Contacts of the helix formed by residues 198 - 210 (chain A) in PDB entry 2CUY
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 MET 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A MET* 3.1 62.1 - - + +
121A ALA* 4.4 4.9 - - - -
122A VAL* 5.3 0.2 - - - -
191A ALA* 4.9 0.2 - - - -
192A PRO* 3.4 38.6 - - - +
193A PHE* 3.8 13.2 - - + -
194A HIS 3.7 12.6 - - - +
195A SER 2.8 13.1 + - - +
197A LEU* 1.3 79.2 - - - +
199A ALA* 1.3 66.0 + - - +
200A PRO* 3.1 4.0 - - - -
201A ALA* 2.8 19.7 + - + +
202A ARG 3.2 8.1 + - - -
244A ILE* 3.7 19.9 - - + +
245A THR* 3.6 3.1 - - + -
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Residues in contact with ALA 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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196A SER* 3.2 18.0 + - - +
198A MET* 1.3 75.7 - - - +
200A PRO* 1.3 68.6 - - + +
202A ARG* 3.1 29.3 + - - +
203A LYS* 3.1 27.4 + - - +
245A THR* 3.3 15.3 - - + +
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Residues in contact with PRO 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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121A ALA* 4.4 21.1 - - + +
196A SER 4.6 0.2 - - - +
197A LEU* 3.2 19.5 - - - +
198A MET 3.3 1.6 - - - -
199A ALA* 1.3 96.0 - - + +
201A ALA* 1.3 61.3 + - - +
203A LYS* 3.6 10.7 + - + +
204A ARG* 3.2 28.8 + - - +
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Residues in contact with ALA 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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117A TYR* 3.7 41.0 - - + +
118A MET* 3.7 19.5 - - + +
121A ALA* 4.6 2.8 - - + +
198A MET* 2.8 20.8 + - + +
200A PRO* 1.3 72.3 - - - +
202A ARG* 1.3 63.2 + - - +
204A ARG* 3.3 5.4 + - - +
205A LEU* 2.9 25.1 + - - +
244A ILE* 4.5 4.5 - - + -
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Residues in contact with ARG 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 MET 3.2 4.7 + - - +
199A ALA* 3.1 18.7 + - - +
201A ALA* 1.3 78.2 - - - +
203A LYS* 1.3 91.7 + - - +
205A LEU* 3.0 8.2 + - - +
206A ALA* 2.9 22.7 + - + +
241A LEU* 3.2 44.4 - - + +
242A GLU* 4.4 4.2 - - - +
244A ILE* 4.1 15.4 - - + +
245A THR* 2.9 33.5 + - + +
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Residues in contact with LYS 203 (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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199A ALA* 3.1 21.1 + - - +
200A PRO* 3.8 10.1 - - + +
202A ARG* 1.3 99.3 - - - +
204A ARG* 1.3 64.8 + - + +
206A ALA* 3.3 18.9 - - - +
207A GLU* 3.7 12.1 + - - +
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Residues in contact with ARG 204 (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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116A ARG* 4.1 6.9 - - - +
117A TYR* 3.3 53.5 + - + +
120A GLU* 2.5 41.4 + - - +
200A PRO 3.2 15.1 + - - +
201A ALA* 3.7 6.7 - - - +
202A ARG 3.2 0.6 - - - -
203A LYS* 1.3 77.3 - - + +
205A LEU* 1.3 66.5 + - - +
207A GLU* 3.2 27.5 + - - +
208A ASP* 3.3 12.1 - - - +
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Residues in contact with LEU 205 (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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93A TRP* 3.9 28.5 - - + -
110A LEU* 3.7 32.8 - - + +
113A LEU* 4.3 4.5 - - + -
114A ARG* 4.0 31.0 - - + +
117A TYR* 3.7 15.2 - - + -
201A ALA 2.9 16.7 + - - +
202A ARG* 3.0 5.8 + - - +
204A ARG* 1.3 76.9 - - - +
206A ALA* 1.3 57.1 + - - +
208A ASP* 3.0 5.6 + - - +
209A LEU* 2.8 31.6 + - + +
240A LEU 5.3 0.4 - - - +
241A LEU* 4.0 14.4 - - + -
244A ILE* 4.7 9.9 - - + -
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Residues in contact with ALA 206 (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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202A ARG* 2.9 12.3 + - + +
203A LYS* 3.3 16.2 - - - +
204A ARG 3.2 0.2 - - - -
205A LEU* 1.3 77.1 - - - +
207A GLU* 1.3 61.7 + - + +
209A LEU* 4.0 1.4 - - - +
210A ALA* 3.1 25.1 + - - +
241A LEU* 3.6 29.8 - - + +
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Residues in contact with GLU 207 (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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203A LYS 3.9 15.3 - - - +
204A ARG* 3.2 18.8 + - - +
205A LEU 3.1 0.8 - - - -
206A ALA* 1.3 80.0 - - + +
208A ASP* 1.3 63.7 + - - +
210A ALA* 3.6 13.8 - - - +
211A GLN* 4.1 12.6 - - - +
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Residues in contact with ASP 208 (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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110A LEU* 4.0 11.1 - - + +
113A LEU* 3.6 27.7 - - + +
117A TYR* 2.8 40.4 + - - -
204A ARG 3.3 7.4 - - - +
205A LEU* 3.0 6.3 + - + +
207A GLU* 1.3 76.1 - - - +
209A LEU* 1.3 64.5 + - - +
210A ALA 3.1 2.3 + - - -
211A GLN* 3.3 20.8 + - - +
212A VAL* 3.7 10.6 - - - +
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Residues in contact with LEU 209 (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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93A TRP* 4.1 13.7 - - + -
110A LEU* 3.8 31.3 - - + +
205A LEU* 2.8 22.0 + - + +
206A ALA 4.0 4.0 - - - +
208A ASP* 1.3 73.2 - - - +
210A ALA* 1.3 63.5 + - - +
212A VAL* 3.0 17.6 + - + +
214A LEU* 4.8 10.1 - - + -
237A ARG* 3.1 49.6 + - + +
240A LEU* 4.4 13.9 - - + -
241A LEU* 3.5 33.4 - - + -
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Residues in contact with ALA 210 (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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206A ALA 3.1 18.6 + - - +
207A GLU* 3.6 11.2 - - - +
208A ASP 3.1 0.4 - - - -
209A LEU* 1.3 76.5 - - - +
211A GLN* 1.3 60.8 + - + +
212A VAL 3.2 1.8 + - - +
237A ARG* 4.0 17.1 + - - +
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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