Contacts of the helix formed by residues 418 - 428 (chain A) in PDB entry 6FQS
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 SER 418 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379A HIS* 2.7 36.3 + - - -
412A GLN* 4.2 2.2 - - - +
416A LYS 4.3 0.2 + - - -
417A LEU* 1.3 76.5 - - - +
419A GLU* 1.3 64.4 + - - +
420A LYS* 3.7 4.3 + - - +
421A GLN* 3.0 23.0 + - - -
422A ALA* 2.9 22.5 + - - +
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Residues in contact with GLU 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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408A MET* 3.2 28.7 - - + +
412A GLN* 3.9 20.7 + - - +
418A SER* 1.3 73.1 - - - +
420A LYS* 1.3 60.3 + - + +
422A ALA* 3.3 2.6 + - - +
423A GLN* 2.9 33.9 + - - +
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Residues in contact with LYS 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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376A ASP* 4.8 15.9 + - - -
379A HIS* 4.8 9.0 - - + +
380A ILE* 3.7 20.0 - - + +
418A SER* 3.2 6.8 + - - +
419A GLU* 1.3 79.2 - - + +
421A GLN* 1.3 62.5 + - - +
423A GLN* 3.3 6.8 + - - +
424A ALA* 3.0 24.8 + - - +
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Residues in contact with GLN 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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379A HIS* 3.0 51.0 + - + +
380A ILE* 4.2 8.0 - - - +
382A GLU* 3.9 10.7 + - - +
383A GLY* 3.3 23.2 - - - +
386A ILE* 5.1 2.8 - - - +
416A LYS 4.7 1.6 - - - +
417A LEU* 3.5 24.4 - - + +
418A SER* 3.0 37.8 + - - +
420A LYS* 1.3 76.8 - - - +
422A ALA* 1.3 62.4 + - - +
424A ALA* 3.3 4.1 + - - +
425A ILE* 3.1 29.7 + - - +
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Residues in contact with ALA 422 (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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408A MET* 3.7 33.0 - - + +
411A LEU* 4.5 13.8 - - + +
412A GLN* 4.4 7.4 - - + -
417A LEU* 4.6 4.0 - - + +
418A SER 2.9 15.9 + - - +
419A GLU 3.6 4.0 - - - +
421A GLN* 1.3 78.0 - - - +
423A GLN* 1.3 63.0 + - - +
425A ILE* 3.2 10.4 + - - +
426A LEU* 3.0 27.8 + - - +
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Residues in contact with GLN 423 (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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404A ASP* 5.2 10.1 - - - +
408A MET* 3.2 30.9 - - + +
419A GLU 2.9 20.0 + - - +
420A LYS* 3.8 5.8 - - - +
422A ALA* 1.3 77.3 - - - +
424A ALA* 1.3 58.1 + - - +
426A LEU* 3.3 14.6 + - - +
427A ASP* 2.9 49.4 + - - +
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Residues in contact with ALA 424 (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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380A ILE* 3.7 31.4 - - + +
384A LEU* 4.5 10.6 - - + +
420A LYS 3.0 17.5 + - - +
421A GLN* 3.6 6.1 - - - +
423A GLN* 1.3 77.0 - - - +
425A ILE* 1.3 61.8 + - - +
427A ASP* 3.2 8.5 + - - +
428A MET* 3.0 22.2 + - - +
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Residues in contact with ILE 425 (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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383A GLY 3.7 7.4 - - - +
384A LEU* 4.1 11.2 - - + -
387A ALA* 3.3 32.8 - - + -
394A ILE* 4.0 30.1 - - + -
398A ILE* 5.1 5.3 - - + +
411A LEU* 4.3 9.2 - - + -
417A LEU* 3.5 33.4 - - + -
421A GLN 3.1 12.3 + - - +
422A ALA* 3.2 8.5 + - - +
424A ALA* 1.3 76.6 - - - +
426A LEU* 1.3 61.7 + - - +
428A MET* 3.2 29.6 + - + +
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Residues in contact with LEU 426 (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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398A ILE* 4.2 32.8 - - + -
404A ASP* 4.4 17.0 - - + +
407A ALA* 4.2 13.0 - - + -
408A MET* 4.2 30.3 - - + +
411A LEU* 4.5 10.3 - - + -
422A ALA 3.0 25.3 + - - +
423A GLN* 3.7 17.0 - - - +
425A ILE* 1.3 77.6 - - - +
427A ASP* 1.3 63.1 + - - +
428A MET 3.5 5.5 + - - +
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Residues in contact with ASP 427 (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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423A GLN* 2.9 34.4 + - - +
424A ALA* 3.2 8.0 + - - +
426A LEU* 1.3 76.5 - - - +
428A MET* 1.3 64.7 + - - +
429A ARG* 3.5 9.7 + - - +
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Residues in contact with MET 428 (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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384A LEU* 3.3 37.7 - - + -
387A ALA* 4.3 16.6 - - + -
388A LEU* 4.3 12.3 - - + -
391A ILE* 6.1 1.3 - - - -
424A ALA 3.0 8.2 + - - +
425A ILE* 3.2 24.4 + - + +
426A LEU 4.0 5.9 - - - +
427A ASP* 1.3 78.0 - - - +
429A ARG* 1.3 64.8 + - - +
430A LEU* 4.1 1.9 + - - +
432A ARG* 3.7 42.0 - - + +
433A LEU* 4.2 18.8 - - - -
441A ILE* 6.0 0.4 - - - -
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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