Contacts of the helix formed by residues 403 - 418 (chain A) in PDB entry 1P9B
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 PRO 403 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389A TRP* 3.8 37.5 - - + -
391A GLU* 3.4 32.1 - - + +
393A ILE* 3.6 19.5 - - + -
396A CYS* 4.9 1.3 - - - -
401A GLU 3.7 3.6 - - - +
402A LEU* 1.3 90.1 - - + +
404A GLU* 1.3 67.2 + - - +
405A ASN* 3.3 2.2 - - + +
406A ALA* 3.0 18.2 + - + +
407A LYS* 3.3 7.6 + - - +
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Residues in contact with GLU 404 (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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402A LEU 3.5 1.5 + - - +
403A PRO* 1.3 72.1 - - - +
405A ASN* 1.3 66.8 + - - +
407A LYS* 2.8 46.1 + - - +
408A LYS* 3.0 38.3 + - - +
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Residues in contact with ASN 405 (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 PHE* 5.3 2.3 - - - +
387A SER* 3.3 37.1 - - - +
388A GLY 2.7 25.9 + - - +
389A TRP* 3.8 15.3 - - + +
403A PRO* 3.3 1.8 - - - +
404A GLU* 1.3 79.4 - - - +
406A ALA* 1.3 59.4 + - - +
408A LYS* 3.7 25.0 + - - +
409A TYR* 3.3 20.4 + - - +
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Residues in contact with ALA 406 (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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340A LEU* 4.4 11.2 - - + -
389A TRP* 3.6 37.6 - - + -
393A ILE* 5.4 0.7 - - + -
402A LEU* 4.3 14.1 - - + -
403A PRO* 3.0 20.8 + - + +
405A ASN* 1.3 76.4 - - - +
407A LYS* 1.3 67.4 + - - +
409A TYR* 3.2 3.8 + - - +
410A ILE* 2.9 29.3 + - - +
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Residues in contact with LYS 407 (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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399A PHE* 3.6 45.8 - - + +
400A ASP* 3.2 33.4 + - - +
402A LEU* 3.1 23.5 + - + +
403A PRO 3.6 9.0 - - - +
404A GLU* 2.8 39.7 + - - +
406A ALA* 1.3 78.1 - - - +
408A LYS* 1.3 52.7 + - + +
410A ILE* 3.2 2.2 + - - +
411A LEU* 2.7 47.9 + - + +
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Residues in contact with LYS 408 (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 PHE* 3.9 12.6 - - + -
404A GLU* 3.0 30.4 + - + +
405A ASN* 3.9 23.8 + - - +
406A ALA 3.3 0.2 - - - -
407A LYS* 1.3 76.7 - - + +
409A TYR* 1.3 54.4 + - - +
411A LEU* 3.9 7.9 - - + +
412A ALA* 2.7 36.7 + - - +
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Residues in contact with TYR 409 (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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276A SER* 2.7 27.6 + - - -
317A TRP* 5.9 0.5 - - - -
318A LEU* 3.5 15.5 + - + +
337A LEU* 4.9 0.9 - - + -
340A LEU* 3.7 23.1 - - + -
343A LEU* 3.6 19.5 - - + +
349A ILE* 3.7 28.0 - - + +
350A LEU 4.9 0.9 + - - -
351A LEU* 3.9 23.3 - - + -
386A PHE* 4.0 28.6 - + + -
389A TRP* 4.5 7.6 - + + -
405A ASN 3.3 11.4 + - - +
406A ALA* 3.2 10.9 + - - +
408A LYS* 1.3 79.7 - - - +
410A ILE* 1.3 62.6 + - - +
412A ALA* 3.3 2.3 + - - +
413A ILE* 3.0 46.3 + - + +
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Residues in contact with ILE 410 (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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337A LEU* 4.1 10.5 - - + -
340A LEU* 3.6 32.1 - - + -
399A PHE* 3.8 28.3 - - + -
402A LEU* 3.8 12.1 - - + -
406A ALA 2.9 16.6 + - - +
407A LYS 3.5 5.4 - - - +
409A TYR* 1.3 76.3 - - - +
411A LEU* 1.3 63.6 + - - +
413A ILE* 3.2 6.6 + - - +
414A GLU* 3.1 19.8 + - + +
421A ILE* 3.4 31.6 - - + +
424A ILE* 3.7 23.1 - - + -
436A LYS* 4.6 8.7 - - - -
