Contacts of the helix formed by residues 431 - 447 (chain A) in PDB entry 1F9O
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 ASP 431 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353A LEU* 5.8 0.9 - - - +
357A LEU* 4.6 5.5 - - - +
425A LEU* 4.7 9.0 - - + +
426A TYR* 3.7 6.1 - - - +
429A THR* 3.0 21.0 + - - +
430A GLY* 1.3 78.9 - - - +
432A ALA* 1.3 64.3 + - - +
433A ARG* 2.7 67.5 + - - +
434A ALA* 3.4 15.1 + - + +
435A LYS* 3.2 18.0 + - - +
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Residues in contact with ALA 432 (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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430A GLY 3.4 4.4 + - - -
431A ASP* 1.3 72.8 + - - +
433A ARG* 1.3 67.1 + - + +
435A LYS* 3.4 6.8 + - - +
436A LYS* 3.0 50.4 + - - +
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Residues in contact with ARG 433 (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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353A LEU* 4.9 9.7 - - - +
354A ASP* 3.0 42.6 + - - +
357A LEU* 3.6 36.3 - - + +
358A GLU* 6.4 2.0 - - - -
361A GLN* 4.7 1.4 - - - +
431A ASP* 2.7 37.4 + - - +
432A ALA* 1.3 76.6 - - + +
434A ALA* 1.3 61.5 + - - +
436A LYS* 3.6 10.2 + - + +
437A LEU* 3.3 28.6 + - + +
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Residues in contact with ALA 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LEU* 4.7 3.3 - - + +
422A VAL* 3.8 27.1 - - + +
425A LEU* 4.7 9.0 - - + -
426A TYR* 3.8 22.0 - - + +
431A ASP* 3.4 18.2 + - + +
433A ARG* 1.3 77.5 - - - +
435A LYS* 1.3 64.9 + - - +
437A LEU* 3.3 4.6 + - - +
438A LEU* 2.9 30.2 + - - +
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Residues in contact with LYS 435 (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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426A TYR* 3.6 44.1 + - + +
430A GLY 5.5 0.4 - - - +
431A ASP 3.2 8.2 + - - +
432A ALA* 3.4 12.1 + - - +
434A ALA* 1.3 78.0 - - - +
436A LYS* 1.3 65.7 + - + +
438A LEU* 3.2 3.5 + - - -
439A ASP* 2.5 69.3 + - - +
512A SER* 5.6 3.4 - - - -
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Residues in contact with LYS 436 (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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361A GLN* 4.2 14.1 - - - +
364A GLN* 4.3 1.6 - - - +
432A ALA* 3.0 41.8 + - - +
433A ARG* 3.9 8.7 - - + +
434A ALA 3.3 0.2 - - - -
435A LYS* 1.3 85.4 - - + +
437A LEU* 1.3 64.5 + - - +
439A ASP* 3.7 6.3 + - - +
440A LYS* 3.6 18.7 + - - +
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Residues in contact with LEU 437 (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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357A LEU* 4.2 24.2 - - + +
360A TYR* 3.5 33.7 - - + +
361A GLN* 3.5 37.9 - - + +
364A GLN* 3.1 31.4 + - + +
370A ILE* 4.7 4.5 - - + -
419A MET* 4.2 11.4 - - + -
422A VAL* 4.5 9.4 - - + -
433A ARG* 3.3 15.5 + - + +
434A ALA* 3.7 5.4 - - - +
435A LYS 3.3 0.4 - - - -
436A LYS* 1.3 78.8 - - - +
438A LEU* 1.3 59.7 + - - +
441A TRP* 3.1 25.3 + - - +
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Residues in contact with LEU 438 (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 MET* 3.6 35.9 - - + +
422A VAL* 3.6 29.2 - - + +
423A ALA* 3.7 15.7 - - + -
426A TYR* 3.8 22.7 - - + -
434A ALA 2.9 20.2 + - - +
435A LYS* 3.8 2.7 - - - +
437A LEU* 1.3 76.8 - - - +
439A ASP* 1.3 59.7 + - - +
441A TRP* 4.5 10.5 - - + -
442A ALA* 2.8 37.3 + - + +
504A THR* 4.7 4.7 - - + -
508A TYR* 3.8 23.6 - - + -
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Residues in contact with ASP 439 (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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435A LYS* 2.5 61.0 + - - +
436A LYS* 4.2 6.3 + - - +
437A LEU 3.5 0.2 - - - -
438A LEU* 1.3 73.2 - - - +
440A LYS* 1.3 60.9 + - - +
442A ALA* 4.2 1.0 - - - +
443A LYS* 3.3 21.8 + - - +
508A TYR* 2.6 37.5 + - - +
512A SER* 5.0 2.1 - - - -
