3.5 21.7 - - - +
334A THR* 2.7 40.9 + - + +
336A LEU* 3.7 18.0 - - + +
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Residues in contact with ARG 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A THR* 3.2 8.1 + - - +
160A GLU* 1.3 75.3 - - - +
162A GLU* 1.3 60.3 + - - +
164A SER* 3.1 3.2 + - - -
165A GLU* 2.9 50.1 + - - +
328A SER 3.5 14.8 - - - +
329A THR* 2.9 24.6 + - - +
330A LYS* 4.6 4.0 - - - +
331A VAL* 2.9 37.9 + - + +
332A PRO* 3.6 5.2 + - - +
333A GLN* 3.5 38.9 + - - +
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Residues in contact with GLU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ARG* 3.3 36.2 + - - +
158A PHE* 3.6 14.0 - - + -
159A THR* 2.8 49.1 + - - +
161A ARG* 1.3 75.8 - - - +
163A ALA* 1.3 56.7 + - - +
165A GLU* 3.5 15.9 + - - +
166A ILE* 3.1 30.8 + - - +
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Residues in contact with ALA 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PHE* 3.7 26.6 - - + -
159A THR 3.3 4.5 + - - +
160A GLU 3.0 11.3 + - - +
162A GLU* 1.3 77.6 - - - +
164A SER* 1.3 59.6 + - - +
166A ILE* 3.1 5.4 + - - +
167A MET* 2.8 34.6 + - + +
256A LEU* 4.3 15.0 - - + -
257A LEU* 4.7 4.5 - - + -
324A TRP* 4.2 9.6 - - + -
336A LEU* 4.4 8.1 - - + -
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Residues in contact with SER 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLU 3.0 9.0 + - - -
161A ARG* 3.1 12.8 + - - -
163A ALA* 1.3 77.1 - - - +
165A GLU* 1.3 53.7 + - - +
167A MET* 3.2 1.7 + - - +
168A LYS* 2.7 34.0 + - - +
324A TRP* 2.9 55.6 + - - -
325A ILE* 4.3 3.8 - - - +
328A SER* 3.4 17.5 + - - -
331A VAL* 4.3 5.8 - - - -
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Residues in contact with GLU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ARG* 2.9 45.1 + - + +
162A GLU* 3.7 16.3 - - - +
164A SER* 1.3 75.5 - - - +
166A ILE* 1.3 65.4 + - + +
168A LYS* 3.2 5.0 + - - +
169A SER* 3.1 19.2 + - - -
328A SER* 3.8 28.3 - - - +
329A THR* 4.7 2.6 + - - +
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Residues in contact with ILE 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU* 3.9 17.7 - - + -
150A ILE* 4.1 4.3 - - + -
158A PHE* 4.0 26.2 - - + -
162A GLU 3.1 15.8 + - - +
163A ALA 3.1 7.4 + - - +
165A GLU* 1.3 74.9 - - - +
167A MET* 1.3 58.8 + - - +
169A SER* 2.8 26.6 + - - -
170A ILE* 3.1 19.1 + - + +
194A TYR* 3.7 23.3 - - - +
203A LEU* 3.7 20.6 - - + -
256A LEU* 3.6 21.3 - - + -
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Residues in contact with MET 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ALA* 2.8 23.3 + - + +
164A SER 3.8 2.9 - - - +
166A ILE* 1.3 72.4 - - - +
168A LYS* 1.3 63.9 + - - +
170A ILE* 3.4 7.7 + - + +
171A GLY* 2.9 21.1 + - - -
249A LEU* 3.6 48.7 - - + +
252A ILE* 4.0 9.6 - - + -
253A MET* 3.7 35.0 - - + -
256A LEU* 3.7 23.3 - - + -
319A PHE* 4.0 12.3 - - + -
324A TRP* 4.4 6.3 - - + -
325A ILE* 4.3 16.8 - - + -
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Residues in contact with LYS 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A SER 2.7 18.1 + - - +
165A GLU* 3.2 11.2 - - - +
166A ILE 3.1 0.2 - - - -
167A MET* 1.3 72.3 - - - +
169A SER* 1.3 63.6 + - - +
171A GLY* 3.0 11.9 + - - -
172A GLU* 3.1 41.2 + - - +
320A MET* 3.7 9.1 - - + +
325A ILE* 3.4 26.2 + - + +
326A MET* 3.9 22.4 + - - +
328A SER* 3.2 25.7 + - - +
329A THR* 6.3 0.4 - - - +
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Residues in contact with SER 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A HIS* 3.3 41.5 + - - +
165A GLU 3.1 6.4 + - - -
166A ILE* 2.8 14.7 + - - -
168A LYS* 1.3 73.9 - - - +
170A ILE* 1.3 68.2 + - - +
172A GLU* 3.4 13.7 + - - +
173A ALA 3.3 13.5 + - - -
203A LEU* 3.8 26.1 + - - +
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Residues in contact with ILE 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU* 4.5 0.9 - - + -
166A ILE* 3.1 33.6 + - + +
167A MET* 3.9 10.3 - - - +
169A SER* 1.3 75.8 + - - +
171A GLY* 1.3 63.8 + - - +
173A ALA* 2.9 19.2 + - + +
174A ILE* 3.1 15.6 + - + +
187A VAL* 4.6 10.5 - - + -
192A LEU* 3.8 33.4 - - + -
203A LEU* 3.9 12.8 - - + -
205A LEU* 5.8 1.6 - - + -
249A LEU* 3.4 26.7 - - + -
252A ILE* 4.1 23.6 - - + -
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Residues in contact with GLY 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A MET 2.9 15.1 + - - -
