Contacts of the helix formed by residues 190 - 202 (chain A) in PDB entry 2IGT
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 ASP 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A GLU* 1.3 79.4 - - + +
191A ALA* 1.3 63.3 + - - +
192A MSE 3.2 5.7 + - - -
193A LYS* 3.0 26.7 + - + +
194A PHE* 3.0 21.7 + - - +
218A GLY* 3.4 20.2 - - - -
219A THR* 3.6 7.7 + - - +
222A GLU* 3.8 18.6 + - - +
224A TRP* 5.4 0.2 - - - -
1001A SAM 2.9 25.2 + - - -
79C ARG* 2.8 45.9 + - - -
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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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139A LEU* 4.4 9.6 - - + +
140A PHE* 3.7 29.2 - - + +
160A VAL* 4.0 17.0 - - + -
190A ASP* 1.3 72.9 - - - +
192A MSE 1.3 58.7 + - - +
194A PHE* 3.4 3.6 + - - +
195A ILE* 3.1 31.4 + - - +
224A TRP* 6.2 0.2 - - + -
233A MSE 3.8 8.1 - - + -
1001A SAM 2.9 27.8 + - + +
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Residues in contact with MSE 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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-2A PHE* 3.9 13.2 - - + -
190A ASP* 3.2 9.3 + - - +
191A ALA* 1.3 76.0 - - - +
193A LYS* 1.3 59.5 + - - +
195A ILE* 3.3 8.5 + - + +
196A GLN* 2.9 30.6 + - + +
224A TRP* 4.1 7.3 - - + -
229A HIS* 3.7 27.4 - - + +
232A LEU* 3.9 13.9 - - + -
233A MSE 3.6 43.8 - - + +
236A ILE* 4.1 15.0 - - + -
79C ARG* 3.5 37.0 - - - +
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Residues in contact with LYS 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* 3.5 24.2 - - + +
190A ASP* 3.0 22.8 + - + +
192A MSE 1.3 75.3 - - - +
194A PHE* 1.3 63.4 + - - +
196A GLN* 3.4 5.9 + - - +
197A ARG* 3.0 61.5 + - + +
220A HIS* 5.1 11.1 - - + +
222A GLU* 2.6 36.3 + - - +
79C ARG* 4.5 3.0 - - - +
82C PHE* 5.3 13.0 - - - -
104C PHE 5.7 3.4 + - - -
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Residues in contact with PHE 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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137A LEU* 3.8 8.5 - - + -
158A THR* 3.8 16.8 - - + -
160A VAL* 3.6 32.5 - - + -
185A ARG* 4.1 7.0 - - - -
187A ILE* 3.7 23.1 - - + -
189A GLU* 3.3 26.2 + - + +
190A ASP 3.0 17.0 + - - +
191A ALA 3.6 3.4 - - - +
193A LYS* 1.3 77.0 - - - +
195A ILE* 1.3 68.8 + - + +
197A ARG* 3.2 4.2 + - - +
198A GLU* 2.8 55.1 + - + +
201A ARG* 3.8 14.8 - - - -
205A TYR* 3.8 9.0 - - - -
1005A GOL 3.4 15.3 - - - -
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Residues in contact with ILE 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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137A LEU* 3.9 4.3 - - + -
139A LEU* 3.7 28.9 - - + -
191A ALA 3.1 18.5 + - - +
192A MSE 3.4 15.0 - - - +
194A PHE* 1.3 81.0 - - + +
196A GLN* 1.3 56.9 + - - +
198A GLU* 3.3 7.2 + - - +
199A GLU 2.8 23.9 + - - -
233A MSE 3.5 49.6 - - + +
236A ILE* 3.3 26.3 - - + +
237A CYS* 4.0 8.1 - - - -
240A ILE* 3.7 22.3 - - + +
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Residues in contact with GLN 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 MSE 2.9 18.8 + - + +
193A LYS* 3.9 5.1 - - - +
195A ILE* 1.3 77.5 - - - +
197A ARG* 1.3 60.0 + - + +
199A GLU* 3.3 11.7 + - - +
200A ARG* 2.9 26.9 + - - +
232A LEU* 5.5 2.4 - - - +
236A ILE* 4.1 23.2 - - + +
81C ARG* 3.9 12.6 + - - +
82C PHE* 2.8 49.9 + - - +
83C PRO 5.3 0.2 - - - -
84C LYS 3.9 10.9 + - - -
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Residues in contact with ARG 197 (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* 3.2 15.0 + - - -
193A LYS* 3.0 51.9 + - + +
194A PHE 3.6 1.3 - - - +
196A GLN* 1.3 75.5 - - + +
198A GLU* 1.3 59.1 + - - +
200A ARG* 3.3 30.7 + - - +
201A ARG* 2.9 53.6 + - - +
1005A GOL 2.9 35.4 + - - +
82C PHE* 6.2 0.2 - - - -
87C LEU* 4.3 9.9 + - + +
88C GLY* 3.9 28.5 - - - -
89C GLU* 4.4 4.9 - - - +
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Residues in contact with GLU 198 (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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185A ARG* 3.6 10.9 + - - -
194A PHE* 2.8 50.6 + - + +
195A ILE* 3.4 11.2 - - - +
197A ARG* 1.3 68.5 - - - +
199A GLU* 1.3 66.1 + - - +
201A ARG* 2.9 38.0 + - - +
202A GLY 3.0 4.3 + - - -
203A SER* 3.0 45.9 + - - -
205A TYR* 2.6 30.4 + - + +
240A ILE* 4.0 14.4 - - + -
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Residues in contact with GLU 199 (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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1A MSE 4.9 5.0 - - - +
195A ILE 2.8 14.4 + - - +
196A GLN* 3.3 17.4 + - - +
198A GLU* 1.3 75.8 - - - +
200A ARG* 1.3 65.4 + - - +
202A GLY* 3.0 14.4 + - - -
203A SER 5.0 0.7 - - - +
236A ILE* 3.8 23.8 - - + +
239A GLU* 3.5 40.8 - - + +
240A ILE* 3.6 15.2 - - + +
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Residues in contact with ARG 200 (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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196A GLN 2.9 13.0 + - - +
197A ARG* 3.6 39.6 + - - +
198A GLU 3.3 0.4 - - - -
199A GLU* 1.3 76.9 - - - +
201A ARG* 1.3 68.5 + - + +
202A GLY* 3.3 1.2 + - - -
85C GLU* 3.5 33.7 - - + +
87C LEU* 3.3 43.9 - - - +
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Residues in contact with ARG 201 (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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185A ARG* 6.1 0.4 - - - +
194A PHE* 3.8 6.1 - - - -
197A ARG* 2.9 33.5 + - - +
198A GLU* 2.9 36.1 + - - +
200A ARG* 1.3 83.9 - - + +
202A GLY* 1.3 60.3 + - - +
203A SER* 3.2 11.8 + - - +
1005A GOL 2.8 53.8 + - - -
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Residues in contact with GLY 202 (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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198A GLU 3.0 2.8 + - - -
199A GLU* 3.0 13.3 + - - -
200A ARG 3.2 2.0 + - - -
201A ARG* 1.3 79.3 - - - +
203A SER* 1.3 64.6 + - - +
204A THR* 3.8 8.9 + - - +
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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