Contacts of the helix formed by residues 190 - 202 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79B ARG* 2.7 45.8 + - - -
189C GLU* 1.3 76.5 - - - +
191C ALA* 1.3 59.2 + - - +
192C MSE 3.2 4.9 + - - -
193C LYS* 2.9 26.9 + - + +
194C PHE* 3.0 28.8 + - - +
218C GLY* 3.5 16.4 - - - -
219C THR* 3.6 7.9 + - - +
222C GLU* 3.7 21.6 + - - +
224C TRP* 5.4 0.2 - - - -
1003C SAM 2.8 24.6 + - - -
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Residues in contact with ALA 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C LEU* 4.4 13.1 - - + +
140C PHE* 3.7 33.2 - - + +
160C VAL* 4.0 15.0 - - + -
190C ASP* 1.3 73.1 - - - +
192C MSE 1.3 63.2 + - - +
194C PHE* 3.3 3.5 + - - +
195C ILE* 3.1 27.2 + - - +
233C MSE 4.0 4.7 - - + -
1003C SAM 2.9 25.9 + - + -
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Residues in contact with MSE 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ARG* 3.5 25.6 - - - +
-2C PHE* 4.0 13.7 - - + -
140C PHE* 5.4 0.2 - - - -
190C ASP* 3.2 7.1 + - - +
191C ALA* 1.3 75.8 - - - +
193C LYS* 1.3 61.0 + - - +
195C ILE* 3.3 6.9 - - + +
196C GLN* 2.9 28.6 + - - +
224C TRP* 4.0 8.0 - - + -
229C HIS* 3.7 26.7 - - + +
232C LEU* 3.9 11.2 - - + -
233C MSE 3.6 44.3 - - + +
236C ILE* 4.1 15.5 - - + -
1018C FMT 3.4 25.1 - - - +
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Residues in contact with LYS 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ARG* 5.3 0.2 - - - +
82B PHE* 5.0 12.3 - - - -
89B GLU* 6.1 2.8 - - - +
104B PHE* 5.6 6.1 + - - +
189C GLU* 3.6 17.0 - - + +
190C ASP* 2.9 21.9 + - + +
192C MSE 1.3 74.3 - - - +
194C PHE* 1.3 66.6 + - - +
196C GLN* 3.9 1.9 - - - +
197C ARG* 3.0 71.0 + - + +
220C HIS* 5.0 10.5 + - - +
222C GLU* 2.8 34.2 + - - +
1018C FMT 3.3 23.4 - - - +
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Residues in contact with PHE 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C LEU* 3.9 10.3 - - + -
158C THR* 3.9 12.6 - - + -
160C VAL* 3.6 31.0 - - + -
185C ARG* 4.2 10.3 - - - -
187C ILE* 3.7 26.5 - - + -
189C GLU* 3.3 25.3 - - - +
190C ASP 3.0 18.7 + - - +
191C ALA 3.3 4.0 + - - +
193C LYS* 1.3 78.5 - - - +
195C ILE* 1.3 66.9 + - + +
197C ARG* 3.3 2.4 + - - +
198C GLU* 2.9 67.2 + - + +
201C ARG* 4.2 5.4 - - - -
205C TYR* 3.7 13.0 - + - -
1011C ACY 3.7 8.3 - - - -
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Residues in contact with ILE 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C LEU* 3.8 4.9 - - + -
139C LEU* 3.7 30.7 - - + -
191C ALA 3.1 14.6 + - - +
192C MSE 3.3 15.3 - - - +
194C PHE* 1.3 79.9 - - + +
196C GLN* 1.3 58.4 + - - +
198C GLU* 3.3 7.3 + - - +
199C GLU 2.9 23.2 + - - -
233C MSE 3.5 46.4 - - + +
236C ILE* 3.3 26.9 - - + +
237C CYS* 3.8 13.7 - - - +
240C ILE* 3.7 21.0 - - + +
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Residues in contact with GLN 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ARG* 3.6 8.0 + - - +
82B PHE* 2.8 42.1 + - - +
85B GLU* 3.9 2.0 - - - +
86B ALA* 3.7 34.6 + - + +
192C MSE 2.9 17.9 + - - +
193C LYS* 4.1 4.0 - - - +
195C ILE* 1.3 77.3 - - - +
197C ARG* 1.3 58.0 + - - +
199C GLU* 3.4 4.7 + - - +
200C ARG* 3.0 22.7 + - - +
232C LEU* 5.6 1.0 - - - +
236C ILE* 3.8 17.9 - - + -
1004C GOL 3.1 34.0 + - - +
1018C FMT 4.3 10.8 - - - -
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Residues in contact with ARG 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B PHE* 6.3 0.2 - - - -
86B ALA* 3.7 18.0 - - + +
87B LEU 3.5 23.6 + - - -
88B GLY* 4.0 4.4 - - - -
89B GLU* 4.0 19.8 - - - +
189C GLU* 3.5 3.2 + - - -
193C LYS* 3.0 54.0 + - + +
194C PHE 3.6 3.6 - - - +
196C GLN* 1.3 74.7 - - - +
198C GLU* 1.3 58.1 + - - +
200C ARG* 3.2 19.7 + - - +
201C ARG* 3.0 49.2 + - - +
1011C ACY 3.1 42.6 + - - +
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Residues in contact with GLU 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C ARG* 4.7 7.1 + - - -
194C PHE* 2.9 48.2 + - + +
195C ILE* 3.5 11.4 - - - +
197C ARG* 1.3 73.7 - - - +
199C GLU* 1.3 58.4 + - - +
201C ARG* 2.8 35.6 + - - +
202C GLY 2.9 23.4 + - - -
203C SER* 3.0 34.7 + - - -
205C TYR* 2.6 27.5 + - + +
240C ILE* 4.0 13.5 - - + -
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Residues in contact with GLU 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C ILE 2.9 12.7 + - - +
196C GLN* 3.4 10.5 - - - +
198C GLU* 1.3 75.6 - - - +
200C ARG* 1.3 62.3 + - - +
202C GLY* 3.1 13.8 + - - +
236C ILE* 3.8 10.9 - - + +
239C GLU* 3.5 29.5 - - + +
240C ILE* 3.5 16.7 - - + +
1004C GOL 2.5 53.4 + - - -
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Residues in contact with ARG 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B GLU* 3.8 30.0 - - + +
86B ALA* 3.0 42.8 + - + +
87B LEU 4.2 0.4 - - - -
88B GLY* 4.2 13.9 - - - +
196C GLN 3.0 14.1 + - - +
197C ARG* 3.2 35.5 + - - +
199C GLU* 1.3 76.9 - - - +
201C ARG* 1.3 75.0 + - - +
202C GLY* 3.5 0.5 + - - -
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Residues in contact with ARG 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C ARG* 5.7 3.4 - - - +
194C PHE* 4.2 6.1 - - - -
197C ARG* 3.0 28.4 + - - +
198C GLU* 2.8 46.6 + - - +
199C GLU 3.2 0.2 - - - -
200C ARG* 1.3 89.4 - - - +
202C GLY* 1.3 60.4 + - - +
203C SER* 3.7 10.2 + - - +
1011C ACY 2.3 44.6 + - - -
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Residues in contact with GLY 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C GLU 2.9 3.6 + - - -
199C GLU* 3.1 13.5 + - - -
200C ARG 3.3 1.0 - - - -
201C ARG* 1.3 79.0 - - - +
203C SER* 1.3 65.3 + - - +
204C THR* 3.8 8.3 + - - +
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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