Contacts of the helix formed by residues 433 - 451 (chain A) in PDB entry 5IG6
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 HIS 433 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429A ASN* 4.0 15.0 - - + -
430A PRO* 3.1 23.5 + - + +
431A PRO 3.4 1.1 - - - +
432A ASP* 1.3 82.0 + - - +
434A ASP* 1.3 71.0 + - + +
435A VAL* 3.0 41.9 + - + +
436A VAL* 3.0 15.8 + - + +
437A ALA* 3.3 9.8 + - - +
505A 6B3 3.2 78.1 + + + -
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Residues in contact with ASP 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A ASP 3.6 4.3 + - - +
433A HIS* 1.3 78.9 + - + +
435A VAL* 1.3 62.3 + - - +
437A ALA* 3.3 11.8 + - + +
438A MET* 3.0 37.6 + - + +
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Residues in contact with VAL 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A PRO* 3.9 30.1 - - + -
372A PHE* 3.8 9.5 - - + -
425A CYS* 3.7 5.7 - - - -
429A ASN* 3.6 33.0 - - - +
433A HIS* 3.0 30.5 + - + +
434A ASP* 1.3 77.6 - - - +
436A VAL* 1.3 59.7 + - - +
438A MET* 3.3 8.4 + - - +
439A ALA* 2.9 27.9 + - - +
505A 6B3 4.1 19.5 - - + +
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Residues in contact with VAL 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A CYS* 4.0 20.4 - - - +
426A TYR* 4.1 19.5 - - + -
429A ASN* 3.6 23.8 - - + +
430A PRO 3.5 21.3 - - - +
431A PRO* 3.5 26.0 - - + +
433A HIS* 3.0 9.1 + - + +
435A VAL* 1.3 75.6 - - - +
437A ALA* 1.3 58.8 + - - +
439A ALA* 3.2 2.2 + - - +
440A ARG* 2.9 41.1 + - - +
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Residues in contact with ALA 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A PRO 5.3 0.4 + - - -
433A HIS 3.3 8.2 + - - +
434A ASP* 3.3 15.7 + - - +
436A VAL* 1.3 78.5 - - - +
438A MET* 1.3 61.4 + - + +
440A ARG* 3.4 11.7 + - - +
441A LYS* 3.2 34.0 + - + +
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Residues in contact with MET 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ALA 3.5 15.0 - - - +
368A TYR* 3.4 30.6 - - + +
370A TRP* 3.3 34.8 - - + +
371A PRO* 3.5 21.8 - - + -
372A PHE* 4.2 6.7 - - + -
434A ASP* 3.0 29.0 + - + +
435A VAL* 3.5 13.0 - - - +
437A ALA* 1.3 75.0 - - + +
439A ALA* 1.3 66.2 + - - +
441A LYS* 3.2 6.0 + - + +
442A LEU* 2.9 23.2 + - - +
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Residues in contact with ALA 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A PHE* 3.6 23.4 - - + -
422A PHE* 3.5 16.5 - - + -
425A CYS* 3.8 11.4 - - + -
426A TYR* 3.7 19.7 - - + -
435A VAL 2.9 16.7 + - - +
436A VAL 3.2 4.9 + - - +
438A MET* 1.3 77.0 - - - +
440A ARG* 1.3 57.7 + - - +
442A LEU 3.3 0.9 + - - -
443A GLN* 2.8 31.7 + - - +
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Residues in contact with ARG 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A TYR* 3.6 23.6 - - + +
431A PRO 5.8 2.0 + - - -
436A VAL* 2.9 32.5 + - - +
437A ALA* 3.8 9.4 - - - +
439A ALA* 1.3 74.9 - - - +
441A LYS* 1.3 59.4 + - + +
444A ASP 3.0 9.2 + - - -
503A GOL 2.8 52.6 + - - +
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Residues in contact with LYS 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A TYR* 3.7 44.6 - - + +
437A ALA* 3.2 20.7 + - + +
438A MET* 3.2 7.9 + - + +
440A ARG* 1.3 78.6 - - + +
442A LEU* 1.3 62.1 + - - +
444A ASP* 3.2 8.2 + - - +
445A VAL* 3.1 23.8 + - - +
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Residues in contact with LEU 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A LEU* 3.8 27.7 - - + +
365A HIS* 4.1 18.4 - - + -
368A TYR* 4.1 12.5 - - + +
369A ALA* 3.8 33.0 - - + -
372A PHE* 4.0 18.6 - - + -
396A LEU* 4.3 17.0 - - + -
421A MET* 4.5 1.3 - - + -
422A PHE* 3.7 22.7 - - + -
438A MET 2.9 16.0 + - - +
439A ALA* 4.7 0.7 - - - -
