Contacts of the helix formed by residues 222 - 228 (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 GLU 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A VAL* 3.9 22.0 - - + +
220A LYS* 3.1 3.0 - - - +
221A PRO* 1.3 82.4 - - + +
223A ILE* 1.3 65.0 + - - +
224A LEU 3.2 3.6 + - - -
225A CYS* 3.3 28.7 + - - +
234A LEU* 3.5 26.8 - - + +
235A SER* 3.1 29.2 + - - +
236A LEU* 3.6 30.4 - - + +
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Residues in contact with ILE 223 (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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121A LYS* 5.0 12.6 - - - +
171A PRO* 6.4 0.9 - - + -
217A PHE 4.0 16.8 - - - +
218A HIS* 3.8 28.7 - - + -
219A ASN* 4.1 13.9 - - - +
220A LYS* 2.9 27.9 + - + +
221A PRO 3.4 0.8 - - - +
222A GLU* 1.3 78.7 - - - +
224A LEU* 1.3 70.8 + - + +
226A ALA* 3.0 17.9 + - + +
234A LEU* 3.7 17.4 - - + +
1296A HEC 3.5 36.8 - - + +
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Residues in contact with LEU 224 (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* 4.3 19.5 - - + -
201A LEU* 4.4 9.0 - - + -
205A MET* 3.6 35.7 - - + -
208A ILE* 4.8 9.4 - - + -
218A HIS* 3.7 31.6 - - + +
221A PRO 5.0 1.6 + - - +
222A GLU 3.3 1.6 - - - -
223A ILE* 1.3 85.7 - - + +
225A CYS* 1.3 62.0 + - - +
227A THR* 2.7 26.5 + - - -
1296A HEC 3.8 38.8 - - + -
1298A HEC 3.6 9.6 - - + +
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Residues in contact with CYS 225 (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* 4.7 0.9 - - - -
222A GLU* 3.5 29.4 - - + +
223A ILE 3.2 0.2 - - - -
224A LEU* 1.3 77.9 - - - +
226A ALA* 1.3 59.3 + - - +
227A THR 3.1 1.3 + - - -
228A CYS 3.3 2.6 + - - -
229A HIS* 3.0 35.0 + - + +
234A LEU* 5.6 1.8 - - + -
235A SER 4.7 7.4 - - - +
238A PRO* 5.7 0.7 - - + -
1298A HEC 1.8 75.5 - - + +
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Residues in contact with ALA 226 (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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118A VAL* 5.2 1.6 - - - +
121A LYS* 5.3 7.2 - - - +
222A GLU 4.0 0.6 + - - -
223A ILE* 3.0 17.7 + - + +
225A CYS* 1.3 76.8 - - - +
227A THR* 1.3 65.7 + - - +
228A CYS 3.1 1.2 + - - -
229A HIS 3.4 16.2 - - - +
230A HIS* 3.6 21.5 - - - +
231A ARG 5.7 0.7 - - - +
232A SER 5.7 0.7 - - - +
234A LEU* 3.7 24.0 - - + +
1296A HEC 4.1 8.8 - - + +
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Residues in contact with THR 227 (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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114A CYS* 3.7 31.6 - - + -
117A ILE* 3.6 37.8 - - + +
118A VAL* 4.0 9.8 - - + +
224A LEU 2.7 20.0 + - - -
225A CYS 3.1 0.2 - - - -
226A ALA* 1.3 78.3 - - - +
228A CYS* 1.3 64.7 + - - +
230A HIS* 4.8 3.6 + - - +
266A GLN* 4.3 3.5 + - - -
1296A HEC 3.3 37.2 - - - +
1298A HEC 4.2 6.7 - - + -
1300A HEC 4.3 2.9 - - + -
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Residues in contact with CYS 228 (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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117A ILE* 4.2 0.4 - - - -
225A CYS 3.3 2.0 + - - -
227A THR* 1.3 89.3 - - - +
229A HIS* 1.3 59.2 + - - +
230A HIS* 3.0 12.1 + - - -
266A GLN* 3.0 41.0 + - - +
1298A HEC 1.8 83.2 - - + -
1299A HEC 3.4 12.9 - - + +
1300A HEC 4.0 10.3 - - - -
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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