Contacts of the helix formed by residues 201 - 212 (chain A) in PDB entry 1QCY
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 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A ILE* 3.4 13.2 - - - +
199A TYR 3.5 1.6 + - - -
200A SER* 1.3 81.8 + - - +
202A THR* 1.3 64.7 + - - +
203A GLU* 3.8 14.2 + - - +
204A GLU* 3.2 33.7 + - - +
205A VAL* 3.1 24.9 + - - +
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Residues in contact with THR 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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169A LEU* 3.7 18.4 - - + +
170A LYS* 4.1 16.2 - - - +
172A MET 2.5 29.8 + - - +
173A ASP* 3.7 2.3 + - - -
174A ILE* 3.0 27.8 + - + +
201A SER* 1.3 73.1 - - - +
203A GLU* 1.3 76.5 + - - +
205A VAL* 3.0 3.9 + - + +
206A LEU* 2.9 33.8 + - + +
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Residues in contact with GLU 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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201A SER* 4.0 11.6 - - - +
202A THR* 1.3 89.2 + - - +
204A GLU* 1.3 63.8 + - + +
206A LEU* 3.4 14.6 + - + +
207A VAL* 3.1 29.0 + - + +
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Residues in contact with GLU 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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198A LYS 4.7 1.2 - - - +
199A TYR* 3.6 29.3 - - + -
200A SER* 3.5 27.8 + - - -
201A SER* 3.2 23.7 + - - +
202A THR 3.2 0.6 - - - -
203A GLU* 1.3 76.3 - - + +
205A VAL* 1.3 66.7 + - - +
207A VAL* 3.2 10.2 + - - +
208A ALA* 3.0 22.0 + - - +
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Residues in contact with VAL 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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169A LEU* 3.4 34.3 - - + -
174A ILE* 3.7 28.3 - - + -
181A VAL* 4.6 16.2 - - + +
194A PHE* 4.3 15.4 - - + -
199A TYR* 3.8 24.9 - - + +
201A SER 3.1 13.1 + - - +
202A THR* 3.0 9.8 + - - +
204A GLU* 1.3 75.4 - - - +
206A LEU* 1.3 52.9 + - - +
208A ALA* 3.0 4.3 + - - +
209A ALA* 2.8 32.4 + - - +
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Residues in contact with LEU 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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166A ASN* 3.8 27.3 - - - +
169A LEU* 3.8 14.8 - - + +
170A LYS* 3.5 43.5 - - + +
202A THR* 2.9 24.7 + - + +
203A GLU* 3.5 16.2 - - + +
205A VAL* 1.3 76.2 - - - +
207A VAL* 1.3 64.2 + - + +
209A ALA* 3.2 4.8 + - - +
210A LYS* 3.1 35.4 + - - +
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Residues in contact with VAL 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 GLU* 3.1 17.4 + - + +
204A GLU* 3.2 10.3 + - - +
206A LEU* 1.3 80.3 - - + +
208A ALA* 1.3 63.8 + - - +
210A LYS* 3.5 13.1 + - - +
211A LYS* 3.4 30.2 + - + +
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Residues in contact with ALA 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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194A PHE* 3.8 14.8 - - + -
199A TYR* 3.2 44.2 - - + +
204A GLU 3.0 6.6 + - - +
205A VAL 3.0 6.8 + - - +
207A VAL* 1.3 74.5 - - - +
209A ALA* 1.3 66.1 + - - +
211A LYS* 3.2 24.3 + - - +
212A ILE* 3.5 13.7 + - - +
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Residues in contact with ALA 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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162A THR* 3.8 13.5 - - - +
165A LEU* 4.3 17.8 - - + +
166A ASN* 5.1 2.7 - - - +
169A LEU* 3.9 24.5 - - + -
183A ILE* 4.7 6.7 - - + -
194A PHE* 4.3 2.4 - - + -
205A VAL* 2.8 19.8 + - + +
206A LEU* 3.7 6.3 - - - +
208A ALA* 1.3 72.7 - - - +
210A LYS* 1.3 62.9 + - + +
211A LYS 3.3 0.5 + - - -
212A ILE* 3.3 28.8 + - - +
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Residues in contact with LYS 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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162A THR* 4.4 19.1 - - - +
166A ASN* 3.4 35.0 + - + +
206A LEU* 3.1 26.3 + - - +
207A VAL* 3.8 8.7 - - - +
208A ALA 3.3 0.2 - - - -
209A ALA* 1.3 76.3 - - + +
211A LYS* 1.3 62.1 + - + +
212A ILE 3.6 1.4 + - - +
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Residues in contact with LYS 211 (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 TYR* 5.0 7.4 + - - -
207A VAL* 3.4 28.1 - - + +
208A ALA* 3.2 18.3 + - - +
209A ALA 3.2 1.2 - - - -
210A LYS* 1.3 78.8 - - + +
212A ILE* 1.3 63.1 + - - +
213A VAL* 3.2 15.4 + - - +
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Residues in contact with ILE 212 (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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149A LEU* 5.0 4.9 - - + -
158A TRP* 2.8 32.5 + - + +
162A THR* 3.8 8.9 - - + +
165A LEU* 4.2 8.3 - - + -
183A ILE* 3.8 41.5 - - + -
185A GLN* 3.8 11.0 - - - +
193A GLU* 3.8 37.2 - - + +
194A PHE* 4.5 4.0 - - + -
208A ALA 3.5 8.7 - - - +
209A ALA* 3.3 22.7 + - - +
210A LYS 4.5 1.0 - - - +
211A LYS* 1.3 76.1 - - - +
213A VAL* 1.3 63.3 + - - +
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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