Contacts of the helix formed by residues 361 - 371 (chain B) in PDB entry 3K0J
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 GLU 361 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B HIS* 4.1 9.8 - - - -
359B PHE* 3.5 19.4 - - - +
360B LYS* 1.3 110.2 - - + +
362B VAL* 1.3 65.3 + - - +
363B SER* 3.5 15.3 - - - +
364B SER* 3.7 13.7 - - - +
365B ALA 3.9 0.7 + - - -
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Residues in contact with VAL 362 (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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308B PRO* 3.8 16.4 - - + -
309B ASN* 3.2 43.7 - - - +
310B HIS* 3.5 30.7 - - + +
361B GLU* 1.3 70.6 + - - +
363B SER* 1.3 67.9 + - - +
364B SER 3.1 2.2 - - - -
365B ALA* 3.1 4.7 + - - +
366B THR* 3.0 22.9 + - - +
386B TYR* 4.9 0.2 - - + -
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Residues in contact with SER 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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361B GLU* 4.0 13.3 - - - +
362B VAL* 1.3 75.8 - - - +
364B SER* 1.3 64.6 + - - +
366B THR* 2.8 24.5 + - - -
367B ASN* 2.6 27.5 - - - +
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Residues in contact with SER 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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337B PHE* 3.2 13.6 + - - +
338B GLY* 3.2 27.7 - - - -
359B PHE* 4.1 18.4 - - - -
361B GLU* 3.7 16.3 + - - +
363B SER* 1.3 84.7 + - - +
365B ALA* 1.3 51.4 - - - +
367B ASN* 3.0 8.2 + - - +
368B ALA* 2.6 37.8 + - - +
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Residues in contact with ALA 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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309B ASN 3.4 23.6 - - - +
310B HIS 3.8 4.0 - - - +
312B ILE* 3.3 26.2 - - + +
359B PHE* 3.4 24.0 - - + -
361B GLU 3.9 0.4 + - - -
362B VAL 3.1 6.7 + - - +
364B SER* 1.3 78.3 - - - +
366B THR* 1.3 57.7 + - - +
368B ALA* 3.5 4.9 - - - -
369B LEU* 2.8 30.0 + - - +
386B TYR* 4.1 2.9 - - + -
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Residues in contact with THR 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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308B PRO* 4.3 7.3 - - - +
362B VAL* 3.0 12.5 + - - +
363B SER* 2.8 17.6 + - - +
365B ALA* 1.3 77.6 - - - +
367B ASN* 1.3 57.4 + - - +
368B ALA 3.1 0.4 - - - -
369B LEU* 3.2 1.7 + - - +
370B ARG* 2.7 38.0 + - + +
386B TYR* 2.3 35.4 + - - +
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Residues in contact with ASN 367 (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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337B PHE* 3.2 17.6 - - + -
363B SER* 2.6 30.1 + - - +
364B SER* 3.4 6.5 - - - +
366B THR* 1.3 80.7 - - - +
368B ALA* 1.3 60.3 + - - +
369B LEU 3.2 0.7 - - - -
370B ARG* 4.4 7.3 - - - +
371B SER* 3.0 31.9 + - - +
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Residues in contact with ALA 368 (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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312B ILE* 4.5 3.4 - - + -
334B PHE* 3.8 10.1 - - + -
337B PHE* 3.4 28.3 - - + -
359B PHE* 3.6 24.0 - - + -
364B SER 2.6 16.4 + - - +
365B ALA* 3.6 6.7 - - - +
367B ASN* 1.3 78.6 - - - +
369B LEU* 1.3 58.9 + - - +
372B MET* 3.3 27.9 - - - +
384B ILE* 3.9 2.4 - - - +
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Residues in contact with LEU 369 (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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312B ILE* 4.6 1.8 - - + -
365B ALA 2.8 14.9 + - - +
366B THR 3.4 4.3 - - - +
368B ALA* 1.3 77.7 - - - +
370B ARG* 1.3 67.5 + - - +
373B GLN* 3.1 49.6 + - + +
384B ILE* 3.4 37.7 - - + +
385B GLN* 3.8 3.4 - - - +
386B TYR* 3.4 54.7 - - + +
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Residues in contact with ARG 370 (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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366B THR* 2.7 24.4 + - + +
367B ASN* 4.4 6.3 - - - +
369B LEU* 1.3 75.6 - - - +
371B SER* 1.3 57.8 + - - +
436C ARG* 3.2 31.6 + - - +
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Residues in contact with SER 371 (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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337B PHE* 3.9 17.5 - - - -
367B ASN* 3.0 21.4 + - - -
370B ARG* 1.3 80.8 - - - +
372B MET* 1.3 65.0 + - - +
373B GLN 3.7 0.2 - - - -
375B PHE* 5.1 2.3 - - - +
436C ARG* 4.4 7.2 + - - +
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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