Contacts of the helix formed by residues 199 - 212 (chain A) in PDB entry 1Y67
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 ASN 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A GLN 4.3 5.2 + - - +
87A ILE 2.7 25.6 + - - +
88A MET 3.9 14.0 + - - +
89A GLY* 5.0 0.8 - - - -
92A GLN* 3.5 25.9 - - - +
197A VAL 3.3 1.4 + - - -
198A VAL* 1.3 71.9 - - - +
200A TRP* 1.3 59.3 + - - +
201A ASP* 3.1 15.2 + - - +
202A GLU* 3.1 27.5 + - + +
203A VAL* 3.1 22.2 + - - +
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Residues in contact with TRP 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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92A GLN* 4.1 3.4 + - - -
98A ASN* 3.5 34.6 + - - +
99A GLN* 3.5 20.9 - - - +
100A PRO* 3.6 31.6 - - + -
104A LEU* 3.6 24.0 - - + -
108A ILE* 4.5 5.6 - - + -
115A PHE* 3.5 21.0 - + - -
118A PHE* 3.8 18.2 - + - -
137A LEU* 4.7 3.1 - - + -
170A LEU* 3.7 21.5 - - + -
195A TRP* 4.0 14.4 + + - -
198A VAL* 3.3 24.1 + - + +
199A ASN* 1.3 70.2 + - - +
201A ASP* 1.3 60.8 + - - +
203A VAL* 3.8 23.9 - - + +
204A SER* 2.8 35.7 + - - +
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Residues in contact with ASP 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLN* 4.9 5.6 + - - +
199A ASN* 3.1 11.0 + - - +
200A TRP* 1.3 79.3 - - - +
202A GLU* 1.3 56.9 + - - +
204A SER* 3.4 6.0 + - - -
205A LYS* 3.0 27.2 + - - +
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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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86A GLN* 3.3 33.4 - - - +
87A ILE* 3.9 6.7 - - + -
199A ASN* 3.1 24.1 + - - +
201A ASP* 1.3 74.7 - - - +
203A VAL* 1.3 66.1 + - - +
205A LYS* 3.2 24.4 + - - +
206A ARG* 2.8 64.5 + - - +
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Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ILE* 4.2 7.9 - - + -
104A LEU* 3.7 17.5 - - + -
137A LEU* 4.8 1.1 - - + -
169A ILE* 3.5 44.1 - - + +
170A LEU* 4.1 13.5 - - + -
198A VAL* 3.9 21.3 - - + -
199A ASN 3.1 14.3 + - - +
200A TRP* 3.4 21.9 + - + +
202A GLU* 1.3 75.1 - - - +
204A SER* 1.3 58.7 + - - +
206A ARG* 3.1 4.3 + - - +
207A TYR* 2.8 26.9 + - - +
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Residues in contact with SER 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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100A PRO* 4.7 2.4 - - - +
101A SER 4.4 7.8 + - - -
104A LEU* 3.4 29.1 - - - +
200A TRP 2.8 23.7 + - - -
201A ASP* 3.7 6.7 - - - -
203A VAL* 1.3 70.7 - - - +
205A LYS* 1.3 59.5 + - - +
207A TYR* 3.4 7.2 + - - +
208A ALA* 3.0 30.8 + - - +
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Residues in contact with LYS 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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201A ASP 3.0 15.4 + - - +
202A GLU* 3.2 29.0 + - - +
204A SER* 1.3 76.6 - - - +
206A ARG* 1.3 63.3 + - + +
208A ALA* 3.4 6.1 + - - +
209A ALA* 3.2 23.4 + - + +
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Residues in contact with ARG 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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83A MET* 3.6 36.0 - - - +
86A GLN* 2.8 34.6 + - - +
87A ILE* 3.9 7.1 - - - +
167A THR* 5.8 0.3 - - - +
168A PRO 4.8 4.3 + - - +
169A ILE* 3.8 34.3 - - + +
202A GLU* 2.8 42.2 + - - +
203A VAL 3.5 5.6 - - - +
205A LYS* 1.3 74.6 - - + +
207A TYR* 1.3 59.8 + - - +
209A ALA* 3.5 6.1 + - - +
210A ALA* 3.0 30.3 + - - +
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Residues in contact with TYR 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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103A GLU* 4.0 26.4 + - + -
104A LEU* 3.9 22.9 - - + -
107A ALA* 3.2 22.9 - - + +
139A VAL* 3.8 18.8 - - + -
142A GLY 4.8 3.2 + - - -
144A LEU* 4.0 23.8 - - + -
169A ILE* 3.9 15.3 - - + +
203A VAL 2.8 16.0 + - - +
204A SER* 3.6 7.2 - - - +
205A LYS 3.3 0.2 - - - -
206A ARG* 1.3 73.5 - - - +
208A ALA* 1.3 70.6 + - + +
210A ALA* 3.2 2.9 + - - +
211A LYS* 3.0 64.1 + - + +
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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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204A SER 3.0 17.0 + - - +
205A LYS* 3.4 6.7 + - - +
207A TYR* 1.3 83.9 - - + +
209A ALA* 1.3 63.6 + - - +
211A LYS* 3.4 5.7 + - - +
212A LEU* 3.3 28.0 + - + +
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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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205A LYS* 3.2 17.0 + - + +
206A ARG* 3.7 7.0 - - - +
208A ALA* 1.3 76.8 - - - +
210A ALA* 1.3 63.0 + - - +
212A LEU* 3.1 29.4 + - + +
213A VAL 4.3 2.9 + - - +
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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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139A VAL* 3.9 34.1 - - + +
142A GLY* 5.8 0.7 - - - -
167A THR* 4.3 24.0 - - + -
169A ILE* 4.4 1.8 - - + -
206A ARG 3.0 17.9 + - - +
207A TYR 3.2 4.2 + - - +
209A ALA* 1.3 76.1 - - - +
211A LYS* 1.3 60.0 + - - +
212A LEU 3.5 0.5 + - - -
213A VAL* 3.6 16.5 + - - +
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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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139A VAL* 4.7 6.3 - - + -
142A GLY* 3.2 34.7 + - - +
207A TYR* 3.0 52.8 + - + +
208A ALA* 3.9 6.3 - - - +
209A ALA 3.2 0.4 - - - -
210A ALA* 1.3 73.1 - - - +
212A LEU* 1.3 58.5 + - + +
213A VAL* 3.0 17.1 + - - +
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Residues in contact with LEU 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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208A ALA* 3.3 18.8 + - + +
209A ALA* 3.1 18.7 + - + +
211A LYS* 1.3 77.0 - - - +
213A VAL* 1.3 70.0 + - - +
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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