Contacts of the helix formed by residues 190 - 202 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A ARG* 2.8 39.2 + - - -
189B GLU* 1.3 79.7 - - - +
191B ALA* 1.3 58.5 + - - +
192B MSE 3.3 4.0 + - - -
193B LYS* 3.0 25.7 + - + +
194B PHE* 3.0 25.1 + - - +
218B GLY* 3.5 13.9 - - - -
219B THR* 3.7 6.9 + - - +
222B GLU* 3.6 25.4 + - - +
224B TRP* 5.4 0.3 - - - -
1002B SAM 2.8 32.1 + - - -
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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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139B LEU* 4.4 12.0 - - + +
140B PHE* 3.7 32.5 - - + +
160B VAL* 4.1 14.4 - - + -
190B ASP* 1.3 72.7 - - - +
192B MSE 1.3 59.6 + - - +
194B PHE* 3.3 3.1 + - - +
195B ILE* 3.0 32.6 + - - +
233B MSE 4.0 4.3 - - + -
1002B SAM 2.9 26.4 + - + -
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Residues in contact with MSE 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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79A ARG* 3.5 26.5 - - - +
-2B PHE* 3.8 14.6 - - + -
140B PHE* 5.4 0.4 - - - -
190B ASP* 3.3 7.3 + - - +
191B ALA* 1.3 75.3 - - - +
193B LYS* 1.3 60.4 + - - +
195B ILE* 3.4 7.5 - - + +
196B GLN* 2.9 28.9 + - - +
224B TRP* 4.0 7.8 - - + -
229B HIS* 3.7 26.5 - - + +
232B LEU* 3.9 12.3 - - + -
233B MSE 3.6 43.6 - - + +
236B ILE* 4.0 16.4 - - + -
1012B FMT 3.4 23.8 - - - +
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Residues in contact with LYS 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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82A PHE* 5.0 11.8 - - - -
89A GLU* 6.1 4.0 - - - +
104A PHE* 5.4 6.3 + - - +
189B GLU* 3.6 16.8 - - + +
190B ASP* 3.0 24.4 + - + +
192B MSE 1.3 77.3 - - - +
194B PHE* 1.3 61.7 + - - +
196B GLN* 3.8 1.9 - - - +
197B ARG* 2.9 69.6 + - + +
220B HIS* 5.0 10.8 + - - +
222B GLU* 2.8 33.2 + - - +
1012B FMT 3.4 23.6 - - - +
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Residues in contact with PHE 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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137B LEU* 3.8 9.9 - - + -
158B THR* 3.9 11.9 - - + -
160B VAL* 3.6 31.2 - - + -
185B ARG* 4.5 6.5 - - - -
187B ILE* 3.8 25.1 - - + -
189B GLU* 3.4 26.9 - - - +
190B ASP 3.0 16.4 + - - +
191B ALA 3.7 3.4 - - - +
192B MSE 3.3 0.2 - - - -
193B LYS* 1.3 77.8 - - - +
195B ILE* 1.3 68.8 + - + +
197B ARG* 3.2 6.2 + - - +
198B GLU* 2.9 62.6 + - + +
201B ARG* 4.1 9.6 - - - -
205B TYR* 3.7 14.6 - - - -
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Residues in contact with ILE 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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137B LEU* 3.8 4.7 - - + -
139B LEU* 3.7 28.0 - - + -
191B ALA 3.0 17.7 + - - +
192B MSE 3.4 15.0 - - - +
194B PHE* 1.3 77.8 - - + +
196B GLN* 1.3 59.0 + - - +
198B GLU* 3.2 6.7 + - - +
199B GLU 2.9 23.7 + - - -
233B MSE 3.5 45.3 - - + +
236B ILE* 3.4 24.3 - - + +
237B CYS* 3.9 13.7 - - - -
240B ILE* 3.7 24.7 - - + +
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Residues in contact with GLN 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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81A ARG* 3.7 13.4 + - - +
82A PHE* 2.8 42.7 + - - +
83A PRO 5.1 1.2 + - - -
84A LYS 5.1 0.2 - - - -
85A GLU* 3.8 4.4 - - - +
86A ALA* 3.6 33.5 + - + +
192B MSE 2.9 17.9 + - - +
193B LYS* 4.0 4.0 - - - +
195B ILE* 1.3 77.4 - - - +
197B ARG* 1.3 57.6 + - - +
199B GLU* 3.3 13.8 + - - +
200B ARG* 3.0 26.2 + - - +
232B LEU* 5.7 1.1 - - - +
236B ILE* 3.9 23.8 - - + +
1012B FMT 4.1 11.9 - - - -
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Residues in contact with ARG 197 (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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86A ALA* 3.8 18.3 - - + +
87A LEU 3.5 24.6 + - - -
88A GLY* 4.0 12.6 - - - -
89A GLU* 4.0 10.1 - - - +
189B GLU* 3.3 24.5 + - - -
193B LYS* 2.9 53.2 + - - +
194B PHE* 3.6 4.7 - - - +
196B GLN* 1.3 74.3 - - - +
198B GLU* 1.3 59.2 + - - +
200B ARG* 3.3 20.9 + - - +
201B ARG* 3.0 59.5 + - - +
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Residues in contact with GLU 198 (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 ARG* 4.0 9.1 + - - -
194B PHE* 2.9 47.0 + - + +
195B ILE* 3.5 11.0 - - - +
197B ARG* 1.3 71.9 - - - +
199B GLU* 1.3 60.9 + - - +
201B ARG* 2.8 32.0 + - - +
202B GLY 2.9 23.6 + - - -
203B SER* 2.9 40.2 + - - -
205B TYR* 2.5 26.6 + - + +
240B ILE* 4.1 12.8 - - + -
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Residues in contact with GLU 199 (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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1B MSE 4.5 6.9 - - - +
195B ILE 2.9 12.7 + - - +
196B GLN* 3.5 17.5 + - - +
197B ARG 3.3 0.2 - - - -
198B GLU* 1.3 77.6 - - - +
200B ARG* 1.3 62.7 + - - +
202B GLY* 3.0 13.6 + - - -
236B ILE* 3.7 23.6 - - + +
239B GLU* 3.7 39.0 - - + +
240B ILE* 3.6 15.8 - - + +
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Residues in contact with ARG 200 (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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85A GLU* 3.8 30.1 - - + +
86A ALA* 2.9 44.8 + - + +
87A LEU 4.3 8.1 - - - -
88A GLY* 4.4 4.6 - - - +
196B GLN 3.0 13.7 + - - +
197B ARG* 3.5 28.8 + - - +
199B GLU* 1.3 75.6 - - - +
201B ARG* 1.3 81.9 + - - +
202B GLY 3.5 0.9 + - - -
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Residues in contact with ARG 201 (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* 5.7 1.2 + - - -
194B PHE* 4.1 13.1 - - - -
197B ARG* 3.0 48.8 + - - +
198B GLU* 2.8 44.8 + - - +
200B ARG* 1.3 92.9 - - - +
202B GLY* 1.3 60.1 + - - +
203B SER* 3.6 9.3 + - - +
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Residues in contact with GLY 202 (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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198B GLU 2.9 3.0 + - - -
199B GLU* 3.0 13.8 + - - -
200B ARG 3.3 1.2 + - - -
201B ARG* 1.3 78.7 - - - +
203B SER* 1.3 64.3 + - - +
204B 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