Contacts of the helix formed by residues 192 - 199 (chain A) in PDB entry 2G4C
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 HIS 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A VAL* 3.4 28.6 - - + +
129A ASP 3.5 21.3 + - - -
130A ALA* 4.5 3.0 + - + -
188A GLY* 2.8 25.8 - - - -
189A ALA 2.8 10.4 + - - +
190A LEU 2.7 1.4 + - - -
191A GLU* 1.3 84.2 + - + +
193A TYR* 1.3 63.1 - - - +
194A VAL 3.0 3.9 + - - -
195A ASN* 3.0 11.8 + - - +
196A CYS* 2.8 28.7 + - - -
208A LEU* 3.8 13.9 - - + -
80C SER* 3.8 25.9 + - - -
97C PRO 5.2 3.8 + - - -
98C GLY* 5.2 2.7 - - - -
99C PHE 4.1 15.2 + - - -
100C GLY* 5.3 2.0 - - - -
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Residues in contact with TYR 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 ALA 3.4 4.2 + - - -
190A LEU 3.0 14.0 + - - +
192A HIS* 1.3 75.5 - - - +
194A VAL* 1.3 54.2 + - - +
197A LEU* 2.6 80.0 + - + +
204A LEU* 4.4 1.1 - - + +
206A TYR* 3.1 32.1 + + - -
208A LEU* 4.3 1.5 - - - +
242A PHE* 3.4 45.8 - + + -
311A LEU* 4.1 13.5 - - + -
315A TYR* 3.9 4.9 - + + +
322A LEU* 3.7 35.9 - - + -
323A HIS* 3.5 5.9 + - - -
324A GLY 3.7 1.7 + - - -
333A PRO* 3.2 30.6 - - + +
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Residues in contact with VAL 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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192A HIS 3.0 2.2 + - - -
193A TYR* 1.3 78.1 - - + +
195A ASN* 1.3 76.1 + - - +
197A LEU* 2.8 22.2 + - - +
198A ASP* 3.5 4.7 + - - +
315A TYR* 3.5 37.6 + - + +
321A LYS* 4.1 39.3 - - + +
322A LEU* 4.0 16.4 - - + -
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Residues in contact with ASN 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 GLU 3.8 19.2 + - - -
192A HIS* 3.0 9.9 + - - +
194A VAL* 1.3 84.5 - - - +
196A CYS* 1.3 63.4 + - - +
198A ASP* 3.5 7.0 - - - +
77C HIS* 3.0 30.9 - - + +
80C SER* 3.8 22.4 + - - +
81C GLY* 5.2 9.5 + - - +
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Residues in contact with CYS 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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126A PHE* 5.4 0.8 - - + -
128A VAL* 4.5 3.4 - - - -
192A HIS* 2.8 33.0 + - - +
193A TYR 3.4 0.2 - - - -
195A ASN* 1.3 73.2 - - - +
197A LEU* 1.3 60.1 + - - +
198A ASP 3.0 6.8 + - - -
199A LEU* 3.5 24.2 + - + +
200A VAL* 4.1 4.7 + - - +
206A TYR* 3.6 20.5 + - + +
208A LEU* 4.0 26.2 - - + -
77C HIS* 5.4 1.1 - - - -
101C PRO* 3.8 37.0 - - - -
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Residues in contact with LEU 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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193A TYR* 2.6 57.5 + - + +
194A VAL* 2.8 9.1 + - - +
196A CYS* 1.3 70.6 - - - +
198A ASP* 1.3 65.7 + - - +
200A VAL* 3.7 3.5 - - + +
201A ASN 3.9 0.3 - - - +
202A LYS* 3.5 47.0 + - + +
204A LEU* 3.6 13.7 - - + -
206A TYR* 3.5 26.2 - - + -
321A LYS 4.5 3.6 - - - +
322A LEU* 3.1 24.2 - - - +
323A HIS 4.1 2.9 - - - -
324A GLY* 4.3 0.4 - - - -
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Residues in contact with ASP 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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194A VAL 3.5 3.7 + - - +
195A ASN 3.5 14.4 - - - +
197A LEU* 1.3 76.9 - - - +
199A LEU* 1.3 54.9 + - - +
200A VAL 2.4 20.2 + - - -
201A ASN* 2.6 25.5 + - - +
202A LYS* 5.9 1.8 - - - -
75C ARG 4.8 2.8 - - - +
77C HIS* 2.9 23.6 + - + -
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Residues in contact with LEU 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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126A PHE* 3.2 48.0 - - + -
196A CYS* 3.5 16.1 - - - +
198A ASP* 1.3 77.7 + - - +
200A VAL* 1.3 58.0 + - - +
201A ASN 3.5 2.2 + - - -
77C HIS* 3.6 36.5 + - + +
101C PRO* 3.8 22.2 - - + -
102C LEU* 4.9 7.0 - - + -
414C TRP* 3.7 36.8 - - + -
435C MET* 5.6 1.8 - - + -
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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