441A LYS* 1.3 76.5 - - - +
443A GLN* 1.3 58.2 + - - +
445A VAL* 3.2 6.1 + - + +
446A PHE* 3.0 26.3 + - - +
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Residues in contact with GLN 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A ARG* 4.1 12.3 + - - +
422A PHE* 3.4 35.7 - - + +
426A TYR* 2.7 39.3 + - - +
439A ALA 2.8 21.4 + - - +
441A LYS 3.2 0.2 - - - -
442A LEU* 1.3 70.4 - - - +
444A ASP* 1.3 60.5 + - - +
446A PHE* 3.2 0.6 + - + -
447A GLU* 2.7 55.0 + - + +
503A GOL 3.5 24.5 + - - +
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Residues in contact with ASP 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ARG 3.0 14.7 + - - +
441A LYS* 3.2 11.2 + - - +
443A GLN* 1.3 78.3 - - - +
445A VAL* 1.3 64.4 + - - +
448A PHE* 3.1 54.8 + - - +
503A GOL 3.4 21.0 + - - -
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Residues in contact with VAL 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ILE* 5.6 0.4 - - + +
359A GLU* 3.9 13.5 - - - +
360A LEU* 3.7 18.6 - - + -
365A HIS* 3.6 45.8 - - + +
368A TYR* 4.3 10.5 - - + +
441A LYS 3.1 14.9 + - - +
442A LEU* 3.4 8.3 - - + +
444A ASP* 1.3 81.7 + - - +
446A PHE* 1.3 63.2 + - - +
448A PHE* 4.2 2.3 - - - +
449A ARG* 3.2 22.3 + - + +
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Residues in contact with PHE 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ILE* 3.6 20.8 - - + +
360A LEU* 4.3 14.1 - - + -
414A PHE* 3.8 24.9 - + - -
415A ALA* 4.0 18.6 - - + -
418A VAL* 3.7 24.5 - - + -
419A ARG* 3.8 18.8 - - + -
422A PHE* 4.3 9.0 - + + -
442A LEU 3.0 13.4 + - - +
443A GLN* 3.5 9.4 - - + +
445A VAL* 1.3 78.1 - - - +
447A GLU* 1.3 89.3 + - + +
449A ARG* 3.9 0.7 - - - +
450A TYR* 2.8 59.7 + + + +
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Residues in contact with GLU 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A ARG* 2.8 44.0 + - - -
443A GLN* 2.7 47.2 + - + +
444A ASP 4.3 1.1 - - - +
446A PHE* 1.3 85.1 - - + +
448A PHE* 1.3 68.0 + - + +
450A TYR* 3.9 3.5 - - - +
451A ALA* 3.0 26.0 + - - +
503A GOL 3.5 17.5 - - - +
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Residues in contact with PHE 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ASP* 3.1 50.2 + - - +
445A VAL* 4.4 1.8 - - - +
447A GLU* 1.3 84.3 - - + +
449A ARG* 1.3 61.3 + - - +
451A ALA* 3.6 10.1 + - + +
452A LYS* 3.6 27.0 + - - +
503A GOL 5.2 3.1 - - - -
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Residues in contact with ARG 449 (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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352A HIS* 2.9 38.6 + - + +
355A GLY* 3.2 40.3 + - - -
356A ILE* 3.6 23.0 - - + +
359A GLU* 2.8 36.1 + - - +
445A VAL* 3.2 18.4 + - + +
446A PHE 4.2 0.4 - - - +
448A PHE* 1.3 74.8 - - - +
450A TYR* 1.3 67.2 + - - +
452A LYS* 3.0 23.2 + - + +
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Residues in contact with TYR 450 (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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352A HIS* 4.3 0.2 - - - -
353A CYS* 4.2 9.9 - - - -
356A ILE* 3.6 18.0 - - + +
411A ALA* 3.4 30.4 + - - +
412A GLN* 3.7 11.3 + - - +
414A PHE* 4.6 0.4 - + - -
415A ALA* 3.6 19.4 - - + +
419A ARG* 3.7 28.5 - - - -
446A PHE* 2.8 46.3 + + + +
447A GLU* 3.9 4.7 - - - +
449A ARG* 1.3 71.8 - - - +
451A ALA* 1.3 59.3 + - + +
453A MET* 3.1 54.3 + - + +
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Residues in contact with ALA 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A GLU 3.0 18.3 + - - +
448A PHE* 3.8 7.9 - - + +
449A ARG 3.1 0.6 - - - -
450A TYR* 1.3 79.1 - - + +
452A LYS* 1.3 58.8 + - + +
453A MET 3.3 2.6 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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