Contacts of the helix formed by residues 196 - 207 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179B TYR 4.0 0.9 - - - -
180B LYS* 3.9 24.0 - - + +
194B ASN 3.5 8.5 + - - +
195B PHE* 1.3 72.0 - - - +
197B HIS* 1.3 53.3 + - - +
198B ARG 3.6 1.6 - - - -
199B ARG* 3.3 36.9 + - - +
200B HIS* 2.8 49.9 + - - -
1300B HEC 3.0 25.6 + - - +
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Residues in contact with HIS 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B ALA* 3.6 14.1 - - + +
178B PRO* 3.0 26.1 + - + +
179B TYR 3.4 6.1 + - - +
181B VAL* 4.0 18.6 - - + -
195B PHE* 2.9 28.3 + + + +
196B THR* 1.3 69.8 - - - +
198B ARG* 1.3 66.2 + - - +
200B HIS* 3.2 5.0 + - - +
201B LEU* 3.1 25.9 + - + +
1298B HEC 2.1 92.4 + + + -
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Residues in contact with ARG 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B PRO* 3.2 24.2 + - + +
175B MET* 3.3 52.9 + - - +
177B ALA* 3.0 20.2 + - - -
178B PRO* 3.3 7.2 + - - +
179B TYR* 3.0 54.0 + - + +
197B HIS* 1.3 79.5 - - - +
199B ARG* 1.3 57.6 + - - +
201B LEU* 3.9 4.9 - - - +
202B THR* 2.7 46.0 + - - +
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Residues in contact with ARG 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B TYR* 4.4 5.0 + - + -
196B THR* 3.3 36.1 + - - +
197B HIS 3.2 0.6 - - - -
198B ARG* 1.3 76.2 - - - +
200B HIS* 1.3 68.2 + - - +
202B THR* 4.0 4.6 - - - -
203B SER* 2.9 28.3 + - - -
1300B HEC 3.6 39.9 + - - +
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Residues in contact with HIS 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B PHE* 3.4 22.6 - + + -
196B THR* 2.8 40.9 + - - +
197B HIS 3.2 4.5 + - - +
199B ARG* 1.3 77.8 - - - +
201B LEU* 1.3 62.3 + - - +
203B SER* 3.6 3.8 - - - -
204B LEU* 2.9 35.0 + - + +
1298B HEC 5.0 4.0 - - + -
1300B HEC 1.9 106.9 + + + -
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Residues in contact with LEU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B VAL 5.3 0.4 - - - +
174B PRO* 3.9 21.5 - - + -
177B ALA* 4.8 4.7 - - + -
197B HIS* 3.1 17.9 + - + +
198B ARG* 3.9 4.5 - - - +
200B HIS* 1.3 75.3 - - - +
202B THR* 1.3 64.7 + - - +
204B LEU* 3.2 6.0 + - + +
205B MET* 2.9 47.0 + - + +
224B LEU* 4.6 13.9 - - + -
1296B HEC 5.0 7.2 - - + -
1298B HEC 3.5 65.6 - - + +
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Residues in contact with THR 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B PRO* 3.4 26.3 - - + +
198B ARG* 2.7 32.5 + - - +
199B ARG* 4.0 4.7 - - - -
201B LEU* 1.3 73.8 - - - +
203B SER* 1.3 62.8 + - - +
205B MET* 3.5 3.5 + - - +
206B GLU* 3.1 31.1 + - + +
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Residues in contact with SER 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ARG* 2.9 21.6 + - - -
200B HIS* 3.6 4.0 - - - -
202B THR* 1.3 80.2 - - - +
204B LEU* 1.3 62.0 + - - +
206B GLU* 3.4 16.8 + - - +
207B ARG* 2.6 44.6 + - - +
1300B HEC 2.7 26.5 + - - +
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Residues in contact with LEU 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B GLU 5.8 0.4 - - - +
114B CYS* 4.4 6.7 - - - -
200B HIS* 2.9 30.2 + - + +
201B LEU* 3.2 8.9 + - + +
203B SER* 1.3 80.1 - - - +
205B MET* 1.3 61.8 + - - +
207B ARG* 3.6 13.5 + - - +
208B ILE* 3.8 13.5 + - - +
274B MET* 3.8 33.7 - - + -
1296B HEC 3.9 33.9 - - + +
1298B HEC 4.4 13.0 - - + -
1300B HEC 3.8 42.4 - - + -
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Residues in contact with MET 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B PRO* 3.5 36.6 - - + +
172B VAL 3.7 14.4 - - - +
173B SER* 5.2 0.4 - - - -
174B PRO* 3.8 29.4 - - + -
201B LEU* 2.9 32.2 + - + +
202B THR* 4.0 4.0 - - - +
204B LEU* 1.3 74.5 - - + +
206B GLU* 1.3 67.3 + - - +
208B ILE* 2.9 20.7 + - + +
209B LYS* 3.0 16.2 + - + +
224B LEU* 3.5 24.9 - - + -
1296B HEC 5.4 0.9 - - + -
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Residues in contact with GLU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B THR* 3.1 25.2 + - + +
203B SER* 3.6 8.7 - - - +
204B LEU 3.3 0.2 - - - -
205B MET* 1.3 76.7 - - - +
207B ARG* 1.3 64.6 + - + +
208B ILE 3.0 1.7 + - - -
209B LYS* 3.2 58.7 + - - +
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Residues in contact with ARG 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ARG* 6.2 2.2 - - - +
110B GLU* 3.8 33.2 - - + +
203B SER* 2.6 43.0 + - - +
204B LEU* 4.1 11.1 - - - +
205B MET 3.3 0.8 - - - -
206B GLU* 1.3 76.1 - - + +
208B ILE* 1.3 61.7 + - + +
210B ASP 5.6 0.2 - - - -
211B ASP* 5.7 0.3 - - - +
274B MET* 3.9 26.0 - - - +
1300B HEC 2.8 34.9 + - - +
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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