Contacts of the strand formed by residues 222 - 227 (chain C) in PDB entry 3IO6
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 222 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C ASN* 4.4 4.7 - - - +
121C LEU* 4.6 1.4 - - - +
144C LYS* 3.5 4.0 - - - -
145C SER* 3.4 27.3 + - - -
146C ALA 3.6 3.5 + - - -
148C MET* 3.7 17.5 + - + +
216C ALA* 3.6 11.9 - - + -
217C PHE* 3.4 46.0 - - + +
220C GLY* 4.6 3.8 - - - -
221C GLU* 1.3 80.1 + - - +
223C ALA* 1.3 63.7 + - - +
224C MET 2.9 25.5 + - - +
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Residues in contact with ALA 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C TYR* 3.2 4.9 - - - +
118C ASN* 2.9 34.7 + - - +
121C LEU* 4.3 14.1 - - + -
122C LEU* 4.1 25.5 - - + +
139C LEU* 3.8 27.4 - - + -
144C LYS* 4.2 1.2 - - - +
145C SER 3.1 6.8 + - - +
146C ALA 4.0 3.6 - - - +
217C PHE* 3.6 1.5 - - - -
222C THR* 1.3 75.2 + - - +
224C MET* 1.3 63.0 + - - +
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Residues in contact with MET 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C LEU* 4.1 24.5 - - + -
116C ILE 3.4 6.3 - - - +
117C TYR* 3.9 9.9 - - + -
122C LEU* 3.7 11.2 - - + -
125C PRO* 5.0 0.2 - - - -
126C PRO* 3.6 41.3 - - + -
132C ILE* 4.2 20.2 - - + -
135C LEU* 3.8 16.2 - - + -
146C ALA 3.2 22.2 + - - +
147C LEU* 3.6 12.7 - - + -
148C MET 3.1 13.7 + - - +
217C PHE* 4.3 2.7 - - - -
222C THR* 2.9 17.2 + - - +
223C ALA* 1.3 85.8 - - - +
225C THR* 1.3 64.8 + - - +
248C PRO* 5.8 0.4 - - - -
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Residues in contact with THR 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C LEU* 3.9 2.8 - - - +
116C ILE* 2.8 53.2 + - + +
147C LEU* 3.9 4.3 - - - -
148C MET 2.7 24.0 + - - -
149C PHE* 4.2 1.9 - - - -
213C ALA* 4.5 7.6 + - - +
214C GLU* 5.2 2.7 + - - -
217C PHE* 3.6 38.6 - - + -
224C MET* 1.3 74.3 - - - +
226C ILE* 1.3 71.9 + - - +
227C ASN* 4.9 6.7 + - + +
235C ILE* 5.6 1.6 - - + -
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Residues in contact with ILE 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C LEU* 4.3 21.3 - - + -
114C SER 3.5 13.2 - - - +
115C LEU* 4.4 11.2 - - + -
129C TRP* 3.7 35.2 - - + -
147C LEU* 4.3 8.3 - - + -
149C PHE* 3.8 45.1 - - + +
150C ASN 5.2 0.3 + - - -
156C PHE* 4.1 19.0 - - + +
159C PRO* 5.8 2.7 - - + -
225C THR* 1.3 81.5 + - - +
227C ASN* 1.3 70.0 + - - +
247C LEU* 3.7 22.9 - - + -
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Residues in contact with ASN 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C LEU* 3.7 12.6 - - - -
114C SER* 3.0 27.6 + - - +
116C ILE* 3.5 24.2 - - + +
156C PHE* 4.5 2.4 - - - -
210C TYR* 3.0 34.1 + - - -
214C GLU* 5.0 8.9 - - - +
225C THR* 4.0 9.7 + - + +
226C ILE* 1.3 78.2 + - - +
228C GLY* 1.3 74.8 + - - +
230C TRP* 2.9 24.9 + - - -
231C ALA* 3.6 15.7 - - + +
232C TRP* 5.0 0.2 + - - -
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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