Contacts of the helix formed by residues 408 - 428 (chain A) in PDB entry 6F0X
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 408 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368A LYS* 6.5 1.1 - - - -
369A LEU* 3.0 46.2 - - + +
372A LEU* 5.7 3.1 - - + -
407A ILE* 1.3 106.2 - - - +
409A GLY* 1.3 58.4 + - - +
410A PHE 4.1 0.6 - - - +
411A LEU* 3.5 21.9 - - + +
412A GLN* 3.3 24.4 + - - +
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Residues in contact with GLY 409 (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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400A VAL* 4.5 4.6 - - - +
405A VAL* 4.3 4.0 + - - -
407A ILE 2.9 8.5 + - - -
408A GLU* 1.3 76.7 - - - +
410A PHE* 1.3 64.7 + - - +
411A LEU 3.1 1.1 - - - -
412A GLN* 3.2 19.3 + - - +
413A ALA* 2.9 24.9 + - - +
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Residues in contact with PHE 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A LEU* 3.4 31.6 - - + -
338A LEU* 3.4 25.8 - - + -
343A ILE* 5.8 0.2 - - + -
344A ILE* 4.9 2.9 - - + -
392A PRO* 4.0 26.0 - - + -
395A ALA* 4.0 18.8 - - + -
396A HIS* 4.1 12.1 - + + -
400A VAL* 4.1 10.5 - - + +
405A VAL* 3.4 50.5 + - + +
407A ILE* 4.9 6.3 - - + -
408A GLU 4.1 0.2 - - - +
409A GLY* 1.3 74.4 - - - +
411A LEU* 1.3 66.9 + - + +
413A ALA* 3.4 5.4 + - - +
414A LEU* 2.9 33.1 + - + +
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Residues in contact with LEU 411 (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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335A LEU* 4.8 16.6 - - + -
369A LEU* 3.8 27.6 - - + +
372A LEU* 3.7 25.8 - - + -
373A LEU* 5.2 9.2 - - + -
376A ILE* 4.5 8.8 - - + +
407A ILE* 3.6 26.7 - - + -
408A GLU* 3.5 31.2 - - + +
409A GLY 3.1 0.6 - - - -
410A PHE* 1.3 88.1 - - + +
412A GLN* 1.3 66.2 + - - +
414A LEU* 3.0 10.8 + - + +
415A SER* 2.9 19.8 + - - -
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Residues in contact with GLN 412 (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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372A LEU* 5.1 2.3 - - - +
408A GLU 3.3 14.3 + - - +
409A GLY* 3.2 25.7 + - - +
411A LEU* 1.3 77.9 - - - +
413A ALA* 1.3 57.7 + - - +
415A SER* 3.1 10.5 + - - -
416A LEU* 2.9 38.5 + - + +
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Residues in contact with ALA 413 (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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395A ALA* 3.6 24.0 - - - +
399A TYR* 3.7 26.2 - - + -
400A VAL* 3.8 10.3 - - + +
409A GLY 2.9 19.5 + - - +
410A PHE 3.5 5.2 - - - +
412A GLN* 1.3 75.8 - - + +
414A LEU* 1.3 66.2 + - - +
416A LEU* 3.2 5.8 + - - +
417A ALA* 2.9 23.2 + - - +
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Residues in contact with LEU 414 (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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331A TYR* 4.2 17.9 - - + -
335A LEU* 6.0 2.0 - - + -
373A LEU* 4.5 9.0 - - + -
376A ILE* 3.7 38.8 - - + -
391A LEU* 3.8 36.6 - - + -
392A PRO* 4.6 4.7 - - + -
395A ALA* 3.8 19.8 - - + +
410A PHE* 2.9 23.4 + - + +
411A LEU* 3.0 14.6 + - + +
413A ALA* 1.3 74.6 - - - +
415A SER* 1.3 63.0 + - - +
417A ALA* 3.1 3.0 + - + +
418A VAL* 2.9 28.6 + - + +
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Residues in contact with SER 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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372A LEU* 6.5 0.9 - - - -
376A ILE* 5.1 6.0 - - - +
379A LYS* 3.0 33.0 + - - +
411A LEU 2.9 11.1 + - - -
412A GLN* 3.1 15.5 + - - -
414A LEU* 1.3 78.4 - - - +
416A LEU* 1.3 67.0 + - - +
418A VAL* 3.2 5.0 + - - +
419A ASP* 2.9 33.5 + - - +
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Residues in contact with LEU 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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399A TYR* 3.5 51.9 + - + +
412A GLN* 2.9 24.5 + - + +
413A ALA* 3.7 4.7 - - - +
415A SER* 1.3 78.4 - - - +
417A ALA* 1.3 56.8 + - - +
419A ASP* 3.2 18.0 - - + +
420A LYS 2.8 23.2 + - - -
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Residues in contact with ALA 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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391A LEU* 4.6 9.6 - - + +
394A LEU* 4.5 12.5 - - + +
395A ALA* 4.2 24.0 - - + +
398A LEU* 5.3 1.3 - - + -
399A TYR* 3.7 11.6 - - + -
413A ALA 2.9 17.6 + - - +
414A LEU* 3.5 5.8 - - + +
416A LEU* 1.3 74.5 - - - +
418A VAL* 1.3 67.1 + - - +
420A LYS* 2.9 8.2 + - - +
421A GLN* 2.9 26.7 + - - +
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Residues in contact with VAL 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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331A TYR* 4.1 3.8 - - - +
