Contacts of the strand formed by residues 225 - 230 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B GLU* 4.4 3.6 - - - +
136B PHE 3.3 16.2 - - - +
137B TYR* 3.5 33.7 + - + -
199B ARG* 5.2 0.3 + - - -
218B HIS* 3.1 13.6 + - - -
219B GLU* 2.8 37.6 + - + +
220B VAL 3.6 1.6 + - - -
221B GLY* 2.8 42.7 + - - +
224B GLY* 1.3 78.3 - - - +
226B ALA* 1.3 62.0 + - - +
271B ASN* 3.8 7.2 - - - +
272B GLY 2.8 27.1 + - - -
273B SER* 3.0 19.6 + - - +
505B P3S 4.2 3.4 + - - -
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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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135B GLU* 3.4 7.1 - - - +
136B PHE* 2.6 64.3 + - + +
138B ILE* 4.2 4.3 - - + -
199B ARG* 3.8 23.3 - - - +
217B HIS 3.5 4.7 - - - -
219B GLU* 3.8 5.5 - - - +
224B GLY 4.2 4.7 - - - +
225B GLN* 1.3 78.6 - - - +
227B GLU* 1.3 62.4 + - - +
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Residues in contact with GLU 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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133B GLU* 2.9 16.0 - - + +
134B ALA 5.2 1.3 - - - +
135B GLU* 3.2 14.6 - - + +
136B PHE* 4.5 2.5 - - - -
216B GLY* 3.2 2.9 - - - -
217B HIS* 2.8 54.7 + - + +
219B GLU* 2.9 6.7 - - + +
226B ALA* 1.3 76.8 - - - +
228B ILE* 1.3 67.1 + - - +
229B ASN* 3.1 26.7 + - - +
502B MG 2.0 30.2 - - - -
504B MG 2.2 27.0 - - - -
505B P3S 3.5 0.2 - - - -
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Residues in contact with ILE 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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132B ALA 5.0 1.6 - - - +
134B ALA 4.8 5.4 + - - +
136B PHE* 4.4 6.0 - - + -
199B ARG* 4.2 18.6 - - + +
202B MET* 3.7 35.2 - - + -
203B LEU* 3.7 21.1 - - + +
206B LEU* 3.7 19.3 - - + -
213B LEU* 3.7 7.9 - - + -
215B LYS 3.3 8.3 - - - +
216B GLY* 3.9 11.0 - - - -
217B HIS 4.9 0.7 - - - +
227B GLU* 1.3 80.3 - - - +
229B ASN* 1.3 72.1 + - - +
230B TYR* 4.7 2.3 - - + -
245B TYR* 3.3 35.0 + - + +
249B ILE* 4.1 10.5 - - + -
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Residues in contact with ASN 229 (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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132B ALA 4.4 2.6 + - - -
133B GLU* 3.8 18.1 - - - +
213B LEU* 3.5 10.1 - - - +
214B GLU* 2.8 31.4 + - + -
215B LYS* 2.7 50.4 + - - +
227B GLU* 3.1 31.4 + - - +
228B ILE* 1.3 82.7 + - - +
230B TYR* 1.3 61.5 - - - +
501B IQ1 4.1 21.4 - - + +
504B MG 4.2 1.4 - - - -
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Residues in contact with TYR 230 (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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132B ALA* 4.6 20.2 + - + +
134B ALA 6.3 0.4 - - - -
206B LEU* 5.6 0.4 - - + -
211B PHE* 3.8 25.4 - + + -
212B ILE 3.2 15.7 - - - +
213B LEU* 4.4 7.4 - - + -
214B GLU* 4.2 5.2 - - - +
228B ILE* 5.0 2.5 - - + -
229B ASN* 1.3 77.2 - - - +
231B GLN* 1.3 79.0 + - - +
232B PHE* 3.6 0.8 + - - -
238B ALA* 4.3 4.8 + - + -
241B ASP* 3.7 26.7 - - + -
242B MET* 3.2 44.3 + - + +
245B TYR* 3.5 43.3 - + + -
501B IQ1 3.4 16.6 - - - +
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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