Contacts of the strand formed by residues 213 - 218 (chain A) 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 LEU 213 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A LEU* 3.8 18.8 - - + +
206A LEU* 3.9 11.0 - - + -
207A ILE* 3.5 39.1 - - + +
211A PHE* 3.5 30.0 + - + +
212A ILE* 1.3 81.2 - - - +
214A GLU* 1.3 64.2 + - - +
228A ILE* 3.7 23.8 - - + -
229A ASN 3.5 17.7 - - - +
230A TYR* 4.4 4.3 - - + -
38F PRO* 3.3 30.9 - - + +
40F SER* 4.8 4.0 + - - +
41F ALA* 4.3 5.4 - - - +
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Residues in contact with GLU 214 (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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212A ILE* 4.8 1.7 - - + +
213A LEU* 1.3 80.2 - - - +
215A LYS* 1.3 67.0 + - + +
229A ASN* 2.9 20.3 + - + +
231A GLN* 3.4 38.1 - - + +
232A PHE* 4.7 3.3 + - - -
501A IQ1 3.2 42.2 + - - +
37F ILE* 3.3 18.4 - - - +
38F PRO* 3.5 9.6 - - - +
41F ALA* 4.5 7.5 - - + +
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Residues in contact with LYS 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A TYR* 5.6 4.0 + - - -
203A LEU* 4.5 6.3 - - - -
213A LEU* 5.1 0.6 - - - +
214A GLU* 1.3 84.3 - - + +
216A GLY* 1.3 58.5 + - - +
217A HIS* 4.2 23.7 + - + -
228A ILE* 3.3 5.1 - - - +
229A ASN* 2.7 59.3 + - + +
501A IQ1 5.8 2.9 - - - -
504A MG 4.4 0.4 - - - -
506A PO4 4.2 18.7 + - - -
35F PHE* 3.7 26.4 - - + -
36F THR 3.1 15.0 - - - +
37F ILE* 4.0 5.8 - - + +
38F PRO* 4.7 1.6 - - - -
52F ALA* 4.5 16.6 + - - +
53F PHE* 5.7 1.8 - - - +
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Residues in contact with GLY 216 (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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199A ARG* 4.5 6.6 + - - -
203A LEU* 4.4 12.5 - - - +
215A LYS* 1.3 75.3 - - - +
217A HIS* 1.3 63.6 + - - +
227A GLU 3.2 10.5 - - - -
228A ILE* 3.8 12.3 - - - -
35F PHE* 3.9 0.3 - - - +
36F THR* 3.0 35.3 + - - +
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Residues in contact with HIS 217 (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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186A TYR* 3.7 16.4 + + - -
187A PHE* 3.8 14.2 - + + -
199A ARG* 3.5 17.8 - - - +
215A LYS* 4.2 33.4 + - + +
216A GLY* 1.3 77.9 - - - +
218A HIS* 1.3 78.5 + - - +
219A GLU* 3.5 25.8 - - + -
226A ALA* 3.4 2.3 - - - -
227A GLU* 2.8 67.2 + - + +
502A MG 4.5 0.2 - - - -
505A P3S 4.6 1.8 + - - -
34F HIS 4.4 1.1 - - - +
35F PHE* 3.5 22.4 - - + +
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Residues in contact with HIS 218 (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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180A VAL* 4.1 16.3 - - + +
185A GLY* 3.1 22.7 + - - +
186A TYR* 4.0 1.0 - - - -
187A PHE* 3.6 21.6 - - + +
193A ASP* 3.3 37.2 - - + +
195A TYR* 4.0 13.1 - + - -
199A ARG* 3.5 19.3 - - - +
217A HIS* 1.3 85.8 + - - +
219A GLU* 1.3 84.2 + - - +
221A GLY 3.5 16.8 - - - -
224A GLY* 4.0 14.5 + - - -
225A GLN 3.0 23.5 + - - -
34F HIS* 5.5 0.4 + - - -
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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