Contacts of the helix formed by residues 402 - 416 (chain A) in PDB entry 4UH6
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 LYS 402 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385A ARG* 3.6 30.9 - - - +
388A GLU* 3.4 24.9 + - - -
400A GLN 5.5 0.9 - - - -
401A LEU* 1.3 74.6 - - - +
403A ASP* 1.3 66.0 + - - +
404A THR* 3.8 13.9 - - - +
405A GLU* 2.9 34.3 + - - +
406A LEU* 2.9 11.6 + - - +
435A ARG* 4.5 0.2 - - - -
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Residues in contact with ASP 403 (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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401A LEU 4.7 0.5 - - - +
402A LYS* 1.3 73.0 - - - +
404A THR* 1.3 65.2 + - + +
406A LEU* 3.2 5.0 + - - +
407A ILE* 3.0 36.1 + - + +
433A ASP* 3.5 13.0 - - + +
435A ARG* 3.0 22.8 + - - +
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Residues in contact with THR 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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370A TYR* 3.3 27.5 + - - +
402A LYS* 3.8 14.4 - - - +
403A ASP* 1.3 77.0 - - + +
405A GLU* 1.3 59.8 + - - +
407A ILE* 3.4 10.2 + - + +
408A TYR* 3.0 28.2 + - - +
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Residues in contact with GLU 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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366A PHE* 3.6 27.0 - - + -
367A ILE* 3.8 11.4 - - + +
370A TYR* 4.2 24.8 - - + -
371A TYR* 4.5 6.9 + - - -
385A ARG* 2.8 53.9 + - - +
401A LEU* 3.7 11.3 - - + +
402A LYS* 2.9 25.0 + - + +
404A THR* 1.3 77.0 + - - +
406A LEU* 1.3 57.4 + - - +
408A TYR* 4.4 4.0 - - - -
409A GLY* 2.8 30.7 + - - -
579A ILE* 4.7 0.3 - - - +
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Residues in contact with LEU 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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401A LEU* 3.9 26.8 - - + +
402A LYS 2.9 11.3 + - - +
403A ASP* 3.5 11.4 - - - +
405A GLU* 1.3 78.1 - - - +
407A ILE* 1.3 57.2 + - + +
409A GLY* 3.8 0.3 - - - -
410A ALA* 3.0 30.1 + - - +
431A VAL* 4.5 7.0 - - + -
433A ASP* 3.9 26.0 - - + +
435A ARG* 3.7 28.3 - - - +
466A ILE* 3.9 32.3 - - + -
579A ILE* 4.2 6.1 - - + +
584A PHE* 4.0 17.3 - - + -
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Residues in contact with ILE 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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403A ASP* 3.0 29.5 + - + +
404A THR* 3.7 8.5 - - + +
405A GLU 3.3 0.2 - - - -
406A LEU* 1.3 78.5 - - + +
408A TYR* 1.3 64.6 + - - +
410A ALA* 3.3 2.8 + - - +
411A LYS* 3.0 51.1 + - + +
431A VAL* 4.1 33.6 - - + +
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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
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366A PHE* 3.6 24.0 - + - -
369A GLN* 2.7 45.3 + - - +
370A TYR* 3.6 30.5 - + + -
373A SER* 3.3 32.4 - - - -
374A ILE* 5.9 0.4 - - + -
404A THR 3.0 17.3 + - - +
405A GLU 3.7 1.8 - - - +
407A ILE* 1.3 78.5 - - - +
409A GLY* 1.3 59.6 + - - +
411A LYS* 3.3 4.8 + - - +
412A HIS* 2.9 75.7 + + + -
707A PRO* 5.1 0.4 - - + -
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Residues in contact with GLY 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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366A PHE* 4.2 2.5 - - - -
405A GLU 2.8 21.2 + - - -
406A LEU 3.8 1.3 - - - -
408A TYR* 1.3 77.4 - - - +
410A ALA* 1.3 56.9 + - - +
412A HIS 3.3 0.5 + - - -
413A ALA* 2.9 26.5 + - - +
579A ILE* 3.8 15.2 - - - +
707A PRO* 3.3 28.5 - - - +
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Residues in contact with ALA 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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406A LEU 3.0 16.9 + - - +
