Contacts of the strand formed by residues 362 - 367 (chain A) in PDB entry 2Y33
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 ARG 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A VAL* 3.4 25.4 - - + +
210A VAL 3.5 3.4 - - - -
211A ASP* 2.7 41.7 + - - +
327A ILE 3.6 1.4 - - - +
328A TYR* 3.3 6.6 - - - -
329A TYR* 2.9 36.5 + - + -
356A ILE* 3.9 14.4 - - - +
357A GLU* 2.9 42.4 + - - +
359A LYS* 3.2 55.7 + - + +
360A PHE 3.2 0.4 - - - +
361A ASP* 1.3 78.6 - - - +
363A LEU* 1.3 65.6 + - - +
364A LEU* 5.3 0.4 - - + -
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Residues in contact with LEU 363 (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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208A CYS 3.8 0.6 - - - +
209A VAL* 3.4 5.2 - - - +
210A VAL* 2.7 52.4 + - + +
213A PHE* 3.8 41.5 - - + -
276A MET* 3.8 17.7 - - + -
279A LEU* 3.9 8.7 - - + -
326A CYS* 3.5 27.6 - - - -
327A ILE 3.4 10.5 - - - +
328A TYR* 4.2 8.3 - - + -
361A ASP 4.1 0.2 + - - -
362A ARG* 1.3 74.6 - - - +
364A LEU* 1.3 61.0 + - - +
365A PHE* 3.5 31.2 - - + -
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Residues in contact with LEU 364 (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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207A ILE* 4.2 6.7 - - + -
208A CYS 3.4 16.6 - - - +
209A VAL* 3.7 10.5 - - + -
325A THR 3.6 0.7 - - - +
326A CYS* 3.3 9.2 - - - +
327A ILE* 2.8 41.3 + - + +
329A TYR* 3.8 18.2 - - + +
343A LEU* 3.3 33.9 - - + -
356A ILE* 3.5 25.8 - - + -
362A ARG* 5.3 1.6 - - + -
363A LEU* 1.3 75.7 - - - +
365A PHE* 1.3 73.7 + - - +
366A PHE* 3.7 23.1 - - + -
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Residues in contact with PHE 365 (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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198A ILE* 4.3 24.2 - - + -
202A MET* 3.8 20.4 - - + +
207A ILE* 3.3 1.0 - - - -
208A CYS* 2.8 42.6 + - + +
210A VAL* 5.0 5.8 - - + -
276A MET* 5.2 2.7 - - - -
279A LEU* 3.7 27.8 - - + -
280A ILE* 3.7 28.3 - - + -
287A LEU* 6.3 0.4 - - + -
324A VAL* 3.9 19.1 - - + -
325A THR 3.4 2.2 - - - -
326A CYS* 3.9 22.4 - - + -
363A LEU* 3.5 28.0 - - + -
364A LEU* 1.3 82.7 - - - +
366A PHE* 1.3 65.5 + - - +
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Residues in contact with PHE 366 (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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202A MET* 4.0 7.5 - - - +
206A GLY 3.1 14.1 - - - +
207A ILE* 4.1 10.3 - - + -
315A ASP* 3.9 1.1 - - - -
324A VAL* 3.8 0.5 - - - +
325A THR* 2.9 65.8 + - + -
327A ILE* 4.0 11.2 - - + -
343A LEU* 4.6 1.8 - - + -
345A ILE* 4.1 13.5 - - + -
364A LEU* 3.7 34.3 - - + -
365A PHE* 1.3 75.4 - - - +
367A TRP* 1.3 89.5 + - - +
368A SER* 4.9 0.7 - - - -
372A ASN* 3.7 12.3 - - + +
374A HIS* 3.6 43.7 - + - -
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Residues in contact with TRP 367 (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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202A MET* 3.6 40.5 + - + -
203A ASN* 4.6 7.4 - - - -
205A HIS 5.1 0.2 - - - -
206A GLY* 3.2 27.8 + - - -
287A LEU* 4.1 26.5 - - + -
288A GLY* 4.3 2.9 - - - -
290A TYR* 3.6 28.3 - + - -
323A CYS 3.5 12.8 - - - +
324A VAL* 3.6 19.1 - - + -
366A PHE* 1.3 79.6 - - - +
368A SER* 1.3 62.6 + - - +
369A ASP* 3.3 6.8 + - - +
371A ARG* 3.4 48.1 - - + +
372A ASN* 3.0 31.9 + - - +
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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