Contacts of the helix formed by residues 199 - 212 (chain A) in PDB entry 4IBR
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 THR 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A ASP* 2.9 40.4 + - + +
198A LEU* 1.3 74.5 - - - +
200A ALA* 1.3 65.0 + - - +
201A ALA* 3.7 7.6 + - - +
202A SER* 3.1 14.4 + - - -
203A ARG* 2.9 22.4 + - - +
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Residues in contact with ALA 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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198A LEU 3.9 0.2 + - - -
199A THR* 1.3 72.5 - - - +
201A ALA* 1.3 62.9 + - - +
203A ARG* 3.4 27.8 - - - +
204A GLN* 3.0 25.9 + - - +
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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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199A THR* 3.2 7.0 + - - +
200A ALA* 1.3 78.2 - - - +
202A SER* 1.3 59.8 + - - +
204A GLN* 3.5 6.0 + - - +
205A GLN* 3.0 27.0 + - - +
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Residues in contact with SER 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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80A LEU* 3.5 32.9 + - - +
83A VAL* 5.0 3.6 - - - +
84A ASP* 2.5 37.0 + - - -
198A LEU* 4.0 7.0 - - - -
199A THR* 3.1 13.1 + - - -
201A ALA* 1.3 76.6 - - - +
203A ARG* 1.3 60.8 + - - +
205A GLN* 3.1 9.9 + - - +
206A LEU* 2.9 23.4 + - - +
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Residues in contact with ARG 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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192A LEU 3.7 17.7 - - - +
193A LEU* 3.1 30.8 - - - +
194A THR* 4.4 9.4 + - - +
195A GLY 3.2 21.0 + - - -
196A GLU* 3.7 20.8 + - - +
198A LEU* 2.8 36.8 + - + +
199A THR* 2.9 7.9 + - - +
200A ALA* 3.4 32.8 - - - +
202A SER* 1.3 76.5 - - - +
204A GLN* 1.3 64.9 + - - +
206A LEU* 3.5 3.9 + - - +
207A ILE* 3.2 22.9 + - - +
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Residues in contact with GLN 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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200A ALA 3.0 19.7 + - - +
201A ALA* 3.6 6.7 - - - +
202A SER 3.2 0.2 - - - -
203A ARG* 1.3 77.8 - - + +
205A GLN* 1.3 60.3 + - - +
207A ILE* 3.4 14.6 - - - +
208A ASP* 2.9 61.5 + - - +
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Residues in contact with GLN 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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80A LEU* 4.3 8.3 - - + -
90A LEU* 3.9 16.5 - - + +
201A ALA 3.0 14.6 + - - +
202A SER* 3.1 11.6 + - - +
204A GLN* 1.3 75.6 - - - +
206A LEU* 1.3 63.9 + - - +
208A ASP* 3.2 13.3 + - - +
209A TRP* 3.0 71.2 + - + +
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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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73A VAL* 3.8 37.7 - - + +
76A CYS* 4.2 10.1 - - + -
77A GLY* 4.3 7.9 - - - +
80A LEU* 3.9 6.3 - - + +
126A ILE* 4.0 20.2 - - + -
192A LEU* 4.0 22.0 - - + -
193A LEU* 3.8 20.6 - - + -
198A LEU* 4.4 11.9 - - + -
202A SER 2.9 14.7 + - - +
203A ARG* 3.8 6.7 - - - +
204A GLN 3.3 0.2 - - - -
205A GLN* 1.3 76.7 - - - +
207A ILE* 1.3 63.3 + - - +
209A TRP* 3.2 11.8 + - + +
210A MET* 3.1 23.5 + - - +
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Residues in contact with ILE 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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50A LEU* 6.3 0.7 - - + -
193A LEU* 4.0 34.0 - - + +
203A ARG 3.2 13.0 + - - +
204A GLN* 3.4 30.3 - - - +
206A LEU* 1.3 78.8 - - - +
208A ASP* 1.3 64.3 + - - +
210A MET* 3.3 3.9 + - + -
211A GLU* 2.8 31.5 + - + +
229A PHE* 4.1 25.8 - - + -
231A ALA* 3.6 16.9 - - + +
247A ALA* 4.4 4.7 - - + -
254A PRO* 4.3 13.7 - - + -
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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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204A GLN* 2.9 48.5 + - - +
205A GLN* 3.4 18.0 + - - +
206A LEU 3.2 0.2 - - - -
207A ILE* 1.3 80.4 - - - +
209A TRP* 1.3 62.1 + - + +
211A GLU* 3.3 19.6 + - - +
212A ALA* 3.2 22.5 + - - +
229A PHE* 6.1 0.2 - - - -
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Residues in contact with TRP 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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76A CYS* 4.1 2.2 - - + -
80A LEU* 3.6 32.8 - - + -
90A LEU* 4.2 10.8 - - + -
119A GLY* 3.6 27.2 + - - -
122A CYS* 3.4 33.0 - - + -
123A SER* 3.9 29.7 - - - -
126A ILE* 3.6 27.4 - - + +
127A THR* 3.2 23.6 - - + +
205A GLN* 3.0 55.4 + - + +
206A LEU* 3.6 13.7 - - + +
208A ASP* 1.3 77.6 - - - +
210A MET* 1.3 62.8 + - - +
212A ALA* 3.1 11.2 + - + -
213A ASP 3.5 0.5 + - - -
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Residues in contact with MET 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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73A VAL* 3.7 38.1 - - + -
126A ILE* 3.8 8.3 - - + -
189A LEU* 4.2 18.6 - - + -
193A LEU* 4.6 16.2 - - + -
206A LEU* 3.1 12.8 + - - +
207A ILE* 3.7 4.3 - - - +
209A TRP* 1.3 73.9 - - - +
211A GLU* 1.3 66.7 + - - +
213A ASP* 3.0 22.2 + - - +
221A ARG* 3.4 0.5 + - - -
231A ALA* 3.5 31.2 - - + +
232A ASP* 3.2 30.8 + - - +
233A LYS 4.2 0.2 - - - +
245A ILE* 4.0 24.0 - - + +
247A ALA 4.9 0.9 - - - +
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Residues in contact with GLU 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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207A ILE 2.8 20.5 + - - +
208A ASP* 3.6 20.8 - - - +
209A TRP 3.3 0.2 - - - -
210A MET* 1.3 73.1 - - - +
212A ALA* 1.3 57.0 + - - +
213A ASP 3.2 0.7 + - - +
221A ARG* 3.0 20.4 + - - -
229A PHE* 3.6 28.5 - - + -
230A ILE 3.6 22.4 - - - +
231A ALA* 3.4 5.1 - - + +
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Residues in contact with ALA 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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127A THR* 3.5 16.0 - - + -
208A ASP 3.2 12.0 + - - +
209A TRP* 3.1 13.6 + - + +
210A MET 3.0 1.0 - - - -
211A GLU* 1.3 74.8 - - - +
213A ASP* 1.3 66.8 + - - +
214A LYS* 3.2 28.0 + - - +
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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