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Residues in contact with LEU 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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399A PHE* 4.2 13.9 - - + -
407A LYS* 2.7 33.0 + - + +
408A LYS* 3.9 7.6 - - + +
410A ILE* 1.3 69.7 - - - +
412A ALA* 1.3 66.1 + - - +
414A GLU* 3.3 23.7 + - - +
415A LYS* 3.0 26.1 + - - +
436A LYS* 3.9 18.4 - - - +
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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
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351A LEU* 4.8 1.3 - - + -
384A GLU* 5.3 0.2 - - - +
386A PHE* 3.4 31.9 - - + -
408A LYS 2.7 23.4 + - - +
409A TYR 3.5 2.9 - - - +
411A LEU* 1.3 72.7 - - - +
413A ILE* 1.3 64.4 + - - +
415A LYS* 3.3 16.3 + - - +
416A TYR* 3.1 40.6 + - + +
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Residues in contact with ILE 413 (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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274A VAL* 5.8 1.8 - - + -
318A LEU* 3.6 31.2 - - + -
320A ILE* 4.6 7.9 - - + -
323A LEU* 5.3 1.8 - - + -
335A ILE* 5.9 2.2 - - + -
337A LEU* 3.8 31.0 - - + -
351A LEU* 4.6 12.6 - - + -
409A TYR* 3.0 30.8 + - + +
410A ILE 3.4 5.6 - - - +
412A ALA* 1.3 77.5 - - - +
414A GLU* 1.3 64.8 + - - +
416A TYR* 3.2 7.0 + - - +
417A LEU* 3.0 45.2 + - + +
421A ILE* 3.9 13.2 - - + -
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Residues in contact with GLU 414 (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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410A ILE* 3.1 14.7 + - - +
411A LEU* 3.5 19.5 - - - +
413A ILE* 1.3 75.5 - - - +
415A LYS* 1.3 54.6 + - - +
417A LEU* 5.1 0.9 - - - -
418A LYS* 2.7 31.7 + - - -
419A THR 3.2 21.8 + - - +
420A PRO* 3.5 8.6 - - - +
421A ILE* 2.7 47.2 + - + +
436A LYS* 2.7 35.1 + - - -
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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
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384A GLU* 5.9 0.4 + - - -
411A LEU 3.0 15.1 + - - +
412A ALA* 3.5 15.0 - - - +
414A GLU* 1.3 77.8 - - - +
416A TYR* 1.3 92.0 + - + +
418A LYS* 3.3 20.0 + - - +
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Residues in contact with TYR 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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320A ILE* 4.1 23.8 - - + -
324A LEU* 3.6 16.5 - - - +
327A LYS* 5.1 0.2 + - - -
351A LEU* 3.9 23.6 - - + -
353A VAL* 3.9 14.6 - - + -
384A GLU* 2.4 37.0 + - - -
412A ALA* 3.1 29.6 + - + +
413A ILE 3.2 3.1 + - - +
415A LYS* 1.3 103.3 + - + +
417A LEU* 1.3 60.7 + - - +
418A LYS* 3.7 5.9 + - - +
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Residues in contact with LEU 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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274A VAL* 5.5 1.3 - - + -
320A ILE* 4.1 18.2 - - + -
323A LEU* 3.6 46.4 - - + +
324A LEU* 3.7 23.6 - - + +
327A LYS* 3.1 19.2 + - + +
335A ILE* 4.8 22.2 - - + -
413A ILE* 3.0 30.7 + - + +
414A GLU* 4.9 0.4 - - - -
416A TYR* 1.3 77.1 - - - +
418A LYS* 1.3 71.5 + - - +
419A THR* 2.8 23.8 + - - +
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Residues in contact with LYS 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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327A LYS* 4.5 10.8 - - - +
414A GLU 2.7 10.4 + - - -
415A LYS* 3.3 13.1 + - - +
416A TYR 4.6 5.4 - - - +
417A LEU* 1.3 80.5 - - - +
419A THR* 1.3 60.9 + - - +
420A PRO* 4.6 2.0 - - - +
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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