Contacts of the strand formed by residues 225 - 230 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F GLU* 4.4 3.4 - - - +
136F PHE 3.3 17.0 - - - +
137F TYR* 3.4 35.8 + - + -
199F ARG* 5.2 0.2 + - - -
218F HIS* 3.2 13.4 + - - -
219F GLU* 2.8 38.6 + - + +
220F VAL 3.5 1.7 + - - -
221F GLY* 2.8 41.4 + - - +
224F GLY* 1.3 79.4 - - - +
226F ALA* 1.3 60.8 + - - +
271F ASN* 3.8 7.6 - - - +
272F GLY 2.9 26.9 + - - -
273F SER* 3.0 20.4 + - - +
505F P3S 4.3 2.4 + - - -
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Residues in contact with ALA 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F GLU* 3.4 7.4 - - - +
136F PHE* 2.6 62.5 + - + +
138F ILE* 4.3 4.7 - - + -
199F ARG* 3.7 27.6 - - - +
217F HIS 3.5 4.9 - - - -
219F GLU* 3.8 5.7 - - - +
224F GLY 4.2 4.9 - - - +
225F GLN* 1.3 76.9 - - - +
227F GLU* 1.3 62.2 + - - +
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Residues in contact with GLU 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F GLU* 3.0 14.6 - - + +
134F ALA 5.2 1.1 - - - +
135F GLU* 3.2 13.5 - - + +
136F PHE* 4.6 2.5 - - - -
199F ARG* 4.9 0.2 - - - -
216F GLY* 3.2 2.9 - - - -
217F HIS* 2.8 62.7 + - + +
219F GLU* 3.0 8.1 - - + +
226F ALA* 1.3 76.4 - - - +
228F ILE* 1.3 69.5 + - - +
229F ASN* 3.0 25.5 + - - +
502F MG 2.0 30.2 - - - -
504F MG 2.1 28.1 - - - -
505F P3S 3.6 0.4 - - - -
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Residues in contact with ILE 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F ALA 5.0 1.0 - - - +
134F ALA 4.8 5.5 + - - +
136F PHE* 4.4 7.1 - - + -
199F ARG* 4.2 18.6 - - + +
202F MET* 3.7 35.7 - - + -
203F LEU* 3.7 25.6 - - + +
206F LEU* 3.7 12.6 - - + -
213F LEU* 3.7 15.3 - - + -
215F LYS 3.3 4.7 - - - +
216F GLY* 3.9 11.0 - - - -
227F GLU* 1.3 80.4 - - - +
229F ASN* 1.3 70.8 + - - +
230F TYR* 4.3 2.8 + - + -
245F TYR* 3.2 34.6 + - + +
249F ILE* 4.1 10.5 - - + -
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Residues in contact with ASN 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F ALA 4.4 3.3 + - - -
133F GLU* 3.8 17.3 - - - +
213F LEU* 3.5 9.1 - - - +
214F GLU* 2.8 36.1 + - + -
215F LYS* 2.7 49.0 + - - +
227F GLU* 3.0 32.4 + - - +
228F ILE* 1.3 81.1 + - - +
230F TYR* 1.3 56.3 + - - +
501F IQ1 3.9 24.6 - - + +
504F MG 4.2 1.7 - - - -
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Residues in contact with TYR 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F ALA* 4.7 19.7 + - + +
134F ALA* 6.2 0.9 - - + -
206F LEU* 5.6 0.4 - - + -
211F PHE* 3.8 23.3 - + + -
212F ILE 3.2 16.8 - - - +
213F LEU* 4.3 7.0 - - + +
214F GLU* 4.3 4.9 - - - +
228F ILE* 4.7 3.4 - - + -
229F ASN* 1.3 76.5 - - - +
231F GLN* 1.3 78.7 + - - +
232F PHE* 3.5 1.0 + - - -
238F ALA* 4.3 4.5 + - + -
241F ASP* 3.7 27.8 - - + -
242F MET* 3.2 44.2 + - + +
245F TYR* 3.5 42.0 - + + -
501F IQ1 3.4 17.3 - - - +
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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