Contacts of the strand formed by residues 363 - 368 (chain A) in PDB entry 3Q8A
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 ASN 363 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A MET* 3.7 0.3 - - - +
267A GLU* 2.9 31.8 + - + +
268A ASN* 3.5 31.5 + - - +
362A ALA* 1.3 74.0 - - - +
364A ILE* 1.3 61.3 + - - +
418A PRO* 3.3 33.6 - - + +
419A ILE 3.0 5.4 - - - +
420A ALA* 3.9 19.8 + - - +
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Residues in contact with ILE 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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264A VAL* 3.7 27.6 - - + -
265A ASP 3.8 4.0 - - - -
266A MET* 3.6 33.0 - - + -
267A GLU* 5.1 0.4 - - - -
362A ALA 4.2 2.0 - - - +
363A ASN* 1.3 80.2 - - - +
365A ARG* 1.3 62.4 + - - +
366A TYR* 5.0 10.1 - - + +
394A ILE* 4.0 22.4 - - + -
418A PRO* 4.4 0.7 - - - -
419A ILE* 2.8 50.5 + - + +
421A LEU* 3.3 35.2 - - + -
450A LEU* 5.8 0.4 - - + -
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Residues in contact with ARG 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A VAL* 3.6 6.1 - - - +
265A ASP* 2.8 36.0 + - + +
267A GLU* 2.8 33.0 + - - +
364A ILE* 1.3 77.9 - - - +
366A TYR* 1.3 70.9 + - - +
410A TYR* 4.2 13.9 - - + -
411A TYR 3.8 5.8 - - - +
412A PRO* 2.8 29.0 + - + +
413A SER 2.6 33.1 + - - -
414A LYS* 4.0 24.5 + - - +
416A LEU 2.8 20.4 + - - -
417A ALA 3.5 6.1 + - - -
418A PRO* 3.0 31.3 - - + +
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Residues in contact with TYR 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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262A VAL* 4.0 15.9 - - + -
263A HIS 3.7 0.9 - - - -
264A VAL* 3.6 28.1 - - + +
364A ILE* 5.0 8.5 - - + -
365A ARG* 1.3 76.9 - - - +
367A VAL* 1.3 65.3 + - - +
378A LEU* 3.3 36.3 - - + +
379A PRO* 4.0 24.9 + - + -
381A THR* 4.7 0.9 + - - -
394A ILE* 4.0 23.6 + - + +
395A LYS 4.9 0.2 - - - -
396A ALA* 4.5 11.4 + - + +
405A LEU* 4.1 18.2 - - + -
410A TYR* 3.2 26.9 - - - +
411A TYR* 2.9 24.9 + - + +
419A ILE* 3.6 23.6 - - + -
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Residues in contact with VAL 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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261A ILE 3.0 1.7 - - - +
262A VAL* 3.0 10.8 - - - +
263A HIS* 2.8 75.3 + - + +
265A ASP* 3.7 17.7 - - + +
366A TYR* 1.3 77.3 - - - +
368A ASN* 1.3 63.1 + - - +
369A THR* 3.4 15.6 + - + -
405A LEU* 4.6 0.9 - - - -
409A ASN 3.9 4.5 - - - +
410A TYR* 3.3 37.5 - - + +
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Residues in contact with ASN 368 (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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260A PRO* 3.9 8.3 - - - +
261A ILE 3.0 19.4 + - - +
262A VAL* 4.6 1.3 - - - +
366A TYR 4.3 0.2 - - - -
367A VAL* 1.3 73.5 - - - +
369A THR* 1.3 55.9 + - - +
370A GLY* 2.9 22.6 + - - -
372A ALA 2.9 24.2 + - - -
373A PRO* 4.0 1.0 - - - +
374A ILE* 4.5 2.2 - - - +
405A LEU* 3.8 24.0 + - + +
406A ALA 3.0 18.8 - - - +
407A PRO* 3.6 15.7 - - - -
408A ASN* 2.7 33.8 + - - -
409A ASN 3.2 10.9 + - - +
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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