Contacts of the helix formed by residues 200 - 213 (chain A) in PDB entry 2R2J
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 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A VAL* 4.4 0.4 - - - -
197A ALA* 3.2 25.4 + - + +
198A MSE 3.2 0.6 - - - -
199A THR* 1.3 78.4 + - - +
201A PHE* 1.3 60.7 + - - +
202A ASP* 3.1 22.4 + - - +
203A VAL* 3.1 28.7 + - + +
204A THR* 2.7 31.9 + - - -
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Residues in contact with PHE 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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88A MSE 3.5 38.1 - - + -
148A VAL* 3.9 14.1 - - + -
151A ARG* 3.2 58.1 - - + +
152A VAL* 3.7 27.4 - - + -
155A ILE* 3.7 13.0 - - + -
199A THR 3.5 4.4 + - - -
200A ASN* 1.3 71.9 + - - +
202A ASP* 1.3 82.4 + - - +
205A TYR* 2.9 36.3 + + + +
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Residues in contact with ASP 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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200A ASN* 3.1 8.5 + - - +
201A PHE* 1.3 94.4 + - - +
203A VAL* 1.3 61.7 + - + +
205A TYR* 3.5 4.1 - - - +
206A ASN* 2.9 43.3 + - - +
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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
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194A TYR* 3.5 21.1 - - + +
196A GLY* 4.6 9.0 - - - -
197A ALA* 5.0 1.8 - - + +
200A ASN* 3.1 29.8 + - + +
202A ASP* 1.3 76.5 - - + +
204A THR* 1.3 55.8 + - - +
206A ASN* 3.2 7.4 + - - +
207A TRP* 2.8 35.2 + - + +
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Residues in contact with THR 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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148A VAL* 3.8 20.2 - - + +
149A PHE* 5.4 2.9 - - + -
152A VAL* 4.5 4.9 - - + -
180A ILE* 3.6 30.7 - - + -
194A TYR* 3.1 25.8 + - + -
197A ALA 3.1 7.1 + - - -
198A MSE 3.8 6.7 - - - +
200A ASN 2.7 22.8 + - - -
201A PHE 4.2 0.2 - - - -
203A VAL* 1.3 75.3 - - - +
205A TYR* 1.3 65.6 - - - +
207A TRP* 3.2 0.9 + - - +
208A ILE* 3.1 32.6 + - + +
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Residues in contact with TYR 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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88A MSE 6.1 2.7 - - - -
91A LYS* 5.7 0.2 - - - +
152A VAL* 3.8 21.6 - - + +
155A ILE* 3.6 27.8 - - + +
156A LEU* 4.0 14.2 - - + +
201A PHE* 2.9 46.6 + + + +
202A ASP* 3.5 4.3 - - - +
204A THR* 1.3 77.8 - - - +
206A ASN* 1.3 67.4 + - - +
208A ILE* 3.4 2.1 + - - +
209A GLN* 2.9 56.3 + - + +
379A FMT 4.0 17.1 + - - -
380A SIN 2.7 39.6 + - - +
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Residues in contact with ASN 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 ASP* 2.9 35.5 + - - +
203A VAL* 3.7 5.8 - - - +
205A TYR* 1.3 79.1 - - - +
207A TRP* 1.3 62.0 + - - +
209A GLN* 3.7 10.4 - - - +
210A ASP* 3.0 24.9 + - - +
379A FMT 3.1 24.6 + - - +
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Residues in contact with TRP 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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134A ILE* 5.1 2.2 - - + -
180A ILE* 3.9 20.2 - - + -
182A TYR* 3.6 22.0 - - + -
192A MSE 3.6 26.5 - - + -
193A VAL 3.6 8.5 + - - -
194A TYR* 3.3 61.3 - + + +
195A LEU 4.9 1.8 - - - +
203A VAL* 2.8 14.2 + - + +
204A THR 3.7 2.0 - - - +
206A ASN* 1.3 71.1 - - - +
208A ILE* 1.3 89.5 + - + +
210A ASP* 3.1 15.5 + - + +
211A LYS* 3.2 48.8 + - + +
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Residues in contact with ILE 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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134A ILE* 4.3 9.4 - - + -
149A PHE* 4.6 11.2 - - + -
152A VAL* 3.8 17.9 - - + -
156A LEU* 3.7 18.6 - - + -
162A PHE* 3.7 23.1 - - + -
180A ILE* 4.1 17.7 - - + -
204A THR* 3.1 35.3 + - + +
205A TYR 3.9 2.5 - - - +
207A TRP* 1.3 97.8 - - + +
209A GLN* 1.3 58.0 + - - +
211A LYS* 3.1 6.6 + - - +
212A CYS* 3.0 31.3 + - - -
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Residues in contact with GLN 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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91A LYS* 4.6 14.5 - - - +
156A LEU* 3.8 17.5 - - + -
205A TYR* 2.9 45.3 + - + +
206A ASN* 3.7 16.5 - - - +
207A TRP 3.1 0.4 - - - -
208A ILE* 1.3 76.4 - - - +
210A ASP* 1.3 60.4 + - - +
212A CYS* 4.3 1.8 - - - -
213A VAL* 3.0 51.7 + - + +
379A FMT 4.4 14.5 + - - +
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Residues in contact with ASP 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 ASN 3.0 13.2 + - - +
207A TRP* 3.3 12.1 - - + +
209A GLN* 1.3 81.0 + - - +
211A LYS* 1.3 86.0 + - - +
213A VAL 3.5 16.7 - - - +
214A PRO* 5.1 1.7 - - - +
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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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132A ARG* 3.3 8.5 + - - -
134A ILE* 5.0 2.0 - - + -
182A TYR* 3.2 65.0 + - + -
192A MSE 4.4 20.1 - - - +
207A TRP* 3.5 56.7 - - + +
208A ILE* 3.1 8.1 + - - +
210A ASP* 1.3 99.1 + - - +
212A CYS* 1.3 56.3 + - - +
213A VAL 5.2 0.2 - - - -
214A PRO* 5.4 0.7 - - - +
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Residues in contact with CYS 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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132A ARG* 3.4 23.4 + - - +
134A ILE* 4.5 1.3 - - - -
156A LEU* 4.3 8.7 - - + -
159A ASP* 4.0 18.3 - - + +
160A CYS* 3.2 39.0 - - - -
208A ILE* 3.0 28.4 + - - +
209A GLN* 3.7 5.8 - - - +
210A ASP 3.3 0.2 - - - -
211A LYS* 1.3 76.8 - - - +
213A VAL* 1.3 70.2 + - + +
214A PRO* 3.1 12.4 - - - +
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Residues in contact with VAL 213 (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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91A LYS* 5.5 6.1 - - - +
156A LEU* 4.7 2.9 - - + -
159A ASP* 4.3 19.5 - - - +
209A GLN* 3.0 40.2 + - + +
210A ASP* 3.5 14.7 - - - +
212A CYS* 1.3 87.6 - - + +
214A PRO* 1.3 65.8 - - + +
217A ARG* 3.5 35.0 - - + +
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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