Contacts of the helix formed by residues 414 - 421 (chain A) in PDB entry 6VW1
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 THR 414 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410A LEU* 3.0 15.4 + - + +
411A SER 2.7 18.2 + - - +
413A ALA* 1.3 78.6 - - - +
415A PRO* 1.3 72.5 - - - +
416A LYS* 4.3 3.8 - - - -
417A HIS* 3.4 11.1 + - - +
418A LEU* 3.0 19.8 + - - +
438A PHE* 4.8 3.6 - - + -
526A GLN* 5.6 0.9 - - - +
540A HIS 3.7 20.2 - - - +
541A LYS 4.7 5.8 - - - -
542A CYS 3.1 28.9 - - - +
543A ASP* 3.5 11.0 - - - +
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Residues in contact with PRO 415 (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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291A ILE* 3.9 22.7 - - + -
413A ALA 3.5 3.8 - - - +
414A THR* 1.3 87.1 - - + +
416A LYS* 1.3 56.4 + - - +
418A LEU* 3.7 10.9 - - + +
419A LYS* 2.9 39.9 + - + +
424A LEU* 4.3 14.1 - - + -
428A PHE* 5.5 1.6 - - + -
430A GLU* 4.6 26.0 - - + +
435A GLU* 5.4 6.1 - - - +
438A PHE* 4.9 16.8 - - + -
540A HIS 5.4 2.5 - - - +
541A LYS* 5.8 5.4 - - + -
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Residues in contact with LYS 416 (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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414A THR* 3.2 4.0 - - - +
415A PRO* 1.3 80.3 - - - +
417A HIS* 1.3 57.5 + - - +
419A LYS* 3.4 7.6 + - - +
420A SER* 2.9 29.3 + - - -
430A GLU* 5.4 5.1 + - - +
535A HIS* 4.2 13.7 + - - -
541A LYS 3.7 20.9 + - - +
543A ASP* 3.6 36.3 + - - +
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Residues in contact with HIS 417 (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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310A GLU* 6.1 0.6 - - - +
314A PHE* 3.7 22.2 - + + +
369A PHE* 4.8 7.2 - + - -
373A HIS* 4.4 9.1 + - - -
411A SER 3.3 19.7 - - - +
412A ALA* 3.7 26.3 - - + +
414A THR* 3.2 7.4 + - - +
416A LYS* 1.3 76.5 - - - +
418A LEU* 1.3 68.0 + - - +
420A SER* 2.9 11.7 + - - -
421A ILE* 2.9 49.5 + - + +
543A ASP* 3.1 16.9 + - - +
545A SER* 3.1 30.1 + - - -
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Residues in contact with LEU 418 (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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291A ILE* 3.7 27.8 - - + -
293A VAL* 4.5 20.6 - - + -
366A MET* 3.7 17.9 - - + -
369A PHE* 4.4 18.2 - - + -
370A LEU* 5.6 0.2 - - + -
412A ALA 3.5 17.3 - - - +
413A ALA 3.5 18.8 - - - +
414A THR 3.0 16.4 + - - +
415A PRO* 3.7 7.9 - - + +
417A HIS* 1.3 76.5 - - + +
419A LYS* 1.3 62.4 + - - +
421A ILE* 3.5 5.3 + - + +
422A GLY 3.3 3.3 + - - -
423A LEU* 3.2 30.8 + - + +
424A LEU* 3.4 15.2 + - + +
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Residues in contact with LYS 419 (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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415A PRO* 2.9 25.1 + - + +
416A LYS* 3.7 7.4 - - - +
418A LEU* 1.3 75.0 - - - +
420A SER* 1.3 61.0 + - - +
422A GLY* 2.9 20.8 + - - -
424A LEU* 3.7 31.5 - - + +
425A SER 3.6 15.5 - - - +
426A PRO* 3.0 34.3 + - + -
428A PHE* 3.4 21.1 + - + -
430A GLU* 4.5 15.7 + - - +
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Residues in contact with SER 420 (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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416A LYS* 2.9 16.1 + - - -
417A HIS* 2.9 24.3 + - - -
419A LYS* 1.3 77.0 - - - +
421A ILE* 1.3 67.9 + - - +
422A GLY* 3.6 0.5 + - - -
543A ASP* 5.0 1.1 + - - -
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Residues in contact with ILE 421 (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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300A GLN* 5.6 0.3 - - - +
302A TRP* 3.7 34.1 - - + -
310A GLU* 3.7 32.4 - - + +
313A LYS* 5.7 5.2 - - + -
369A PHE* 5.0 6.3 - - + -
417A HIS* 2.9 47.8 + - + +
418A LEU* 4.0 6.7 - - + +
419A LYS 3.1 0.2 - - - -
420A SER* 1.3 83.9 - - - +
422A GLY* 1.3 57.9 + - - +
423A LEU* 4.2 10.8 - - + -
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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