Contacts of the helix formed by residues 191 - 199 (chain A) in PDB entry 3C33
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 SER 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A LEU* 3.5 7.7 - - - +
109A GLY 2.7 35.7 + - - +
111A SER* 4.5 2.7 - - - -
189A MET 3.5 2.2 + - - -
190A GLU* 1.3 72.0 - - - +
192A THR* 1.3 61.3 + - - +
194A ILE* 3.2 12.2 + - - +
195A GLU* 2.9 38.5 + - - +
206A GLN* 4.1 9.2 - - - +
210A LEU* 3.7 25.8 - - - +
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Residues in contact with THR 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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16A TYR* 3.7 12.4 + - - -
106A MET* 3.9 20.4 - - + -
107A THR 4.4 5.4 - - - +
108A LEU* 3.9 20.3 - - + +
190A GLU 4.5 0.2 + - - -
191A SER* 1.3 77.5 + - - +
193A SER* 1.3 61.7 + - - +
195A GLU* 3.4 20.3 + - - +
196A TYR* 3.2 6.6 + - - +
216A TYR* 3.5 27.0 + - - -
247A LYS* 3.8 12.6 - - - +
251A TRP* 2.8 29.5 + - - -
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Residues in contact with SER 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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13A GLU* 5.9 2.1 - - - +
14A GLU 5.3 3.7 + - - -
15A PRO* 6.4 0.7 - - - -
16A TYR* 4.6 13.6 - - - -
173A SER* 5.7 1.7 + - - -
189A MET* 3.9 25.1 - - - -
190A GLU* 3.0 12.6 + - - +
192A THR* 1.3 75.8 + - - +
194A ILE* 1.3 66.9 - - - +
196A TYR* 3.2 8.3 + - - +
197A VAL* 2.9 28.4 + - - +
216A TYR* 4.5 10.2 + - - -
251A TRP* 5.7 0.7 - - - -
401A KAI 5.8 4.2 - - - +
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Residues in contact with ILE 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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111A SER* 3.6 33.0 - - - +
112A ILE 3.7 13.9 - - - +
113A LEU* 3.9 10.8 - - + +
189A MET* 3.5 46.4 - - + +
190A GLU 3.1 4.5 + - - +
191A SER* 3.2 9.8 + - - +
193A SER* 1.3 76.1 - - - +
195A GLU* 1.3 57.7 + - + +
197A VAL* 3.1 4.0 + - - -
198A THR* 2.8 45.9 + - + +
206A GLN* 3.7 29.6 - - + +
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Residues in contact with GLU 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 SER* 2.9 25.6 + - - +
192A THR* 3.5 17.1 - - - +
194A ILE* 1.3 75.8 - - + +
196A TYR* 1.3 63.6 + - - +
198A THR* 3.4 8.2 + - - -
199A GLN* 3.2 29.8 + - + +
206A GLN* 5.1 6.3 - - - +
247A LYS* 2.7 36.1 + - - -
251A TRP* 3.9 9.4 - - + -
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Residues in contact with TYR 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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14A GLU* 3.3 39.9 + - + +
15A PRO* 3.5 46.1 - - + +
18A MET* 4.7 4.7 - - - +
192A THR 3.2 5.0 + - - +
193A SER* 3.4 11.0 - - - +
195A GLU* 1.3 80.6 - - - +
197A VAL* 1.3 72.2 + - + +
199A GLN* 3.5 3.6 + - - +
200A ARG* 3.0 73.9 + - - +
250A TRP 3.6 6.7 - - - -
251A TRP* 3.5 22.8 - + + +
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Residues in contact with VAL 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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113A LEU* 4.1 15.5 - - + -
177A ILE* 3.5 33.4 - - + -
189A MET* 4.4 7.9 - - + -
193A SER* 2.9 21.5 + - - +
194A ILE* 3.7 5.6 - - - +
196A TYR* 1.3 86.0 - - + +
198A THR* 1.3 57.1 + - - +
200A ARG* 2.9 18.2 + - - +
201A ASN* 2.9 36.9 + - - +
204A LEU* 3.9 22.4 - - + -
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Residues in contact with THR 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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113A LEU* 3.9 8.1 - - + -
194A ILE* 2.8 39.3 + - + +
195A GLU* 3.4 9.5 + - - -
197A VAL* 1.3 68.0 - - - +
199A GLN* 1.3 68.3 + - - +
200A ARG 3.1 2.0 + - - -
201A ASN 3.6 17.3 + - - +
202A CYS* 4.5 0.5 - - - -
204A LEU* 3.7 22.9 - - + +
205A THR* 3.7 20.0 - - - +
206A GLN 4.1 1.1 - - - +
256A CYS* 4.0 12.1 - - - -
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Residues in contact with GLN 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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195A GLU* 3.2 21.2 + - + +
196A TYR 3.6 1.6 - - - +
198A THR* 1.3 78.8 + - - +
200A ARG* 1.3 80.5 + - - +
202A CYS* 5.0 0.5 - - - -
251A TRP* 3.5 16.6 - - + +
252A ARG* 3.8 17.5 - - - +
253A GLY* 3.0 36.6 + - - +
254A ASN 4.5 3.6 + - - -
255A GLY* 4.8 7.3 + - - +
256A CYS* 4.2 12.6 - - - -
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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