Contacts of the helix formed by residues 189 - 195 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A GLY* 4.8 2.0 - - - -
186A ARG* 3.1 29.3 + - - -
187A PRO 3.2 2.8 + - - -
188A GLY* 1.3 80.1 - - - +
190A PRO* 1.3 72.3 - - - +
191A ALA 3.3 2.9 - - - -
192A ASP 3.2 2.1 + - - -
193A ARG* 2.9 30.2 + - - +
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Residues in contact with PRO 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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155A LEU* 3.7 7.8 - - + +
156A HIS 3.3 34.3 - - - +
158A GLU* 4.1 16.8 - - + +
161A THR 3.6 17.3 - - - +
162A PHE* 3.4 21.5 - - - +
186A ARG* 4.0 11.2 - - - +
189A GLY* 1.3 82.7 - - - +
191A ALA* 1.3 55.0 + - - +
193A ARG* 3.3 16.9 + - - +
194A GLU* 2.9 30.7 + - - +
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Residues in contact with ALA 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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155A LEU* 3.9 18.1 - - + +
162A PHE 3.0 17.9 + - - +
163A GLY 4.0 9.4 - - - +
164A PHE* 3.9 23.3 - - + -
185A VAL* 4.2 8.8 - - + +
189A GLY 3.3 0.4 - - - -
190A PRO* 1.3 72.6 - - - +
192A ASP* 1.3 65.1 + - - +
194A GLU* 3.5 1.9 + - - +
195A GLY* 3.0 20.3 + - - -
196A THR 4.4 1.7 + - - -
197A ILE* 4.4 17.4 + - + +
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Residues in contact with ASP 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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163A GLY 5.1 0.2 + - - -
185A VAL* 3.7 16.2 - - + +
186A ARG 3.3 19.9 + - - +
187A PRO* 3.4 11.1 - - - +
188A GLY* 2.9 22.6 + - - +
189A GLY 3.2 7.4 + - - +
191A ALA* 1.3 77.6 - - - +
193A ARG* 1.3 64.5 + - - +
195A GLY* 3.2 16.1 + - - -
197A ILE 6.0 0.2 - - - -
198A LYS* 5.4 5.5 + - - -
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Residues in contact with ARG 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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158A GLU* 5.1 9.7 - - - +
188A GLY* 2.7 33.2 + - - +
189A GLY* 2.9 21.8 + - - +
190A PRO* 3.7 14.2 - - - +
192A ASP* 1.3 77.6 - - + +
194A GLU* 1.3 63.3 + - - +
195A GLY* 3.5 1.0 + - - -
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Residues in contact with GLU 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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152A GLU 5.5 0.3 - - - +
153A VAL* 3.5 22.9 - - - +
154A THR 3.9 12.0 + - - +
155A LEU* 3.3 28.4 - - + +
190A PRO 2.9 9.2 + - - +
191A ALA 4.1 1.5 - - - +
192A ASP 3.3 0.2 - - - -
193A ARG* 1.3 78.8 - - - +
195A GLY* 1.3 55.6 + - - +
196A THR* 2.8 47.9 + - - -
197A ILE* 4.3 1.6 + - - +
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Residues in contact with GLY 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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191A ALA 3.0 11.4 + - - -
192A ASP* 3.2 14.8 + - - -
193A ARG 4.3 0.9 - - - -
194A GLU* 1.3 76.9 - - - +
196A THR* 1.3 62.2 + - - +
197A ILE 3.7 2.9 - - - -
198A LYS* 3.8 19.5 + - - -
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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