Contacts of the helix formed by residues 196 - 207 (chain A) in PDB entry 1OFY
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 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A TYR* 4.1 4.9 - - - -
180A LYS* 5.0 3.1 - - + +
194A ASN 3.4 8.0 + - - +
195A PHE* 1.3 72.0 - - - +
197A HIS* 1.3 53.8 + - - +
198A ARG 3.4 1.8 - - - -
199A ARG* 3.2 26.5 + - - -
200A HIS* 2.8 59.6 + - - -
1300A HEC 3.7 14.8 + - + +
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Residues in contact with HIS 197 (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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177A ALA* 3.6 14.1 - - + +
178A PRO* 3.2 24.1 + - + +
179A TYR 3.6 5.8 + - - +
181A VAL* 3.9 20.6 - - + -
195A PHE* 2.9 26.3 + + + +
196A THR* 1.3 70.5 - - - +
198A ARG* 1.3 62.6 + - - +
200A HIS* 3.4 2.3 + - - +
201A LEU* 3.1 24.2 + - + +
1298A HEC 2.0 97.1 + + + -
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Residues in contact with ARG 198 (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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174A PRO* 3.1 23.5 + - + +
175A MET* 3.4 46.5 + - - +
177A ALA* 2.9 22.4 + - - -
178A PRO* 3.6 9.8 - - - +
179A TYR* 3.0 51.9 + - + +
197A HIS* 1.3 75.7 - - - +
199A ARG* 1.3 63.5 + - - +
201A LEU* 4.5 4.0 - - - +
202A THR* 2.6 43.9 + - - +
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Residues in contact with ARG 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A TYR* 4.6 5.7 + - + -
196A THR* 3.2 29.3 + - - +
198A ARG* 1.3 79.6 - - - +
200A HIS* 1.3 56.7 + - - +
202A THR* 3.7 4.3 - - - -
203A SER* 3.0 33.1 + - - -
1300A HEC 2.8 60.3 + - - +
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Residues in contact with HIS 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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195A PHE* 3.5 23.8 - + + -
196A THR* 2.8 40.4 + - - +
197A HIS 3.6 5.2 - - - +
199A ARG* 1.3 73.3 - - - +
201A LEU* 1.3 66.6 + - - +
203A SER* 3.2 6.1 + - - -
204A LEU* 2.9 32.8 + - + +
1298A HEC 5.0 3.8 - - + -
1300A HEC 2.0 104.1 + + + -
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Residues in contact with LEU 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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172A VAL 5.4 0.4 - - - +
174A PRO* 4.1 21.8 - - + -
177A ALA* 4.8 4.3 - - + -
197A HIS* 3.1 14.9 + - + +
198A ARG* 4.2 3.6 - - - +
200A HIS* 1.3 79.1 - - - +
202A THR* 1.3 63.5 + - - +
204A LEU* 3.3 5.2 + - + +
205A MET* 3.0 51.2 + - + +
224A LEU* 4.4 15.9 - - + +
1296A HEC 4.8 7.4 - - + -
1298A HEC 3.3 68.8 - - + +
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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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174A PRO* 3.4 26.7 - - + +
175A MET* 5.5 3.5 - - + +
198A ARG* 2.6 29.6 + - - +
199A ARG* 3.7 5.2 - - - -
201A LEU* 1.3 76.8 - - - +
203A SER* 1.3 58.7 + - - +
205A MET* 3.5 3.6 + - - +
206A GLU* 3.0 30.4 + - + +
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Residues in contact with SER 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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199A ARG* 3.0 19.4 + - - -
200A HIS 3.6 3.4 - - - -
202A THR* 1.3 75.1 - - - +
204A LEU* 1.3 67.3 + - - +
206A GLU* 3.2 13.5 + - - +
207A ARG* 2.5 45.9 + - - +
1300A HEC 2.8 24.5 + - - -
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Residues in contact with LEU 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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110A GLU 5.1 1.7 - - - +
114A CYS* 4.2 14.6 - - - -
200A HIS 2.9 26.1 + - - +
201A LEU* 3.8 5.6 - - - +
203A SER* 1.3 78.9 - - - +
205A MET* 1.3 59.2 + - - +
207A ARG* 3.7 21.8 + - - +
208A ILE* 3.9 4.3 - - - +
274A MET* 3.7 36.6 - - + -
1296A HEC 3.8 36.0 - - + +
1298A HEC 4.5 11.9 - - + -
1300A HEC 3.6 40.6 - - + -
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Residues in contact with MET 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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171A PRO* 3.5 36.6 - - + +
172A VAL 3.9 13.7 - - - +
173A SER* 5.3 0.4 - - - -
174A PRO* 3.8 29.6 - - + -
201A LEU* 3.0 32.5 + - + +
202A THR* 3.8 4.0 - - - +
204A LEU* 1.3 74.5 - - + +
206A GLU* 1.3 65.9 + - - +
208A ILE* 3.1 11.3 + - - +
209A LYS* 3.1 23.6 + - - +
224A LEU* 3.6 23.3 - - + -
1296A HEC 5.4 0.4 - - + -
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Residues in contact with GLU 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 THR* 3.0 20.7 + - + +
203A SER* 3.2 6.6 + - - +
205A MET* 1.3 78.7 - - - +
207A ARG* 1.3 66.7 + - - +
208A ILE 3.1 5.4 + - - -
209A LYS* 3.0 58.3 + - - +
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Residues in contact with ARG 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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110A GLU* 3.8 34.6 + - + +
203A SER* 2.5 42.3 + - - +
204A LEU* 3.8 14.4 - - - +
205A MET 3.3 0.2 - - - -
206A GLU* 1.3 84.9 + - - +
208A ILE* 1.3 60.1 + - + +
209A LYS 3.7 0.2 - - - -
274A MET* 3.8 22.0 - - - +
1300A HEC 3.2 40.8 + - - +
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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