Contacts of the strand formed by residues 362 - 366 (chain B) in PDB entry 3A3K
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 GLY 362 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287B ASN* 3.2 20.9 + - - -
357B PHE 4.0 0.2 - - - +
358B GLN* 3.5 14.1 + - - -
359B GLY 2.9 32.9 + - - -
360B VAL 3.1 2.8 - - - -
361B THR* 1.3 80.6 + - - +
363B TYR* 1.3 65.3 + - - -
364B LEU* 3.6 3.5 + - - +
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Residues in contact with TYR 363 (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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356B SER* 3.7 21.0 - - - -
357B PHE 3.8 7.0 - - - -
358B GLN* 3.8 14.9 - - - +
361B THR 4.0 2.6 + - - +
362B GLY* 1.3 73.1 - - - -
364B LEU* 1.3 60.5 + - - +
365B LYS* 3.4 31.9 - - + +
372B ARG* 3.9 8.1 + - - -
375B ASP* 5.4 5.6 - - - +
397B THR* 3.6 26.6 - - - +
461B NAG 3.3 67.1 + - + +
462B NAG 3.3 38.9 + - - +
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Residues in contact with LEU 364 (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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126B THR* 5.6 4.9 - - - +
323B ASP* 3.9 31.6 - - + +
327B LEU* 4.7 5.8 - - + -
355B ARG 5.2 0.2 - - - +
356B SER* 3.2 3.8 - - - -
357B PHE* 2.9 64.0 + - + +
359B GLY 5.0 0.4 - - - +
361B THR* 4.2 8.7 - - - +
362B GLY 4.7 4.0 - - - +
363B TYR* 1.3 81.7 - - - +
365B LYS* 1.3 61.8 + - - +
366B ILE* 3.8 32.5 - - + -
372B ARG* 3.5 29.8 - - + +
373B ASP 5.7 0.7 - - - -
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Residues in contact with LYS 365 (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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354B ASN* 3.9 26.9 + - - -
355B ARG* 3.8 2.9 - - - +
356B SER* 4.1 17.0 - - - +
363B TYR* 3.4 28.5 - - + +
364B LEU* 1.3 74.0 - - - +
366B ILE* 1.3 74.5 + - - +
367B ASP* 4.6 0.4 - - - +
372B ARG* 3.3 4.5 - - - +
373B ASP* 2.8 48.1 + - - +
397B THR* 3.5 25.0 - - + +
462B NAG 5.2 5.0 + - - +
506B SO4 3.8 16.9 + - - -
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Residues in contact with ILE 366 (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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124B THR* 4.4 3.4 - - + -
125B ARG 3.8 9.4 - - - +
126B THR* 4.4 9.0 - - + -
327B LEU* 3.8 21.8 - - + -
352B MET 3.4 26.9 - - - +
353B TRP* 3.9 6.3 - - + -
354B ASN* 3.0 23.2 + - - -
355B ARG 3.1 11.3 + - - +
364B LEU* 3.8 21.5 - - + -
365B LYS* 1.3 77.4 - - - +
367B ASP* 1.3 61.8 + - - +
370B GLY* 3.6 33.4 - - - +
371B ASP 3.8 1.8 - - - +
372B ARG* 3.8 21.3 - - + -
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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