Contacts of the helix formed by residues 199 - 207 (chain A) in PDB entry 1QXP
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 CYS 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A TRP* 3.0 18.3 - - - -
198A GLY* 1.3 79.4 - - - +
200A THR* 1.3 67.8 + - - +
201A SER* 2.9 13.7 + - - -
202A GLU* 3.2 33.5 + - + +
203A ALA 3.2 16.6 + - - -
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Residues in contact with THR 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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106A TRP* 3.4 45.5 - - + +
109A ALA* 4.3 14.4 - - + -
110A ALA* 4.6 6.6 - - - +
199A CYS* 1.3 73.1 - - - +
201A SER* 1.2 65.1 + - - +
203A ALA* 3.4 5.7 - - - +
204A PHE* 3.0 30.0 + - - +
338A LEU* 3.3 25.6 - - - +
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Residues in contact with SER 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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199A CYS* 2.9 10.4 + - - -
200A THR* 1.2 85.4 + - - +
202A GLU* 1.3 66.6 + - - +
204A PHE* 2.9 20.1 + - - +
205A GLU* 3.1 16.9 + - - +
212A THR* 2.7 33.5 + - - +
338A LEU* 4.2 22.7 - - - -
340A ILE* 5.1 0.2 - - - -
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Residues in contact with GLU 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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106A TRP* 5.8 0.7 - - + -
185A TYR* 5.0 1.1 - - - +
198A GLY* 3.9 9.9 - - - +
199A CYS* 3.2 38.7 - - + +
201A SER* 1.3 77.4 + - - +
203A ALA* 1.3 65.6 + - - +
205A GLU* 2.9 8.0 + - - +
206A ASP* 2.8 22.5 + - - +
469A LEU* 5.5 2.6 - - - +
470A ARG* 3.2 66.7 + - - +
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Residues in contact with ALA 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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106A TRP* 4.5 4.1 - - + -
107A LEU* 4.4 13.5 - - + -
110A ALA* 3.6 21.3 - - + -
185A TYR* 3.9 15.8 + - + -
199A CYS 3.2 7.4 + - - +
200A THR* 3.4 13.2 - - - +
202A GLU* 1.3 75.6 - - - +
204A PHE* 1.3 67.8 + - - +
206A ASP* 2.7 7.3 + - - +
207A PHE* 2.7 33.9 + - + -
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Residues in contact with PHE 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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109A ALA 4.8 0.7 - - - -
110A ALA* 4.6 18.6 - - + -
113A SER* 3.6 36.1 - - - -
114A LEU* 5.5 3.8 - - + -
200A THR* 3.0 18.2 + - - -
201A SER* 2.9 16.2 + - - +
203A ALA* 1.3 80.1 - - - +
205A GLU* 1.3 53.6 + - - +
207A PHE* 3.3 6.1 + - + +
208A THR* 2.5 45.2 + - + +
237A LEU* 3.1 39.3 - - + -
239A GLY* 5.7 7.9 - - - -
338A LEU* 6.1 1.6 - - + -
340A ILE* 3.1 40.4 - - + -
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Residues in contact with GLU 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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144A TRP* 3.5 9.7 - - + +
201A SER* 3.1 8.8 + - - +
202A GLU* 2.9 9.6 + - - +
204A PHE* 1.3 78.4 - - - +
206A ASP* 1.4 59.4 + - - +
208A THR* 3.5 6.1 - - - -
209A GLY* 2.8 31.5 + - - -
210A GLY 2.8 26.7 - - - +
211A VAL* 3.4 2.0 - - - -
212A THR* 2.9 33.1 + - + +
340A ILE* 4.7 0.9 - - - -
414A MET* 3.5 15.5 - - - +
470A ARG* 4.0 15.0 + - - +
471A GLU* 2.1 39.8 - - - +
501A ARG* 4.7 0.2 - - - +
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Residues in contact with ASP 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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143A LEU* 3.6 6.5 - - + -
144A TRP* 2.8 51.4 + - - +
145A GLN* 3.3 17.7 + - - +
146A PHE* 5.2 1.0 + - - -
185A TYR* 2.1 43.0 + - + +
189A ASN* 5.9 0.3 + - - -
202A GLU* 2.8 6.2 + - - +
203A ALA 2.7 9.5 + - - +
205A GLU* 1.4 81.0 - - - +
207A PHE* 1.4 56.3 + - + -
208A THR 3.4 0.4 - - - -
470A ARG* 2.9 40.1 + - - -
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Residues in contact with PHE 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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107A LEU* 4.4 4.7 - - + -
110A ALA* 3.9 33.4 - - + -
111A ILE* 4.0 18.8 - - + -
114A LEU* 4.4 18.8 - - + +
120A ILE 4.4 5.5 - - - +
123A ARG* 5.2 1.7 + - - +
124A VAL* 3.2 33.0 - - + +
142A GLN 5.4 0.2 - - - -
143A LEU* 3.9 24.7 - - + -
149A TRP* 4.6 5.0 - - - -
181A LEU* 4.3 17.9 - - + -
185A TYR* 4.2 35.9 - + + -
203A ALA* 2.7 22.6 + - + +
204A PHE* 3.3 5.6 + + + +
206A ASP* 1.4 75.1 - - - +
208A THR* 1.3 69.3 + - + +
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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