Contacts of the helix formed by residues 409 - 432 (chain A) in PDB entry 5ID6
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 SER 409 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A GLN* 3.6 7.6 - - - +
407A ASP 3.9 3.2 + - - -
408A LEU* 1.3 71.1 - - - +
410A VAL* 1.3 62.1 + - - +
411A VAL* 3.2 25.6 - - - +
412A GLU* 3.5 15.5 + - - +
413A LYS* 3.1 24.2 + - - +
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Residues in contact with VAL 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ILE* 3.7 42.4 - - + +
352A PHE* 4.2 3.4 - - + -
397A LEU* 3.9 39.7 - - + +
400A LEU* 4.0 23.3 - - + +
401A GLN* 3.4 17.5 + - + +
404A ALA* 4.0 12.3 - - + -
408A LEU 3.2 5.6 + - - +
409A SER* 1.3 72.0 + - - +
411A VAL* 1.3 64.8 + - + +
413A LYS* 3.5 2.2 + - - +
414A LEU* 3.1 25.0 + - + +
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Residues in contact with VAL 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A PHE* 3.7 38.5 - - + +
329A ASP* 3.3 26.2 - - - +
333A SER* 5.8 7.9 - - - -
397A LEU* 4.8 11.2 - - + -
401A GLN* 5.2 3.9 - - + +
409A SER* 3.2 14.6 - - - +
410A VAL* 1.3 81.3 - - + +
412A GLU* 1.3 61.3 + - - +
414A LEU* 3.3 8.0 + - - +
415A LYS* 2.9 26.0 + - - +
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Residues in contact with GLU 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ASP* 2.7 34.8 - - - +
409A SER* 3.4 20.9 + - - +
410A VAL 3.3 0.4 - - - -
411A VAL* 1.3 79.9 - - - +
413A LYS* 1.3 64.3 + - - +
415A LYS* 3.2 24.3 + - - +
416A GLU* 3.1 36.4 + - + +
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Residues in contact with LYS 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ASP* 2.6 33.3 + - - +
351A ILE* 4.1 22.2 + - + +
408A LEU* 6.1 1.6 - - + -
409A SER 3.1 17.0 + - - +
410A VAL* 4.0 4.9 - - - +
412A GLU* 1.3 76.3 - - - +
414A LEU* 1.3 61.8 + - - +
416A GLU* 3.5 18.2 + - - +
417A ILE* 3.2 47.4 + - + +
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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
----------------------------------------------------------
328A PHE* 4.2 10.3 - - + -
338A VAL* 5.6 0.9 - - + -
347A ILE* 3.8 16.4 - - + -
351A ILE* 3.7 33.9 - - + -
397A LEU* 3.6 31.0 - - + -
400A LEU* 5.8 0.2 - - + -
410A VAL 3.1 16.9 + - - +
411A VAL 3.4 5.8 - - - +
413A LYS* 1.3 76.0 - - - +
415A LYS* 1.3 64.7 + - - +
417A ILE* 3.1 8.5 + - + +
418A ILE* 3.0 34.3 + - + +
469A TYR* 4.2 13.5 - - - +
473A PHE* 4.1 26.2 - - + -
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Residues in contact with LYS 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A PHE* 3.2 22.7 - - + +
326A LYS* 3.5 22.7 + - + +
328A PHE* 4.0 15.9 - - + -
329A ASP* 2.8 42.7 + - - +
411A VAL 2.9 12.4 + - - +
412A GLU* 3.2 26.8 + - - +
414A LEU* 1.3 76.5 - - - +
416A GLU* 1.3 58.9 + - + +
418A ILE* 3.5 4.9 + - - +
419A ILE* 2.9 50.3 + - + +
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Residues in contact with GLU 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A GLU* 3.1 26.4 + - + +
413A LYS* 3.5 19.8 + - - +
414A LEU 3.2 0.2 - - - -
415A LYS* 1.3 80.9 - - + +
417A ILE* 1.3 58.7 + - - +
419A ILE* 4.1 7.3 - - + +
420A GLN* 3.1 26.2 + - - +