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Residues in contact with LYS 440 (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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364A GLN* 3.8 24.0 - - + +
365A SER 3.2 11.6 + - - -
366A ALA* 3.1 25.5 + - - +
367A GLU 3.9 7.1 - - - +
368A GLY* 4.1 5.8 - - - -
436A LYS 3.6 9.9 + - - +
437A LEU 3.6 0.8 + - - -
438A LEU 3.2 0.6 - - - -
439A ASP* 1.3 78.0 - - - +
441A TRP* 1.3 63.8 + - - +
443A LYS* 3.4 8.3 + - - +
444A TRP* 3.2 20.6 + - - +
478A TYR* 2.9 34.3 + - + +
480A GLY* 3.8 8.5 + - - -
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Residues in contact with TRP 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A GLN* 3.7 1.7 - - - +
368A GLY 3.3 28.0 - - - +
369A ALA* 3.9 5.2 - - - -
370A ILE* 4.3 4.3 - - + -
412A PHE* 4.9 1.3 - + - -
415A GLN* 3.1 51.8 + - + -
416A VAL* 4.0 20.4 - - + -
419A MET* 3.6 37.0 - - + +
437A LEU 3.1 19.5 + - - +
438A LEU* 4.2 4.9 - - + +
440A LYS* 1.3 73.0 - - - +
442A ALA* 1.3 75.2 + - + +
444A TRP* 3.1 15.2 + + - +
445A ILE* 3.1 35.1 + - + +
501A LEU* 4.1 12.6 - - + -
504A THR* 3.7 28.5 - - + -
505A LEU* 5.0 4.3 - - + -
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Residues in contact with ALA 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A LEU* 2.8 21.7 + - + +
439A ASP 4.2 1.6 - - - +
441A TRP* 1.3 84.1 - - + +
443A LYS* 1.3 62.4 + - - +
445A ILE* 3.4 9.0 - - - +
446A ASN* 3.1 34.1 + - - +
505A LEU* 4.6 5.2 - - + -
508A TYR* 3.7 31.9 - - + +
517A SER* 4.4 6.1 - - - +
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Residues in contact with LYS 443 (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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367A GLU 6.2 0.4 - - - -
439A ASP 3.3 18.6 + - - +
440A LYS* 3.7 8.1 - - - +
441A TRP 3.2 0.4 - - - -
442A ALA* 1.3 78.0 - - - +
444A TRP* 1.3 67.6 + - - +
446A ASN* 3.6 6.2 + - + +
447A GLY* 3.6 12.3 + - - -
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Residues in contact with TRP 444 (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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367A GLU* 3.6 40.9 + - + +
368A GLY* 4.2 2.2 - - - -
369A ALA* 3.7 31.0 - - + -
412A PHE* 4.1 31.0 - + - -
415A GLN* 4.2 5.4 - - + -
440A LYS 3.2 7.3 + - - +
441A TRP* 3.1 30.8 + + - +
443A LYS* 1.3 81.3 - - - +
445A ILE* 1.3 77.5 + - + +
447A GLY* 3.2 9.2 + - - -
448A GLU* 3.6 29.7 + - + +
460A PRO* 5.0 3.1 - - + -
463A ILE* 5.1 5.6 - - + -
486A VAL* 3.9 27.4 - - + +
488A VAL* 4.4 17.6 - - + +
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Residues in contact with ILE 445 (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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412A PHE* 3.6 32.1 - - + -
441A TRP* 3.1 29.0 + - + +
442A ALA* 3.4 17.5 - - - +
444A TRP* 1.3 92.3 - - + +
446A ASN* 1.3 70.7 + - - +
448A GLU* 3.0 13.0 + - + -
449A ILE* 3.3 11.9 - - + +
460A PRO* 3.9 23.3 - - + -
501A LEU* 3.7 32.3 - - + -
505A LEU* 4.5 4.3 - - + -
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Residues in contact with ASN 446 (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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442A ALA 3.1 25.2 + - - +
443A LYS* 4.1 6.3 - - - +
444A TRP 3.2 0.6 - - - -
445A ILE* 1.3 76.8 - - - +
447A GLY* 1.3 60.4 + - - +
448A GLU 3.2 1.0 + - - -
449A ILE* 4.0 11.3 + - - +
505A LEU* 3.7 22.0 - - - +
514A ASP* 4.0 8.7 + - - -
516A THR* 4.2 14.8 - - + +
517A SER* 3.5 25.9 + - - +
520A ASN* 3.0 33.2 + - - +
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Residues in contact with GLY 447 (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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443A LYS 3.6 6.4 + - - -
444A TRP 3.2 8.5 + - - -
446A ASN* 1.3 78.6 - - - +
448A GLU* 1.3 67.1 + - - +
449A ILE 3.5 2.0 - - - +
450A LYS* 3.5 14.0 + - - -
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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