Contacts of the helix formed by residues 410 - 429 (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 ASP 410 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ASP* 3.9 19.1 - - - +
350A LEU* 3.7 16.7 - - - +
408A TYR* 3.5 2.2 - - - +
409A ARG* 1.3 86.5 + - - +
411A ALA* 1.3 65.4 + - - +
412A GLN* 3.4 21.1 + - - +
413A GLU* 2.9 44.4 + - - +
414A PHE 3.4 8.7 + - - -
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Residues in contact with ALA 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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346A ASP* 5.1 0.4 + - - -
349A GLN* 4.1 13.3 + - + +
350A LEU* 4.1 4.3 - - - +
353A CYS* 3.5 20.2 - - - -
410A ASP* 1.3 72.8 - - - +
412A GLN* 1.3 67.7 + - - +
414A PHE* 3.2 5.1 + - - +
415A ALA* 2.9 26.2 + - - +
450A TYR* 3.4 6.5 + - - +
453A MET* 3.4 40.6 - - + -
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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
----------------------------------------------------------
346A ASP* 5.0 2.0 + - - -
349A GLN* 4.6 8.1 + - - +
410A ASP* 3.3 19.4 + - - +
411A ALA* 1.3 93.0 - - - +
413A GLU* 1.3 57.7 + - - +
415A ALA* 3.3 3.1 + - - +
416A ALA* 3.0 30.0 + - - +
450A TYR* 3.8 15.0 + - - +
453A MET* 4.4 7.4 - - - +
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Residues in contact with GLU 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A LYS* 5.0 0.7 + - - +
407A ASP* 3.8 8.2 - - - +
408A TYR* 3.6 24.6 - - + -
409A ARG* 2.9 29.6 + - - +
410A ASP* 2.9 23.7 + - - +
411A ALA 3.2 0.2 - - - -
412A GLN* 1.3 75.3 - - - +
414A PHE* 1.3 62.8 + - - +
416A ALA* 3.4 7.2 + - - +
417A ASP* 3.3 18.1 + - - +
504A GOL 3.8 30.0 + - - +
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Residues in contact with PHE 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A LEU* 4.8 0.7 - - + -
353A CYS* 3.3 55.4 - - + -
356A ILE* 4.6 4.5 - - + -
357A LEU* 4.2 15.0 - - + -
360A LEU* 5.8 0.4 - - + -
399A VAL* 3.6 31.4 - - + -
403A MET* 3.6 21.5 - - + -
408A TYR* 3.6 22.7 - + + -
410A ASP 3.4 8.0 + - - +
411A ALA 3.2 6.2 + - - +
413A GLU* 1.3 79.0 - - - +
415A ALA* 1.3 67.3 + - - +
417A ASP* 3.1 13.0 + - - +
418A VAL* 3.1 24.9 + - + +
446A PHE* 3.8 23.6 - + - -
450A TYR* 4.6 4.0 - + - -
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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 ALA 2.9 9.3 + - - +
412A GLN* 3.8 4.5 - - - +
414A PHE* 1.3 83.0 - - - +
416A ALA* 1.3 57.3 + - - +
418A VAL* 3.3 1.0 + - - +
419A ARG* 2.9 53.2 + - - +
446A PHE* 4.0 13.2 - - + -
450A TYR* 3.6 36.1 - - + +
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Residues in contact with ALA 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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412A GLN 3.0 17.4 + - - +
413A GLU* 3.7 7.6 - - - +
414A PHE 3.2 0.2 - - - -
415A ALA* 1.3 77.0 - - - +
417A ASP* 1.3 58.3 + - - +
419A ARG* 3.8 2.5 - - - +
420A LEU* 2.9 28.8 + - - +
501A CL 4.1 20.1 - - + +
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Residues in contact with ASP 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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394A MET* 3.3 36.6 - - + +
399A VAL* 4.3 2.0 - - + -
402A LYS* 2.8 28.9 + - - +
408A TYR* 2.7 34.2 + - - +
413A GLU* 3.3 6.2 + - - +
414A PHE 3.1 7.4 + - - +
416A ALA* 1.3 78.0 - - - +
418A VAL* 1.3 65.6 + - - +
420A LEU* 3.2 11.9 + - - +
421A MET 3.0 18.0 + - - -
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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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357A LEU* 5.9 0.2 - - + -
360A LEU* 4.4 13.9 - - + -
396A LEU* 5.1 2.7 - - + -
399A VAL* 4.3 16.6 - - + -
414A PHE* 3.1 44.3 + - + +
415A ALA 3.3 4.9 + - - +
417A ASP* 1.3 73.8 - - - +
419A ARG* 1.3 62.7 + - - +
421A MET* 3.2 25.7 + - + +
422A PHE* 3.3 31.7 + - + -
446A PHE* 3.7 27.1 - - + -
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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
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415A ALA* 2.9 35.3 + - - +
416A ALA* 3.9 3.6 - - - +
418A VAL* 1.3 74.7 - - - +
420A LEU* 1.3 57.9 + - - +
422A PHE* 3.2 8.9 + - - +
423A SER* 2.8 35.0 + - - +
443A GLN* 4.1 9.1 + - - +
446A PHE* 3.8 8.3 - - + -
447A GLU* 2.8 42.6 + - - +
450A TYR* 3.7 23.8 - - - -
501A CL 3.2 29.0 - - - +