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Residues in contact with ILE 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ASP* 3.5 31.0 - - + +
413A LYS* 3.2 49.9 + - + +
414A LEU* 3.1 16.6 + - + +
416A GLU* 1.3 76.5 - - - +
418A ILE* 1.3 64.8 + - - +
420A GLN* 3.3 7.7 - - - +
421A LYS* 3.2 31.9 + - - +
469A TYR* 3.4 31.2 - - + +
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Residues in contact with ILE 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LEU 5.3 0.4 - - - +
322A GLU* 6.1 0.4 - - - -
325A PHE* 3.8 54.5 - - + -
328A PHE* 4.6 2.7 - - + -
414A LEU* 3.0 33.4 + - + +
415A LYS* 3.9 4.0 - - - +
417A ILE* 1.3 75.7 - - - +
419A ILE* 1.3 69.2 + - + +
421A LYS* 3.0 17.7 + - - +
422A VAL* 3.2 15.2 + - + +
466A PHE* 4.3 7.6 - - + -
469A TYR* 4.2 12.8 - - + -
470A ILE* 3.6 24.9 - - + -
473A PHE* 4.3 19.1 - - + -
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Residues in contact with ILE 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A GLU* 5.0 12.1 - - + +
325A PHE* 5.4 1.3 - - + -
326A LYS* 3.4 46.4 - - + +
415A LYS* 2.9 42.1 + - + +
416A GLU* 4.4 6.5 - - + +
418A ILE* 1.3 79.3 - - + +
420A GLN* 1.3 65.2 + - - +
422A VAL* 3.0 11.5 + - + +
423A ASP* 3.0 36.7 + - - +
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Residues in contact with GLN 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A GLU 3.1 19.8 + - - +
417A ILE* 3.3 8.9 - - - +
418A ILE 3.1 0.2 - - - -
419A ILE* 1.3 81.7 - - - +
421A LYS* 1.3 72.4 + - - +
423A ASP* 3.2 11.7 + - + +
424A GLU* 3.0 28.7 + - - +
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Residues in contact with LYS 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ASP* 5.3 0.8 + - - -
417A ILE* 3.2 20.6 + - - +
418A ILE* 3.0 11.7 + - - +
420A GLN* 1.3 90.4 - - - +
422A VAL* 1.3 59.8 + - - +
424A GLU* 3.5 8.5 + - + +
425A ILE* 3.3 25.4 + - - +
462A SER 4.8 1.8 - - - +
465A SER* 3.7 25.1 - - - +
466A PHE* 4.0 26.0 - - + -
469A TYR* 3.9 43.1 - - + -
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Residues in contact with VAL 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ILE* 4.8 11.4 - - + -
321A LEU 5.8 0.2 - - - -
322A GLU* 3.7 47.8 - - + +
418A ILE* 3.2 21.3 - - + +
419A ILE* 3.0 13.3 + - + +
421A LYS* 1.3 73.1 - - - +
423A ASP* 1.3 73.4 + - - +
425A ILE* 3.0 21.7 + - - +
426A TYR* 3.0 21.9 + - + -
466A PHE* 3.5 26.0 - - + -
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Residues in contact with ASP 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A GLU* 4.3 6.9 - - - +
326A LYS* 5.8 0.5 + - - -
419A ILE* 3.0 30.8 + - - +
420A GLN* 3.5 12.4 - - + +
422A VAL* 1.3 86.4 - - - +
424A GLU* 1.3 56.2 + - - +
426A TYR* 3.3 13.2 + - - +
427A LYS* 3.1 28.1 + - - +
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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
----------------------------------------------------------
420A GLN* 3.0 23.9 + - - +
421A LYS* 3.7 13.5 - - + +
422A VAL 3.1 0.4 - - - -
423A ASP* 1.3 73.7 - - - +
425A ILE* 1.3 63.7 + - - +
427A LYS* 4.2 18.3 - - - +
428A VAL* 3.0 49.3 + - - +
462A SER* 4.3 15.3 - - - +
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Residues in contact with ILE 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ILE* 4.5 17.0 - - + -
