Contacts of the helix formed by residues 189 - 195 (chain B) in PDB entry 2JIL
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 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158B GLU* 5.1 1.1 - - - -
163B GLY* 4.8 3.1 - - - -
186B ARG* 3.1 29.6 + - - +
187B PRO 3.2 2.2 + - - -
188B GLY* 1.3 81.3 - - - +
190B PRO* 1.4 67.8 - - - +
191B ALA 3.3 2.2 - - - -
192B ASP 3.1 2.4 + - - -
193B ARG* 2.8 34.9 + - - +
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Residues in contact with PRO 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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155B LEU* 3.8 12.5 - - + +
156B HIS 3.4 30.1 - - - +
158B GLU* 3.7 11.2 - - + +
161B THR 3.7 15.7 - - - +
162B PHE* 3.3 24.9 - - - +
186B ARG* 3.9 11.0 - - - +
189B GLY* 1.4 82.0 - - - +
191B ALA* 1.3 61.9 + - - +
193B ARG* 3.3 25.7 + - - +
194B GLU* 3.1 24.1 + - - +
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Residues in contact with ALA 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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155B LEU* 3.9 15.3 - - + -
162B PHE 3.1 13.4 + - - +
163B GLY 3.9 9.6 - - - +
164B PHE* 3.8 24.0 - - + -
185B VAL* 4.1 10.8 - - + +
189B GLY 3.3 0.4 - - - -
190B PRO* 1.3 78.1 - - - +
192B ASP* 1.3 66.1 + - - +
194B GLU* 3.5 2.4 + - - +
195B GLY* 3.0 21.3 + - - -
196B THR 4.4 1.2 + - - -
197B ILE* 4.3 16.7 + - + +
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Residues in contact with ASP 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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185B VAL* 3.5 16.6 - - + +
186B ARG 3.3 20.8 + - - +
187B PRO* 3.5 10.1 - - - +
188B GLY* 2.8 23.6 + - - +
189B GLY 3.1 6.7 + - - +
191B ALA* 1.3 77.6 - - - +
193B ARG* 1.3 63.4 + - - +
195B GLY* 3.2 15.8 + - - -
198B LYS* 5.5 5.2 + - - -
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Residues in contact with ARG 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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202A ARG* 4.7 10.6 + - - -
156B HIS* 4.4 6.3 + - - +
158B GLU* 3.0 40.9 - - - +
188B GLY* 3.3 26.4 + - - +
189B GLY 2.8 16.4 + - - +
190B PRO* 3.5 22.5 + - - +
191B ALA 3.3 0.2 - - - -
192B ASP* 1.3 75.1 - - - +
194B GLU* 1.3 61.2 + - - +
195B GLY* 4.4 0.3 - - - -
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Residues in contact with GLU 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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167A ARG* 4.5 3.6 + - - -
179A PRO* 4.4 8.0 - - - +
181A VAL* 5.6 2.8 - - - +
202A ARG* 5.4 5.2 + - - -
153B VAL* 3.4 22.2 - - - +
154B THR 3.9 18.8 + - - +
155B LEU* 3.5 22.3 - - + +
190B PRO 3.1 7.8 + - - +
191B ALA 4.1 1.5 - - - +
193B ARG* 1.3 76.3 - - - +
195B GLY* 1.3 55.9 + - - +
196B THR* 2.8 45.5 + - - -
197B ILE* 4.3 1.2 + - - +
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Residues in contact with GLY 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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178A ARG* 4.3 0.3 - - - -
179A PRO* 3.1 29.9 - - - +
202A ARG* 6.2 0.2 - - - -
191B ALA 3.0 11.4 + - - -
192B ASP* 3.2 15.7 + - - -
193B ARG 4.4 0.4 - - - -
194B GLU* 1.3 75.6 - - - +
196B THR* 1.3 61.5 + - - +
197B ILE 3.6 2.5 - - - -
198B LYS* 3.4 20.5 + - - -
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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