Contacts of the strand formed by residues 225 - 230 (chain C) in PDB entry 3ZXR
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 GLN 225 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135C GLU* 4.4 3.4 - - - +
136C PHE 3.3 16.6 - - - +
137C TYR* 3.4 33.7 + - + -
218C HIS* 3.1 15.1 + - - -
219C GLU* 2.8 42.1 + - + +
220C VAL 3.5 1.6 + - - -
221C GLY* 2.9 40.9 + - - +
224C GLY* 1.3 78.3 - - - +
226C ALA* 1.3 57.0 + - - +
271C ASN* 3.9 7.6 + - - +
272C GLY 2.9 26.7 + - - -
273C SER* 3.0 20.0 + - - +
505C P3S 4.3 2.5 + - - -
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Residues in contact with ALA 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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135C GLU* 3.5 6.4 - - - +
136C PHE* 2.7 64.0 + - + +
138C ILE* 4.3 4.3 - - + -
199C ARG* 3.7 24.5 - - - +
217C HIS 3.4 5.4 - - - -
219C GLU* 3.8 5.6 - - - +
224C GLY 4.1 4.9 - - - +
225C GLN* 1.3 77.9 - - - +
227C GLU* 1.3 63.9 + - - +
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Residues in contact with GLU 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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133C GLU* 3.0 15.1 - - + +
134C ALA 5.1 1.6 - - - +
135C GLU* 3.1 13.9 - - + +
136C PHE* 4.5 2.7 - - - -
215C LYS 4.7 0.2 - - - -
216C GLY* 3.2 3.1 - - - -
217C HIS* 2.8 59.2 + - + +
219C GLU* 2.9 6.1 - - + +
226C ALA* 1.3 77.7 - - - +
228C ILE* 1.3 67.3 + - - +
229C ASN* 3.0 28.1 + - - +
502C MG 2.1 31.5 - - - -
504C MG 2.3 25.5 - - - -
505C P3S 3.6 0.2 - - - -
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Residues in contact with ILE 228 (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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132C ALA 5.1 1.4 - - - +
134C ALA 4.8 4.7 + - - +
136C PHE* 4.4 6.0 - - + -
199C ARG* 4.1 17.3 - - + +
202C MET* 3.7 36.8 - - + -
203C LEU* 3.7 20.9 - - + +
206C LEU* 3.6 24.0 - - + -
213C LEU* 3.8 7.9 - - + -
215C LYS 3.3 3.4 - - - -
216C GLY* 3.9 10.8 - - - -
217C HIS 5.0 0.2 - - - +
227C GLU* 1.3 81.1 - - - +
229C ASN* 1.3 72.1 + - - +
230C TYR* 4.3 3.3 + - + -
245C TYR* 3.2 35.0 + - + +
249C ILE* 4.1 10.8 - - + -
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Residues in contact with ASN 229 (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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132C ALA 4.4 3.1 + - - -
133C GLU* 3.9 14.8 - - - +
213C LEU* 3.4 9.3 - - - +
214C GLU* 2.8 31.7 + - + +
215C LYS* 2.6 48.4 + - + +
227C GLU* 3.0 32.6 + - - +
228C ILE* 1.3 81.0 + - - +
230C TYR* 1.3 61.8 + - - +
501C IQ1 3.9 26.3 - - + +
504C MG 4.3 1.2 - - - -
506C PO4 4.6 0.2 + - - -
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Residues in contact with TYR 230 (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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132C ALA* 4.7 21.1 + - + +
134C ALA* 6.1 0.7 - - + -
211C PHE* 3.8 24.9 - + + -
212C ILE 3.2 15.9 - - - +
213C LEU* 4.4 7.6 - - + -
214C GLU* 4.3 6.1 - - - +
228C ILE* 4.6 3.6 - - + -
229C ASN* 1.3 75.9 - - - +
231C GLN* 1.3 78.7 + - - +
232C PHE* 3.5 1.0 + - - -
238C ALA* 4.3 4.9 + - + -
241C ASP* 3.7 26.5 - - + -
242C MET* 3.2 43.8 + - + +
245C TYR* 3.5 42.8 - + + -
501C IQ1 3.5 17.0 - - - +
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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