Contacts of the helix formed by residues 180 - 196 (chain B) in PDB entry 2J16
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 SER 180 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111B HIS* 3.9 25.6 + - - -
145B SER* 3.1 12.5 + - - -
178B ASN* 3.4 3.1 + - - -
179B PRO* 1.3 75.2 - - - +
181B ILE* 1.3 60.7 + - - +
182B GLY* 3.8 4.6 + - - -
183B LEU* 2.8 45.3 + - - +
184B ILE* 3.0 10.6 + - - +
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Residues in contact with ILE 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B PRO 3.6 1.7 + - - +
180B SER* 1.3 72.5 - - - +
182B GLY* 1.3 62.6 + - - +
183B LEU 3.2 0.2 + - - -
184B ILE* 3.2 13.4 + - + +
185B PHE* 3.0 50.9 + - + -
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Residues in contact with GLY 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B HIS* 5.9 1.8 - - - -
112B ASP* 6.6 0.2 - - - -
180B SER* 3.1 6.5 + - - -
181B ILE* 1.3 78.5 - - - +
183B LEU* 1.3 60.0 + - - +
185B PHE* 3.6 10.2 + - - +
186B GLN* 3.3 30.0 + - - +
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Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B TRP* 5.3 1.6 - - + -
110B GLU 5.5 2.0 - - - +
111B HIS* 4.2 14.1 - - - +
113B SER 4.8 2.5 - - - +
115B ILE* 4.1 33.0 - - + -
145B SER* 3.3 25.6 - - - +
146B ARG* 4.0 22.9 - - + -
149B THR* 3.8 23.7 - - + +
179B PRO* 4.6 0.4 - - + -
180B SER* 2.8 22.1 + - - +
182B GLY* 1.3 76.5 - - - +
184B ILE* 1.3 58.3 + - - +
186B GLN* 3.2 22.6 + - - +
187B LEU* 3.0 30.2 + - - +
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Residues in contact with ILE 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ILE* 6.3 0.2 - - + -
163B LEU* 3.9 13.4 - - + +
167B TYR* 5.5 7.6 - - + -
179B PRO* 3.3 48.9 - - + +
180B SER 3.0 9.2 + - - +
181B ILE* 3.2 14.1 + - + +
183B LEU* 1.3 72.9 - - - +
185B PHE* 1.3 65.8 + - + +
187B LEU* 3.1 16.3 + - + +
188B MET* 3.1 41.9 + - + +
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Residues in contact with PHE 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B ILE* 3.0 46.1 + - + -
182B GLY* 3.7 11.4 - - - +
184B ILE* 1.3 75.8 - - + +
186B GLN* 1.3 61.4 + - + +
188B MET* 3.3 37.1 + - + +
189B GLU* 3.2 25.9 + - - +
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Residues in contact with GLN 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ASP 4.6 3.2 + - - -
113B SER 2.6 23.9 + - - -
114B GLN* 3.3 25.9 - - - +
115B ILE* 2.9 44.3 + - + +
116B ALA* 4.2 5.0 + - + +
119B LEU* 5.0 2.8 - - - +
182B GLY 3.3 20.1 + - - +
183B LEU* 3.2 20.2 + - - +
185B PHE* 1.3 75.6 - - + +
187B LEU* 1.3 60.1 - - - +
189B GLU* 3.3 22.4 + - - +
190B TRP* 3.0 24.6 + - - +
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Residues in contact with LEU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ILE* 5.2 0.2 - - + -
119B LEU* 5.0 3.8 - - + -
149B THR* 3.7 43.5 - - + +
152B ILE* 3.8 17.7 - - + -
153B ALA* 3.8 24.0 - - + +
156B MET* 3.4 17.9 - - - +
163B LEU* 3.7 28.5 - - + -
179B PRO* 5.5 0.7 - - + -
183B LEU 3.0 17.0 + - - +
184B ILE* 3.1 20.1 + - + +
186B GLN* 1.3 74.8 - - - +
188B MET* 1.3 58.9 + - - +
190B TRP* 3.2 9.9 + - + +
