Contacts of the helix formed by residues 407 - 422 (chain A) in PDB entry 5I35
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 407 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403A ALA 3.3 6.9 + - - +
404A LEU* 3.1 18.8 + - - +
405A GLU 3.2 0.6 - - - +
406A CYS* 1.3 75.1 - - + +
408A TYR* 1.3 58.5 + - - +
409A GLN* 3.2 15.2 + - - +
410A ARG* 3.0 35.2 + - + +
411A GLU* 3.0 24.4 + - - +
440A PRO 4.9 0.7 - - - -
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Residues in contact with TYR 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ALA* 5.1 2.1 - - - +
341A ILE* 3.6 21.0 - - + +
342A GLY* 5.7 0.7 - - - -
358A LYS* 3.0 44.3 + - + +
359A ILE 5.2 0.3 - - - -
360A GLN* 3.5 31.6 + - + +
405A GLU* 3.6 21.3 - - + -
406A CYS 3.3 3.4 + - - -
407A ASP* 1.3 69.5 + - - +
409A GLN* 1.3 59.5 + - - +
411A GLU* 3.7 24.7 - - - -
412A ALA* 2.9 28.9 + - - +
439A SER 3.7 11.2 - - - +
440A PRO 3.3 14.3 + - - +
441A HIS 3.5 23.8 - - - -
442A VAL 3.6 5.8 - - - +
443A LEU* 3.6 20.7 - - + +
700A ANP 5.2 1.2 + - - -
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Residues in contact with GLN 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ASP* 3.2 9.2 + - - +
408A TYR* 1.3 73.8 - - - +
410A ARG* 1.3 66.6 + - - +
412A ALA* 3.2 6.9 + - - +
413A ALA* 3.0 23.4 + - - +
416A ARG* 4.9 1.2 + - - -
439A SER 4.5 3.4 - - - +
440A PRO* 3.8 40.8 - - + +
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Residues in contact with ARG 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A LEU* 3.2 42.5 + - - +
407A ASP* 3.0 29.0 + - - +
409A GLN* 1.3 77.0 - - - +
411A GLU* 1.3 61.7 + - - +
413A ALA* 3.2 8.2 + - - +
414A CYS* 3.0 46.2 + - - -
484A PHE* 6.4 0.6 - - - -
508A PHE 4.3 4.0 + - - -
509A GLY* 3.8 15.8 + - - -
511A THR* 3.2 29.7 + - - +
512A ARG* 4.2 11.5 - - - +
513A GLU 5.4 1.2 - - - +
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Residues in contact with GLU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A LYS* 2.8 31.5 + - - -
405A GLU 4.4 4.2 - - - +
407A ASP 3.0 16.5 + - - +
408A TYR* 3.7 23.2 - - - +
409A GLN 3.3 0.4 - - - -
410A ARG* 1.3 77.8 - - - +
412A ALA* 1.3 55.4 + - - +
414A CYS* 3.2 3.0 + - - +
415A ALA* 3.0 29.5 + - - +
443A LEU* 3.1 22.0 - - + +
507A ASP* 4.2 3.2 - - - +
508A PHE* 3.6 18.7 + - + +
509A GLY* 3.6 36.0 + - - +
700A ANP 4.6 1.0 + - - -
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Residues in contact with ALA 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A TYR 2.9 17.7 + - - +
409A GLN* 3.2 7.4 + - - +
411A GLU* 1.3 74.6 - - - +
413A ALA* 1.3 58.6 + - - +
414A CYS 3.4 0.2 + - - -
415A ALA* 3.6 2.1 + - - +
416A ARG* 3.0 56.8 + - - +
433A ILE* 4.2 10.3 - - + +
438A CYS* 5.0 5.2 - - + -
443A LEU* 3.6 20.2 - - + +
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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
----------------------------------------------------------
409A GLN 3.0 12.5 + - - +
410A ARG* 3.2 10.1 + - - +
412A ALA* 1.3 78.6 - - - +
414A CYS* 1.3 57.6 + - - +
416A ARG* 3.5 16.6 + - - +
417A LYS* 3.0 29.5 + - - +
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Residues in contact with CYS 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A ARG* 3.0 50.4 + - - -
411A GLU 3.7 3.4 - - - +
413A ALA* 1.3 74.9 - - - +
415A ALA* 1.3 61.1 + - - +
417A LYS* 3.2 12.3 + - - +
418A PHE* 2.8 28.6 + - - +
484A PHE* 5.3 8.1 - - - -
508A PHE* 3.6 20.4 - - - +
511A THR* 3.7 26.0 - - + +
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Residues in contact with ALA 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A GLU* 3.0 16.8 + - + +
412A ALA 3.7 4.3 - - - +
414A CYS* 1.3 76.5 - - - +
