Contacts of the helix formed by residues 222 - 228 (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 GLU 222 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172B VAL* 3.6 28.6 - - + +
220B LYS* 3.1 2.8 + - - +
221B PRO* 1.3 78.8 - - + +
223B ILE* 1.3 62.1 + - - +
224B LEU 3.3 3.8 + - - -
225B CYS* 3.4 24.8 + - - +
234B LEU* 3.6 25.8 - - + +
235B SER* 3.1 31.2 + - - +
236B LEU* 3.5 33.7 + - + +
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Residues in contact with ILE 223 (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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121B LYS* 5.1 4.7 - - - +
171B PRO* 6.2 1.3 - - + -
217B PHE 4.0 15.9 - - - +
218B HIS* 3.9 26.7 - - + -
219B ASN 4.1 3.1 - - - +
220B LYS* 3.0 55.4 + - + +
221B PRO 3.4 1.0 - - - +
222B GLU* 1.3 78.0 - - - +
224B LEU* 1.3 67.7 + - + +
226B ALA* 2.9 28.9 + - + +
234B LEU* 3.8 13.5 - - + +
1296B HEC 3.4 39.1 - - + +
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Residues in contact with LEU 224 (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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171B PRO* 4.1 24.9 - - + -
201B LEU* 4.6 9.4 - - + -
205B MET* 3.5 32.1 - - + -
208B ILE* 4.9 7.2 - - + -
218B HIS* 3.8 33.0 - - + +
221B PRO 5.0 1.2 + - - -
222B GLU 3.3 1.0 - - - -
223B ILE* 1.3 78.2 - - + +
225B CYS* 1.3 65.5 + - - +
227B THR* 2.7 26.7 + - - -
1296B HEC 3.9 39.2 - - + +
1298B HEC 3.6 8.5 - - + +
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Residues in contact with CYS 225 (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* 4.5 0.4 - - - -
222B GLU* 3.5 28.9 - - - +
223B ILE 3.2 0.2 - - - -
224B LEU* 1.3 79.3 - - - +
226B ALA* 1.3 55.3 + - - +
227B THR 3.0 3.0 + - - -
228B CYS 3.3 2.8 + - - -
229B HIS* 3.0 35.8 + - + -
234B LEU* 5.7 0.9 - - + -
235B SER 4.7 6.1 - - - +
238B PRO* 5.7 0.7 - - + -
1298B HEC 1.8 77.1 - - + +
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Residues in contact with ALA 226 (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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118B VAL* 5.4 2.6 - - - +
121B LYS* 5.5 6.1 - - - +
222B GLU 4.1 0.6 + - - -
223B ILE* 2.9 19.0 + - + +
225B CYS* 1.3 76.7 - - - +
227B THR* 1.3 66.1 + - - +
228B CYS 3.1 1.0 + - - -
229B HIS 3.4 17.0 - - - +
230B HIS* 3.6 22.4 - - - +
231B ARG 5.8 0.2 - - - +
232B SER 5.8 0.9 - - - +
234B LEU* 3.9 21.5 - - + +
1296B HEC 4.2 8.1 - - + +
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Residues in contact with THR 227 (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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114B CYS* 3.8 29.6 - - + -
117B ILE* 3.6 38.1 - - + +
118B VAL* 4.0 11.4 - - + +
224B LEU 2.7 20.3 + - - -
226B ALA* 1.3 78.1 - - - +
228B CYS* 1.3 66.8 + - - +
230B HIS* 4.7 4.2 + - - +
266B GLN* 4.3 1.9 - - - +
1296B HEC 3.3 36.5 - - - +
1298B HEC 4.3 3.8 - - + -
1300B HEC 4.4 3.1 - - + -
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Residues in contact with CYS 228 (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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117B ILE* 4.2 1.8 - - - -
225B CYS 3.3 1.6 + - - -
227B THR* 1.3 89.5 - - - +
229B HIS* 1.3 59.7 + - - +
230B HIS* 3.0 13.9 + - - -
266B GLN* 3.1 37.0 - - - +
1298B HEC 1.8 81.9 - - + -
1299B HEC 3.5 13.4 - - + +
1300B HEC 4.0 11.0 - - - -
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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