376A ILE* 4.5 3.4 - - + -
379A LYS* 4.5 7.4 - - + +
380A SER* 3.4 28.7 - - - +
383A LEU* 4.0 4.7 - - + -
391A LEU* 3.6 35.6 - - + +
414A LEU* 2.9 19.8 + - + +
415A SER* 3.6 7.2 - - - +
417A ALA* 1.3 74.5 - - - +
419A ASP* 1.3 66.1 + - - +
421A GLN* 3.1 5.1 + - - +
422A PHE* 3.0 51.5 + - + -
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Residues in contact with ASP 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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379A LYS* 5.3 8.3 + - - +
415A SER* 2.9 32.1 + - - +
416A LEU* 3.2 28.0 - - + +
417A ALA 3.1 0.2 - - - -
418A VAL* 1.3 79.7 - - - +
420A LYS* 1.3 57.0 + - - +
422A PHE* 3.3 7.0 + - - +
423A GLU* 2.9 43.9 + - + +
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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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398A LEU* 3.1 49.7 - - + +
399A TYR* 4.0 14.7 + - - +
416A LEU 2.8 13.3 + - - +
417A ALA* 2.9 10.5 + - - +
419A ASP* 1.3 75.4 - - - +
421A GLN* 1.3 68.0 + - - +
423A GLU* 3.7 12.2 - - - +
424A GLU* 2.9 61.8 + - + +
148B HIS* 3.5 15.5 + - - -
315B ILE* 6.4 0.2 - - - -
317B GLN* 3.3 24.9 + - - +
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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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383A LEU* 4.7 9.6 - - + -
387A VAL* 4.1 32.6 - - + +
391A LEU* 4.5 10.5 - - + -
394A LEU* 3.3 29.7 - - + +
417A ALA 2.9 16.4 + - - +
418A VAL* 3.5 8.1 - - - +
420A LYS* 1.3 79.1 - - - +
422A PHE* 1.3 58.5 + - - +
424A GLU* 3.2 17.8 + - - +
425A ARG* 2.9 36.7 + - - +
314B ASP 4.5 5.6 + - - -
315B ILE* 5.3 0.4 - - - +
316B LYS* 5.1 18.4 - - - +
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Residues in contact with PHE 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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379A LYS 3.6 19.5 - - - -
380A SER* 4.0 0.7 - - - -
381A GLU* 3.2 31.4 - - + -
382A GLY 5.7 0.4 - - - -
383A LEU* 3.4 33.4 - - + -
418A VAL* 3.0 41.1 + - + +
419A ASP* 3.8 5.8 - - - +
421A GLN* 1.3 75.4 - - - +
423A GLU* 1.3 66.0 + - - +
424A GLU 3.1 0.2 + - - -
425A ARG* 3.3 13.9 + - + +
426A LYS* 2.9 21.8 + - - +
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Residues in contact with GLU 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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419A ASP* 2.9 30.7 + - + +
420A LYS* 3.7 12.5 - - - +
422A PHE* 1.3 76.4 - - + +
424A GLU* 1.3 61.1 + - + +
426A LYS* 3.2 12.0 - - - +
427A LYS* 2.8 25.1 + - - +
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Residues in contact with GLU 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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420A LYS* 2.9 61.1 + - + +
421A GLN* 3.8 18.9 + - - +
423A GLU* 1.3 77.8 - - + +
425A ARG* 1.3 56.8 + - - +
426A LYS 3.1 0.7 - - - -
427A LYS* 3.2 11.2 - - + +
428A LEU* 2.7 34.8 + - - +
178B HIS* 5.8 1.9 - - + +
316B LYS* 3.3 42.6 + - + +
317B GLN* 4.0 5.4 + - - +
318B TYR* 4.9 7.3 + - + -
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Residues in contact with ARG 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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382A GLY 4.3 5.7 + - - -
383A LEU* 2.4 60.4 + - - +
387A VAL* 4.1 6.5 - - - +
421A GLN* 2.9 18.6 + - - +
422A PHE* 3.6 14.6 - - + +
424A GLU* 1.3 75.5 - - - +
426A LYS* 1.3 61.1 + - - +
427A LYS 3.2 0.5 + - - -
428A LEU* 3.4 16.1 + - - +
429A ALA 4.6 2.1 + - - +
311B ASP* 4.0 22.6 + - - +
316B LYS* 4.8 23.0 - - + +
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Residues in contact with LYS 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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422A PHE 2.9 13.3 + - - +
423A GLU* 3.2 15.0 - - - +
425A ARG* 1.3 77.0 - - - +
427A LYS* 1.3 58.8 + - - +
428A LEU 3.5 0.2 - - - -
429A ALA* 3.9 8.8 + - - -
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Residues in contact with LYS 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 GLU 2.8 14.6 + - - +
424A GLU* 2.8 16.6 + - + +
426A LYS* 1.3 75.6 - - - +
428A LEU* 1.3 57.2 + - - +
429A ALA* 2.9 16.5 + - - +
178B HIS* 4.5 4.1 - - + -
302B THR* 5.8 0.9 - - - +
318B TYR* 4.3 36.1 - - + -
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Residues in contact with LEU 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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424A GLU 2.7 16.1 + - - +
425A ARG* 3.4 12.4 + - - +
427A LYS* 1.3 71.4 - - - +
429A ALA* 1.3 69.5 + - - +
178B HIS* 4.8 7.2 - - + -
302B THR* 4.0 28.1 + - - +
303B GLU* 4.6 3.1 - - - -
316B LYS* 5.9 9.2 - - + +
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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