Contacts of the helix formed by residues 180 - 196 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A ASP* 3.3 23.7 + - - +
145A SER* 4.3 4.0 + - - -
178A ASN 3.7 1.6 + - - -
179A PRO* 1.3 78.0 - - - +
181A ILE* 1.3 59.9 + - - +
182A GLY* 3.3 6.2 + - - -
183A LEU* 3.0 26.4 + - - +
184A ILE* 3.0 26.1 + - - +
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Residues in contact with ILE 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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180A SER* 1.3 71.2 - - - +
182A GLY* 1.3 60.4 + - - +
184A ILE* 3.3 10.2 + - + +
185A PHE* 2.9 64.2 + - + -
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Residues in contact with GLY 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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112A ASP* 5.5 5.6 - - - -
180A SER* 3.1 7.6 + - - -
181A ILE* 1.3 79.5 - - - +
183A LEU* 1.3 57.1 + - - +
185A PHE* 3.5 7.7 + - - +
186A GLN* 3.1 34.9 + - - +
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Residues in contact with LEU 183 (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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112A ASP* 3.9 26.9 - - + +
115A ILE* 3.9 30.1 - - + -
145A SER* 3.6 25.6 - - - +
146A ARG* 4.1 5.2 - - + +
149A THR* 3.4 34.8 - - + +
179A PRO* 4.0 2.5 - - + -
180A SER* 3.0 33.7 + - - +
182A GLY* 1.3 73.2 - - - +
184A ILE* 1.3 61.3 + - - +
186A GLN* 3.1 10.1 - - - +
187A LEU* 3.0 32.6 + - - +
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Residues in contact with ILE 184 (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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163A LEU* 4.0 16.1 - - + +
167A TYR* 4.7 15.9 - - + -
179A PRO* 3.7 30.3 - - + +
180A SER 3.0 19.8 + - - +
181A ILE* 3.3 13.2 + - + +
183A LEU* 1.3 77.0 - - - +
185A PHE* 1.3 59.4 + - + +
187A LEU* 3.0 20.3 + - + +
188A MET* 2.9 33.6 + - + +
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Residues in contact with PHE 185 (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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181A ILE* 2.9 51.0 + - + +
182A GLY* 3.7 7.0 - - - +
184A ILE* 1.3 73.9 - - + +
186A GLN* 1.3 62.0 + - - +
188A MET* 3.2 33.6 + - + +
189A GLU* 3.0 32.3 + - - +
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Residues in contact with GLN 186 (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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112A ASP 2.7 29.6 - - - +
113A SER* 3.4 24.4 + - - +
115A ILE* 4.3 10.1 - - + +
116A ALA* 3.9 29.5 - - + +
119A LEU* 4.7 5.2 - - + +
149A THR* 5.3 2.9 - - + -
182A GLY 3.1 19.6 + - - +
183A LEU* 3.1 18.0 - - + +
185A PHE* 1.3 78.4 - - - +
187A LEU* 1.3 58.6 + - + +
189A GLU* 3.3 18.7 + - - +
190A TRP* 3.0 26.4 + - - +
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Residues in contact with LEU 187 (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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119A LEU* 5.1 2.9 - - + -
149A THR* 3.5 41.1 - - + +
152A ILE* 3.8 26.0 - - + -
153A ALA* 3.8 25.4 - - + +
156A MET* 3.3 16.3 - - - +
163A LEU* 3.7 21.1 - - + -
179A PRO* 5.4 0.7 - - + -
183A LEU 3.0 18.6 + - - +
184A ILE* 3.0 24.0 + - + +
186A GLN* 1.3 73.8 - - - +
188A MET* 1.3 60.0 + - - +
190A TRP* 3.4 6.5 - - + +
191A GLU 3.0 22.5 + - - -
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Residues in contact with MET 188 (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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163A LEU* 3.7 17.9 - - + -
184A ILE* 2.9 20.3 + - + +
185A PHE* 3.2 43.0 + - + +
187A LEU* 1.3 74.8 - - - +
189A GLU* 1.3 64.6 + - - +
191A GLU* 3.2 18.3 + - - +
192A VAL* 3.2 19.3 + - - +
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Residues in contact with GLU 189 (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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116A ALA* 4.4 17.9 - - + +
185A PHE* 3.0 14.5 + - - +
186A GLN* 3.3 22.9 + - - +
188A MET* 1.3 75.7 - - - +
190A TRP* 1.3 61.3 + - - +
192A VAL* 3.2 10.8 + - - +
193A ALA* 3.1 21.8 + - - +
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Residues in contact with TRP 190 (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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116A ALA 5.2 2.5 - - - -
119A LEU* 3.6 32.8 - - + -
120A PRO* 3.7 37.0 - - + -
123A THR* 3.9 12.1 - - + -
153A ALA* 3.0 36.0 + - + +
156A MET* 3.8 20.9 - - + -
157A LYS* 3.5 32.3 - - + -
186A GLN 3.0 14.5 + - - +
187A LEU* 3.4 11.7 - - + +
189A GLU* 1.3 76.3 - - - +
191A GLU* 1.3 60.0 + - - +
193A ALA* 3.3 14.0 + - + +
194A LEU* 3.0 45.6 + - + +
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Residues in contact with GLU 191 (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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156A MET* 3.6 18.3 - - + +
161A LEU 4.3 1.6 - - - +
162A SER* 3.2 15.6 - - - -
163A LEU* 3.0 39.5 + - - +
187A LEU 3.0 8.4 + - - +
188A MET* 3.2 12.8 + - - +
190A TRP* 1.3 72.9 - - - +
192A VAL* 1.3 67.0 + - + +
194A LEU* 3.0 16.4 + - + +
195A ASN* 3.1 37.2 + - - +
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Residues in contact with VAL 192 (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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188A MET 3.2 14.5 + - - +
189A GLU* 3.2 9.8 + - - +
191A GLU* 1.3 77.1 - - + +
193A ALA* 1.3 63.4 + - - +
195A ASN* 3.2 8.3 + - - +
196A ALA* 3.1 26.9 + - + +
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Residues in contact with ALA 193 (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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189A GLU 3.1 12.2 + - - +
190A TRP* 3.6 21.5 - - + +
192A VAL* 1.3 76.6 - - - +
194A LEU* 1.3 62.4 + - - +
196A ALA* 4.2 13.2 + - - +
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Residues in contact with LEU 194 (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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156A MET* 3.9 10.8 - - + +
157A LYS* 3.7 57.4 - - + +
190A TRP* 3.0 47.6 + - + +
191A GLU* 3.0 15.5 + - + +
193A ALA* 1.3 80.1 - - - +
195A ASN* 1.3 66.4 + - - +
196A ALA 3.4 0.4 + - - -
197A LYS 4.1 4.9 + - - -
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Residues in contact with ASN 195 (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 ASN* 5.1 6.1 - - - +
191A GLU* 3.1 36.5 + - - +
192A VAL* 3.2 6.9 + - - +
194A LEU* 1.3 80.6 - - - +
196A ALA* 1.3 62.7 + - - +
197A LYS 3.2 2.8 + - - -
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Residues in contact with ALA 196 (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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192A VAL* 3.1 19.2 + - + +
193A ALA* 4.2 8.5 + - - +
194A LEU 3.4 0.6 - - - -
195A ASN* 1.3 78.2 - - - +
197A 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