416A ARG* 1.3 61.6 + - - +
418A PHE* 3.2 1.7 + - - +
419A ARG* 2.9 25.8 + - - +
430A VAL* 3.9 7.1 - - + +
431A PRO 5.5 0.9 - - - +
433A ILE* 3.7 24.7 - - + -
443A LEU* 5.8 1.6 - - + -
445A THR* 5.7 1.3 - - + -
508A PHE* 3.6 34.7 - - + +
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Residues in contact with ARG 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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409A GLN 4.9 1.0 + - - -
412A ALA* 3.0 48.6 + - - +
413A ALA* 3.8 14.1 - - - +
415A ALA* 1.3 72.7 - - - +
417A LYS* 1.3 61.7 + - - +
419A ARG* 3.3 10.0 + - - +
420A ASP* 3.2 26.2 + - - +
433A ILE* 3.7 26.7 - - + +
435A ASP* 2.8 37.3 + - - +
438A CYS* 4.8 4.8 - - - +
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Residues in contact with LYS 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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413A ALA 3.0 18.5 + - - +
414A CYS* 3.5 14.8 + - - +
415A ALA 3.2 0.2 - - - -
416A ARG* 1.3 76.4 - - - +
418A PHE* 1.3 85.5 + - - +
419A ARG 3.2 0.3 + - - -
420A ASP* 3.3 20.0 + - + +
421A LEU* 3.4 26.7 + - + +
484A PHE* 2.9 73.1 - - + +
511A THR* 3.7 6.5 - - - +
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Residues in contact with PHE 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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414A CYS 2.8 15.6 + - - +
415A ALA 3.9 2.5 - - - +
417A LYS* 1.3 94.7 - - - +
419A ARG* 1.3 63.7 + - - +
421A LEU* 3.3 6.7 + - + +
422A LEU* 3.2 42.3 + - + +
430A VAL* 4.2 2.2 - - + +
474A LEU* 5.1 2.7 - - + -
478A GLU* 3.7 35.4 - - + -
482A PHE* 4.6 15.3 - + - -
484A PHE* 4.2 13.9 - - + -
485A MSE 4.4 3.1 - - - -
486A GLN* 4.2 21.3 - - + -
505A LEU* 4.5 9.6 - - + -
508A PHE* 3.5 36.6 - + + -
511A THR* 4.3 4.7 - - + -
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Residues in contact with ARG 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ALA 2.9 17.7 + - - +
416A ARG* 3.5 9.4 - - - +
417A LYS 3.1 0.2 - - - -
418A PHE* 1.3 77.2 - - - +
420A ASP* 1.3 64.9 + - - +
422A LEU* 3.3 2.9 + - - +
423A LYS* 3.1 19.5 + - - +
429A TYR* 5.7 2.0 - - - -
430A VAL* 3.1 42.7 + - + +
431A PRO* 4.3 2.4 - - - +
432A GLU* 3.4 55.9 + - - +
433A ILE* 5.3 1.6 - - - +
446A GLU* 4.2 4.9 + - - -
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Residues in contact with ASP 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 ARG 3.2 15.3 + - - +
417A LYS* 3.4 14.2 - - + +
419A ARG* 1.3 75.8 - - - +
421A LEU* 1.3 59.3 + - + +
423A LYS* 2.9 55.5 + - - +
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Residues in contact with LEU 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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417A LYS* 3.4 35.9 + - + +
418A PHE* 3.3 16.4 + - + +
420A ASP* 1.3 79.6 - - + +
422A LEU* 1.3 65.4 + - + +
423A LYS 3.5 1.3 + - - +
425A HIS* 5.6 0.3 - - - -
477A ARG* 5.3 3.3 + - - -
482A PHE* 4.0 58.4 - - + -
483A HIS 5.4 1.6 - - - +
484A PHE* 4.3 8.5 - - + -
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Residues in contact with LEU 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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418A PHE* 3.2 27.7 + - + +
419A ARG 3.6 3.8 - - - +
420A ASP 3.1 0.8 - - - -
421A LEU* 1.3 80.9 - - + +
423A LYS* 1.3 67.4 + - - +
424A GLY 3.1 0.7 + - - -
425A HIS* 2.9 50.9 + - + +
428A PHE* 4.0 21.4 - - + +
429A TYR* 5.0 3.6 - - - +
430A VAL* 4.2 13.7 - - + -
474A LEU* 4.3 19.7 - - + -
477A ARG* 4.9 1.3 - - - +
482A PHE* 4.7 8.3 - - + -
505A LEU* 3.8 30.3 - - + -
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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