407A ILE 3.8 4.0 - - - +
409A GLY* 1.3 72.3 - - - +
411A LYS* 1.3 67.4 + - - +
413A ALA* 3.3 6.1 + - - +
414A TRP* 3.2 20.4 + - - +
429A LEU* 4.2 5.0 - - + +
431A VAL* 4.0 18.6 - - + -
464A ILE* 4.3 11.4 - - + -
466A ILE* 4.1 18.8 - - + -
577A LEU* 4.5 13.5 - - + -
579A ILE* 3.9 1.0 - - - +
709A PHE* 4.4 4.1 - - - -
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Residues in contact with LYS 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ILE* 3.0 40.6 + - + +
408A TYR* 3.8 6.5 - - - +
410A ALA* 1.3 74.5 - - - +
412A HIS* 1.3 57.9 + - + +
414A TRP* 3.4 5.3 + - - +
415A ARG* 2.9 26.2 + - - +
426A TRP* 3.5 34.9 - - + +
427A SER* 3.1 33.2 + - - +
429A LEU* 3.7 35.0 + - + +
431A VAL* 4.9 0.9 - - + -
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Residues in contact with HIS 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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369A GLN* 4.4 2.2 + - - +
373A SER* 5.5 2.0 - - - -
408A TYR* 2.9 72.6 + + + +
409A GLY 4.0 2.7 - - - +
410A ALA 3.2 0.2 - - - -
411A LYS* 1.3 78.2 - - + +
413A ALA* 1.3 58.7 + - - +
415A ARG* 3.3 39.9 - - - -
416A ASN* 2.8 41.1 + - - +
426A TRP* 3.6 20.2 - + - -
674A ARG* 3.9 11.0 + - - -
707A PRO* 4.1 17.7 - - + -
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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
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409A GLY 2.9 11.7 + - - +
410A ALA 3.3 2.9 + - - +
412A HIS* 1.3 74.8 - - - +
414A TRP* 1.3 62.0 + - - +
416A ASN* 3.3 3.6 + - - +
417A ALA* 3.1 22.2 + - - +
577A LEU* 3.5 31.6 - - + -
707A PRO 3.3 13.5 + - - +
708A SER* 3.8 12.1 - - - +
709A PHE* 3.5 25.2 + - + -
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Residues in contact with TRP 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 ALA 3.2 6.4 + - - +
411A LYS 3.5 7.0 - - - +
413A ALA* 1.3 75.3 - - - +
415A ARG* 1.3 66.6 + - - +
416A ASN 3.0 1.6 - - - -
417A ALA* 3.0 13.1 + - - +
420A CYS* 3.4 12.6 - - + -
422A GLY 3.7 17.0 - - - -
423A ARG* 3.1 17.6 - - + +
425A GLN* 3.4 36.1 - - + -
426A TRP* 3.5 21.8 - - + -
428A LYS 3.7 3.8 - - - -
429A LEU* 4.0 11.2 - - + -
462A SER* 3.7 19.5 - - - -
709A PHE* 3.5 7.3 - - - -
750A HEM 3.3 90.4 + + + -
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Residues in contact with ARG 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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411A LYS 2.9 18.2 + - - +
412A HIS* 3.2 33.5 + - - +
414A TRP* 1.3 75.3 - - - +
416A ASN* 1.3 57.7 + - - +
423A ARG* 3.2 25.9 + - - +
426A TRP* 3.4 53.9 - - + +
666A HIS* 5.2 2.2 + - + -
670A GLU* 2.8 42.3 + - - +
673A CYS* 3.9 10.1 - - - -
674A ARG* 3.5 48.3 + - - +
677A CYS* 5.5 0.7 - - - -
678A PRO* 5.3 0.9 - - - +
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Residues in contact with ASN 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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369A GLN* 5.6 0.4 + - - -
412A HIS* 2.8 20.2 + - - +
413A ALA 3.6 2.5 - - - +
414A TRP 3.0 0.4 - - - -
415A ARG* 1.3 77.7 - - - +
417A ALA* 1.3 58.1 + - - +
418A SER* 2.9 11.3 + - - -
423A ARG* 4.0 3.8 - - - +
674A ARG* 2.8 39.4 + - - +
678A PRO* 4.1 13.4 - - - +
703A TYR 5.1 2.4 - - - +
704A ARG* 6.0 0.2 - - - -
705A LEU* 3.5 35.6 + - + +
706A THR 3.7 11.5 + - - -
707A PRO* 3.0 29.5 + - - +
708A SER* 5.3 1.7 - - - -
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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
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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