191B GLU 2.9 23.0 + - - -
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Residues in contact with MET 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B LEU* 3.7 16.4 - - + +
184B ILE* 3.1 32.8 + - + +
185B PHE* 3.4 43.3 - - + +
187B LEU* 1.3 74.3 - - - +
189B GLU* 1.3 58.1 + - - +
191B GLU* 3.1 12.6 + - - +
192B VAL* 3.0 32.6 + - + +
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Residues in contact with GLU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B GLN* 4.8 9.3 - - - +
116B ALA* 4.7 16.9 - - + +
185B PHE* 3.2 14.7 + - - +
186B GLN* 3.3 24.2 - - - +
188B MET* 1.3 76.5 - - - +
190B TRP* 1.3 58.0 + - - +
192B VAL* 3.3 9.9 + - - +
193B ALA* 3.0 28.5 + - - +
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Residues in contact with TRP 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ALA* 4.8 5.2 - - - -
119B LEU* 3.6 36.1 - - + -
120B PRO* 3.9 36.1 - - + -
123B THR* 4.1 10.3 - - + -
153B ALA* 3.1 36.1 + - + -
156B MET* 3.9 14.1 - - + -
157B LYS* 3.9 19.7 - - + -
186B GLN 3.0 13.6 + - - +
187B LEU* 3.2 10.7 + - + +
189B GLU* 1.3 75.0 - - - +
191B GLU* 1.3 58.2 + - - +
193B ALA* 3.4 14.3 + - + +
194B LEU* 2.9 73.8 + - + +
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Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B MET* 3.5 17.5 - - + +
161B LEU 5.7 0.4 - - - +
162B SER* 3.4 29.0 - - - -
163B LEU* 3.6 26.4 - - - +
187B LEU 2.9 8.0 + - - +
188B MET* 3.1 13.2 + - - +
190B TRP* 1.3 74.3 - - - +
192B VAL* 1.3 63.6 + - + +
194B LEU* 3.5 5.5 + - + +
195B ASN* 2.8 45.7 + - - +
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Residues in contact with VAL 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B MET* 3.0 18.6 + - + +
189B GLU* 3.3 10.5 + - - +
191B GLU* 1.3 75.2 - - + +
193B ALA* 1.3 58.7 + - - +
195B ASN* 3.4 5.1 + - - +
196B ALA* 2.9 30.5 + - + +
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Residues in contact with ALA 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B GLU 3.0 13.9 + - - +
190B TRP* 3.4 24.5 - - + +
192B VAL* 1.3 78.9 - - - +
194B LEU* 1.3 61.3 + - - +
196B ALA* 3.2 22.0 + - - +
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Residues in contact with LEU 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B MET* 3.8 14.1 - - + +
157B LYS* 3.6 51.1 - - + +
160B ASN* 6.3 0.9 - - - +
161B LEU 5.7 0.4 - - - +
190B TRP* 2.9 63.8 + - + +
191B GLU* 4.0 4.9 - - + +
192B VAL 3.4 0.2 - - - -
193B ALA* 1.3 76.4 - - + +
195B ASN* 1.3 65.1 + - - +
196B ALA 3.8 0.5 + - - -
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Residues in contact with ASN 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B ASN* 4.9 10.4 + - - -
191B GLU* 2.8 42.3 + - - +
192B VAL* 3.7 5.3 - - - +
194B LEU* 1.3 78.6 - - - +
196B ALA* 1.3 57.2 + - - +
197B LYS 3.1 10.3 + - - -
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Residues in contact with ALA 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B VAL* 2.9 20.5 + - + +
193B ALA* 3.2 15.5 + - - +
195B ASN* 1.3 76.4 - - - +
197B LYS 1.2 46.3 + - - +
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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