Contacts of the helix formed by residues 202 - 212 (chain A) in PDB entry 4IXU
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 ASP 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A ASN* 2.8 26.5 + - - +
155A SER* 4.7 4.1 + - - -
200A ASP* 4.9 1.4 - - - +
201A VAL* 1.3 74.7 - - - +
203A PRO* 1.3 75.7 - - + +
204A PRO* 3.9 12.6 - - + -
205A GLU* 2.8 31.1 + - + +
206A HIS* 2.9 11.3 + - - +
406A 38I 2.8 63.5 + - + +
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Residues in contact with PRO 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 VAL 3.8 3.1 - - - +
202A ASP* 1.3 86.4 - - + +
204A PRO* 1.4 70.2 - - + +
206A HIS* 3.2 9.9 + - + +
207A PHE* 3.1 20.8 + - - +
406A 38I 4.3 16.4 - - + -
329C GLY* 5.5 6.5 - - - -
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Residues in contact with PRO 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ASN* 3.8 15.9 - - - +
153A THR* 3.5 39.0 - - + +
202A ASP* 3.6 6.3 - - + -
203A PRO* 1.4 99.0 - - + +
205A GLU* 1.3 56.7 + - - +
207A PHE* 3.3 9.5 + - + +
208A ILE* 3.0 33.0 + - - +
406A 38I 5.4 3.8 - - + -
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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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146A ALA* 3.7 8.2 + - + -
147A ASP* 3.1 14.7 + - - -
148A ILE* 3.1 42.3 + - + +
149A ASN* 3.5 33.9 + - - +
161A GLY 4.2 0.2 - - - +
200A ASP 4.3 2.1 - - - +
201A VAL* 3.6 14.8 - - + -
202A ASP* 2.8 39.7 + - + +
204A PRO* 1.3 73.9 - - - +
206A HIS* 1.3 61.8 + - - +
208A ILE* 3.1 5.0 + - - +
209A LEU* 2.9 33.3 + - - +
406A 38I 3.9 6.5 + - - -
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Residues in contact with HIS 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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201A VAL* 3.6 6.8 - - + +
202A ASP 2.9 11.3 + - - +
203A PRO* 3.2 9.4 + - + +
205A GLU* 1.3 76.3 - - - +
207A PHE* 1.3 66.3 - - - +
209A LEU* 3.3 5.4 + - - +
210A LYS* 3.0 47.2 + - + +
216A TYR* 4.3 4.2 + - - -
328C GLU* 3.0 46.9 + - - +
329C GLY 3.6 24.5 + - - -
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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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203A PRO 3.1 13.1 + - - +
204A PRO* 3.4 13.5 - - + +
206A HIS* 1.3 81.7 - - - +
208A ILE* 1.3 61.6 + - + +
210A LYS* 3.8 3.8 - - + +
211A ASN* 2.7 72.1 + - + +
212A TYR* 5.4 2.5 - + - -
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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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148A ILE* 3.4 53.2 - - + +
149A ASN* 4.9 0.2 - - - -
150A THR* 4.2 18.2 - - + -
153A THR* 4.7 12.1 - - + +
171A LEU* 4.0 11.0 - - + -
204A PRO 3.0 22.5 + - - +
205A GLU* 3.1 7.4 + - - +
207A PHE* 1.3 84.7 - - + +
209A LEU* 1.3 64.3 + - - +
212A TYR* 2.9 53.8 + - + +
214A ILE* 4.3 1.8 - - + -
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Residues in contact with LEU 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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146A ALA* 4.2 4.5 - - + -
148A ILE* 4.3 11.2 - - + -
195A TYR* 3.7 31.6 - - + -
198A LEU* 4.1 17.7 - - + -
201A VAL* 4.2 18.4 - - + -
205A GLU 2.9 21.1 + - - +
206A HIS* 3.8 6.7 - - - +
208A ILE* 1.3 75.2 - - - +
210A LYS* 1.3 63.5 + - - +
213A ASP* 3.2 2.6 + - - -
214A ILE* 2.9 52.1 + - + +
216A TYR* 4.1 33.0 - - + -
328C GLU 5.5 0.9 - - - +
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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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206A HIS* 3.0 45.0 + - + +
207A PHE* 3.9 3.6 - - + +
209A LEU* 1.3 77.7 - - + +
211A ASN* 1.3 64.5 + - - +
213A ASP* 3.2 15.1 + - - +
216A TYR* 3.2 36.5 + - + +
328C GLU* 3.9 4.2 + - - -
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Residues in contact with ASN 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 PHE* 2.7 52.4 + - + +
208A ILE 4.1 1.8 - - - +
210A LYS* 1.3 74.7 - - - +
212A TYR* 1.3 89.6 + - + +
213A ASP* 3.4 0.9 + - - +
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Residues in contact with TYR 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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170A GLU* 3.4 41.7 + - + -
171A LEU* 3.5 27.0 - - + +
173A ASP* 4.5 0.3 + - - -
174A LYS* 3.9 30.8 + - - +
190A SER* 3.4 23.4 + - - -
207A PHE* 5.4 3.1 - + - -
208A ILE* 2.9 41.6 + - + +
211A ASN* 1.3 99.7 + - + +
213A ASP* 1.3 70.6 + - - +
214A ILE* 3.2 15.8 + - + -
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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