421A LYS 3.3 12.9 + - - +
422A VAL* 3.0 12.6 + - - +
424A GLU* 1.3 78.5 - - - +
426A TYR* 1.3 63.8 + - + +
428A VAL* 3.2 2.6 + - - +
429A TYR* 2.9 58.4 + - + -
462A SER* 3.3 35.7 - - - +
463A VAL* 3.7 21.3 - - + -
466A PHE* 3.7 29.4 - - + -
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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
----------------------------------------------------------
310A LYS* 4.6 6.5 + - - +
315A PHE* 3.5 39.0 - + - -
318A ILE* 3.8 24.7 + - + +
319A LYS* 3.4 22.6 - - + +
322A GLU* 3.2 35.6 + - - +
422A VAL* 3.0 23.2 + - + -
423A ASP* 3.3 14.5 + - - +
425A ILE* 1.3 79.3 - - + +
427A LYS* 1.3 62.6 + - - +
429A TYR* 3.4 6.6 + + - +
430A GLY* 3.2 17.2 + - - -
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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
----------------------------------------------------------
423A ASP 3.1 17.1 + - - +
424A GLU* 4.3 18.8 + - - +
426A TYR* 1.3 75.7 - - - +
428A VAL* 1.3 72.8 + - + +
430A GLY* 3.2 10.2 + - - -
431A SER* 3.1 24.2 + - - +
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Residues in contact with VAL 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A GLU* 3.0 40.3 + - - +
425A ILE 3.2 4.5 + - - +
427A LYS* 1.3 87.7 - - + +
429A TYR* 1.3 56.3 + - - +
431A SER* 3.3 12.2 + - - -
432A SER* 2.3 32.7 + - - +
458A ASP* 3.9 14.8 - - + +
459A LEU* 3.6 38.1 - - + +
462A SER* 4.2 9.2 - - - +
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Residues in contact with TYR 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LEU* 2.5 46.6 + - - +
309A ASN 4.4 6.3 - - - -
310A LYS* 3.5 31.4 - - + +
315A PHE* 3.4 38.6 + + - +
318A ILE* 5.1 2.0 - - + +
425A ILE* 2.9 42.9 + - + -
426A TYR* 3.6 6.7 - - - +
427A LYS 3.2 0.2 - - - -
428A VAL* 1.3 77.7 - - - +
430A GLY* 1.3 62.8 + - - +
432A SER* 3.0 15.6 + - - -
433A GLU* 3.0 18.8 + - - +
436A PHE* 4.0 22.0 - + - -
459A LEU* 4.0 19.6 - - + +
463A VAL* 4.8 3.1 - - + +
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Residues in contact with GLY 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A LYS* 4.9 2.1 - - - +
426A TYR 3.2 10.8 + - - -
427A LYS* 3.2 5.3 + - - -
429A TYR* 1.3 78.5 - - - +
431A SER* 1.3 59.2 + - - +
432A SER 3.2 0.7 + - - -
433A GLU* 3.7 17.4 + - - +
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Residues in contact with SER 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A LYS* 3.1 24.1 + - - +
428A VAL* 3.3 12.9 + - - -
429A TYR 3.1 1.0 - - - -
430A GLY* 1.3 75.6 - - - +
432A SER* 1.3 59.9 + - - +
433A GLU 3.5 0.4 - - - -
435A LEU* 5.9 0.2 - - - +
455A ILE* 3.9 18.3 - - - +
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Residues in contact with SER 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A PHE* 5.5 0.7 - - - -
428A VAL* 2.3 34.2 + - - +
429A TYR 3.0 4.9 + - - -
431A SER* 1.3 79.3 - - - +
433A GLU* 1.3 65.3 + - - +
434A LYS 3.3 2.7 - - - -
435A LEU* 3.0 26.3 + - - +
436A PHE* 3.9 8.9 - - - -
455A ILE* 3.5 27.0 + - - +
459A LEU* 3.9 23.3 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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