168A LYS 3.0 4.9 + - - -
170A ILE* 1.3 75.6 - - - +
172A GLU* 1.3 50.1 + - - +
174A ILE* 3.1 4.3 + - - +
175A GLN* 2.6 37.6 + - - +
249A LEU* 4.6 3.3 - - - +
316A ILE* 3.8 13.2 - - - +
319A PHE* 4.2 5.4 - - - -
320A MET* 3.8 17.7 - - - -
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Residues in contact with GLU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A CYS* 4.7 3.6 - - - -
116A HIS* 3.3 30.4 + - + -
168A LYS* 3.1 40.7 + - - +
169A SER* 3.4 13.3 - - - +
170A ILE 3.3 0.2 - - - -
171A GLY* 1.3 70.6 - - - +
173A ALA* 1.3 54.3 + - - +
175A GLN* 3.1 6.5 + - - +
176A TYR* 2.7 37.7 + - - +
320A MET* 3.4 20.3 - - + +
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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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114A CYS* 4.1 11.4 - - - -
116A HIS* 3.7 29.3 - - + +
117A ILE* 3.9 11.9 - - + +
169A SER 3.3 2.9 + - - +
170A ILE* 2.9 13.0 + - + +
172A GLU* 1.3 79.5 - - - +
174A ILE* 1.3 64.2 + - - +
176A TYR* 3.6 2.1 - - - +
177A LEU* 3.0 28.1 + - - +
205A LEU* 4.3 15.0 - - + -
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Residues in contact with ILE 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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170A ILE* 3.1 20.7 + - + +
171A GLY 3.1 6.3 + - - +
173A ALA* 1.3 72.7 - - - +
175A GLN* 1.3 68.4 + - - +
177A LEU* 3.2 11.1 + - + +
178A HIS* 2.7 53.4 + - + +
187A VAL* 3.8 28.9 - - + -
205A LEU* 4.2 12.1 - - + -
245A ASP* 4.2 17.3 - - + +
246A MET* 4.5 3.8 - - - -
249A LEU* 4.6 11.9 - - + -
316A ILE* 3.6 20.0 - - + -
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Residues in contact with GLN 175 (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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171A GLY 2.6 22.4 + - - +
172A GLU* 3.5 7.6 - - - +
174A ILE* 1.3 73.6 - - - +
176A TYR* 1.3 68.8 + - - +
178A HIS* 3.2 0.9 + - - +
179A SER* 3.0 27.2 + - - -
316A ILE* 3.4 22.1 - - + +
317A THR* 4.6 24.0 + - - +
320A MET* 3.5 30.6 - - + +
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Residues in contact with TYR 176 (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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110A ARG 4.2 2.9 + - - -
111A ALA* 4.2 13.2 - - + -
113A GLN* 3.3 25.2 - - + +
114A CYS* 3.5 45.8 - - + -
115A PRO* 5.3 3.1 - - + -
117A ILE* 4.7 2.7 - - + -
172A GLU 2.7 19.6 + - - +
173A ALA 3.6 3.6 - - - +
175A GLN* 1.3 74.3 - - - +
177A LEU* 1.3 66.5 + - - +
179A SER* 2.8 24.2 + - - -
180A ILE* 3.1 43.4 + - + +
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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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111A ALA* 3.7 31.0 - - + -
117A ILE* 4.1 7.2 - - + -
173A ALA 3.0 15.4 + - - +
174A ILE* 3.3 13.5 - - + +
176A TYR* 1.3 76.8 - - + +
178A HIS* 1.3 66.4 + - + +
180A ILE* 2.9 17.6 + - + +
182A ILE* 3.0 45.9 + - + +
184A HIS* 3.5 43.1 - - + +
205A LEU* 4.2 11.4 - - + -
208A PHE* 4.0 6.7 - - + -
245A ASP* 5.3 0.2 - - - +
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Residues in contact with HIS 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ILE* 2.7 44.0 + - + +
175A GLN 4.1 1.3 - - - +
177A LEU* 1.3 76.4 - - + +
179A SER* 1.3 57.7 + - - +
181A ASN* 2.8 17.7 + - - +
182A ILE 3.3 18.4 - - - -
242A LYS* 3.2 70.3 + - + +
245A ASP* 2.7 25.2 + - + -
246A MET* 4.5 7.8 - - + -
316A ILE* 4.1 21.2 + - + +
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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
----------------------------------------------------------
175A GLN* 3.0 19.3 + - - -
176A TYR* 2.8 17.8 + - - -
178A HIS* 1.3 77.7 - - - +
180A ILE* 1.3 65.0 + - - +
181A ASN* 3.3 4.8 + - - +
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Residues in contact with ILE 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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110A ARG* 3.7 45.2 + - + +
111A ALA* 4.5 1.8 - - - -
176A TYR* 3.5 40.6 - - + +
177A LEU* 2.9 15.7 + - - +
179A SER* 1.3 88.0 + - - +
181A ASN* 1.3 72.7 + - - +
182A ILE* 3.4 21.4 + - + -
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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
------------------------------------------------------------
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