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Residues in contact with LEU 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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392A HIS* 3.5 44.2 - - + +
394A MET* 3.8 20.6 - - + -
416A ALA 2.9 19.7 + - - +
417A ASP* 3.2 19.0 + - - +
419A ARG* 1.3 73.7 - - - +
421A MET* 1.3 64.1 + - - +
423A SER* 3.2 8.0 + - - -
424A ASN* 2.9 39.3 + - - +
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Residues in contact with MET 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A PHE* 3.8 32.5 - - + -
394A MET* 3.4 30.9 - - + +
395A ASP* 3.7 20.9 - - - -
396A LEU* 3.7 30.1 - - + -
399A VAL* 5.6 0.7 - - - -
417A ASP 3.0 12.1 + - - +
418A VAL* 3.3 15.0 - - + +
420A LEU* 1.3 79.2 - - - +
422A PHE* 1.3 101.8 + - + +
424A ASN* 3.4 11.7 + - - +
425A CYS* 3.4 11.1 + - - +
442A LEU* 4.5 1.8 - - + -
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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
----------------------------------------------------------
360A LEU* 5.4 0.9 - - + -
372A PHE* 4.9 5.2 - + - -
418A VAL* 3.3 38.6 + - + -
419A ARG* 3.2 6.9 + - - +
421A MET* 1.3 99.5 - - + +
423A SER* 1.3 62.2 + - - +
425A CYS* 3.0 17.7 + - - +
426A TYR* 3.0 23.0 + - + +
439A ALA* 3.5 34.1 - - + -
442A LEU* 3.7 22.7 - - + -
443A GLN* 3.4 60.3 - - + +
446A PHE* 4.3 7.0 - + + -
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Residues in contact with SER 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 ARG* 2.8 22.4 + - - +
420A LEU* 3.2 10.4 + - - -
422A PHE* 1.3 75.6 - - - +
424A ASN* 1.3 60.1 + - - +
426A TYR* 3.2 13.9 + - - +
427A LYS* 2.8 32.4 + - - +
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Residues in contact with ASN 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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386A TYR* 4.0 4.5 - - - +
390A ILE* 3.5 33.3 - - + +
392A HIS 2.9 24.1 + - - +
394A MET 3.5 5.5 - - - +
420A LEU* 2.9 35.3 + - - +
421A MET* 3.6 5.6 - - - +
422A PHE 3.2 0.2 - - - -
423A SER* 1.3 77.1 - - - +
425A CYS* 1.3 57.9 + - - +
427A LYS* 3.3 2.1 + - - +
428A TYR* 3.0 32.9 + - - +
502A CL 3.3 28.9 - - + +
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Residues in contact with CYS 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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372A PHE* 4.1 11.2 - - + -
421A MET 3.4 7.9 + - - +
422A PHE 3.0 10.6 + - - +
424A ASN* 1.3 80.1 - - - +
426A TYR* 1.3 62.4 + - - +
429A ASN* 3.0 48.9 + - - +
435A VAL* 3.7 39.3 - - - -
436A VAL* 4.0 6.4 - - - +
439A ALA* 3.8 16.8 - - + -
505A 6B3 4.2 6.5 - - + +
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Residues in contact with TYR 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* 3.0 24.1 + - + +
423A SER* 3.2 11.6 + - - +
425A CYS* 1.3 79.4 - - - +
427A LYS* 1.3 60.9 + - - +
429A ASN 3.8 10.2 - - - +
436A VAL* 4.1 19.5 - - + -
439A ALA* 3.6 24.7 + - + -
440A ARG* 3.6 37.5 - - + -
443A GLN* 2.7 28.9 + - - +
503A GOL 3.7 4.7 + - - -
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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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389A ILE* 2.8 43.0 + - + +
390A ILE* 3.9 9.9 - - + -
391A LYS* 5.4 7.7 - - - +
423A SER 2.8 17.1 + - - +
424A ASN* 3.7 5.6 - - - +
426A TYR* 1.3 79.6 - - - +
428A TYR* 1.3 62.7 + - - +
429A ASN 4.6 1.2 - - - +
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Residues in contact with TYR 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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383A LEU* 3.6 36.6 - - + +
385A ASP* 2.6 39.2 + - - -
386A TYR* 3.7 39.3 - + + -
389A ILE* 3.9 27.6 - - + +
390A ILE* 4.2 4.5 - - + -
424A ASN 3.0 17.5 + - - +
427A LYS* 1.3 81.5 - - - +
429A ASN* 1.3 82.1 + - - +
430A PRO* 4.1 3.2 - - + +
505A 6B3 4.1 8.5 - + - -
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Residues in contact with ASN 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A CYS* 3.0 27.7 + - - +
426A TYR 3.8 13.5 - - - +
427A LYS 4.6 1.0 - - - +
428A TYR* 1.3 89.9 - - - +
430A PRO* 1.3 74.0 - - + +
431A PRO* 3.6 3.8 - - - +
433A HIS* 4.0 10.2 - - + -
435A VAL* 3.6 15.9 - - - +
436A VAL* 3.6 16.6 - - + +
505A 6B3 2.7 54.7 + - - +
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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