Contacts of the strand formed by residues 222 - 227 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ASN* 4.3 2.3 + - - +
121A LEU* 4.0 9.2 - - - +
145A SER* 3.2 31.3 + - - -
146A ALA 3.5 3.8 + - - -
147A LEU 3.7 1.0 + - - -
148A MET* 3.8 16.5 + - + +
213A ALA 4.7 0.4 - - - +
216A ALA* 3.3 10.5 + - + -
217A PHE* 3.6 44.1 - - + +
220A GLY 4.5 1.6 - - - -
221A GLU* 1.3 80.2 + - - +
223A ALA* 1.3 64.9 + - - +
224A MET 3.5 21.2 + - - +
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Residues in contact with ALA 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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117A TYR* 3.3 2.1 - - - +
118A ASN* 2.7 32.1 + - - -
121A LEU* 4.1 22.6 - - + +
122A LEU* 4.2 18.2 - - + -
139A LEU* 3.7 27.6 - - + -
145A SER 2.9 8.1 + - - -
146A ALA 3.6 8.5 - - - +
217A PHE* 3.4 4.6 - - - -
222A THR* 1.3 73.0 + - - +
224A MET* 1.3 61.0 + - - +
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Residues in contact with MET 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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115A LEU* 3.8 23.3 - - + -
116A ILE 3.4 4.5 - - - -
117A TYR* 3.8 11.4 - - + -
122A LEU* 3.8 13.0 - - + -
126A PRO* 3.5 39.9 - - + -
132A ILE* 3.9 24.9 - - + -
135A LEU* 4.1 11.0 - - + -
146A ALA* 2.8 28.7 + - + +
147A LEU* 3.6 13.2 - - + -
148A MET 3.1 21.8 + - - +
217A PHE* 4.5 2.2 - - - -
222A THR* 3.5 8.3 + - - +
223A ALA* 1.3 80.0 - - - +
225A THR* 1.3 65.0 + - - +
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Residues in contact with THR 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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115A LEU* 3.8 3.6 - - - +
116A ILE* 2.9 52.7 + - + +
147A LEU* 3.8 4.9 - - - -
148A MET 2.7 24.0 + - - -
149A PHE* 4.1 2.1 - - - -
213A ALA* 4.3 8.0 + - - +
214A GLU* 5.7 0.6 - - - -
217A PHE* 3.8 37.0 - - + -
224A MET* 1.3 75.4 - - - +
226A ILE* 1.3 71.9 + - - +
227A ASN* 5.0 6.9 + - + +
235A ILE* 5.8 0.4 - - + -
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Residues in contact with ILE 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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113A LEU* 4.2 24.0 - - + -
114A SER 3.5 11.7 - - - +
115A LEU* 4.9 5.2 - - + -
129A TRP* 3.8 34.1 - - + -
147A LEU* 4.3 8.1 - - + -
149A PHE* 3.7 40.5 - - + +
150A ASN 5.1 0.5 + - - -
156A PHE* 3.6 25.8 - - + +
159A PRO* 5.6 4.0 - - + -
225A THR* 1.3 83.0 + - - +
227A ASN* 1.3 68.2 + - - +
247A LEU* 3.7 23.8 - - + -
248A PRO* 5.8 0.7 - - + -
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Residues in contact with ASN 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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113A LEU* 3.7 12.1 - - - -
114A SER* 3.2 24.4 + - - +
116A ILE* 3.4 27.8 - - + +
156A PHE* 3.9 3.0 - - - -
210A TYR* 3.1 38.3 + - - -
213A ALA* 6.4 0.2 - - - +
214A GLU* 5.1 8.1 - - - +
225A THR* 4.0 10.5 + - + +
226A ILE* 1.3 77.6 + - - +
228A GLY* 1.3 74.7 + - - +
230A TRP* 3.1 24.1 + - - -
231A ALA* 3.7 12.2 - - + +
232A TRP* 5.0 0.5 + - - -
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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