Contacts of the helix formed by residues 438 - 457 (chain A) in PDB entry 3H13
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 438 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A LYS 4.1 4.0 - - - +
437A ARG* 1.3 87.9 - - + +
439A LEU* 1.3 67.3 + - - +
440A LEU* 4.4 7.0 - - + +
441A ASP* 3.0 44.4 + - - +
442A LEU* 3.1 11.1 + - - +
474A LYS* 4.1 29.6 - - + +
475A LEU 3.2 14.1 - - - +
476A ILE* 3.7 17.0 - - + -
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Residues in contact with LEU 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A MET* 3.7 29.2 - - + -
356A PHE* 4.1 19.7 - - + -
402A PHE* 3.6 42.0 - - + -
427A LEU* 5.4 2.5 - - + -
431A LEU* 3.8 27.4 - - + -
437A ARG 3.5 2.9 + - - -
438A PRO* 1.3 71.0 - - - +
440A LEU* 1.3 57.1 + - - +
442A LEU* 3.1 12.1 + - + +
443A HIS* 2.9 28.5 + - + +
471A LEU* 6.0 0.2 - - + -
475A LEU* 2.8 28.0 + - + +
476A ILE* 4.6 0.8 - - - +
477A LEU* 4.6 9.4 - - + +
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Residues in contact with LEU 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A PHE* 3.9 12.7 - - + -
438A PRO* 3.2 5.7 - - + +
439A LEU* 1.3 79.8 - - - +
441A ASP* 1.3 61.5 + - - +
443A HIS* 3.3 5.2 + - - +
444A ILE* 3.1 37.4 + - + +
467A LEU* 3.8 29.8 - - + -
469A HIS* 3.6 34.5 - - + +
471A LEU* 5.3 9.1 - - + +
475A LEU* 4.7 1.0 + - - +
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Residues in contact with ASP 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A ARG* 4.2 19.0 + - - +
438A PRO* 3.0 38.3 + - + +
440A LEU* 1.3 78.0 - - - +
442A LEU* 1.3 64.7 + - - +
444A ILE* 3.3 12.2 + - - +
445A GLU* 3.2 27.5 + - - +
474A LYS* 5.6 0.7 + - - -
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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
----------------------------------------------------------
430A LYS* 4.0 25.6 - - + +
431A LEU* 3.5 30.7 - - + -
434A GLU* 3.7 50.0 - - + +
435A ARG* 5.2 1.1 - - - -
437A ARG* 4.0 22.4 - - + +
438A PRO 3.1 11.3 + - - +
439A LEU* 3.1 13.3 + - + +
441A ASP* 1.3 74.8 - - - +
443A HIS* 1.3 59.8 + - - +
445A GLU* 3.2 16.0 + - - +
446A LEU* 2.9 27.1 + - - +
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Residues in contact with HIS 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A PHE* 5.0 5.4 - + - -
402A PHE* 3.8 24.7 - + + -
404A SER* 2.7 29.3 + - - -
423A TYR* 4.6 3.0 - - - -
427A LEU* 5.1 4.9 - - + -
439A LEU* 2.9 17.5 + - + +
440A LEU* 3.6 7.2 - - - +
441A ASP 3.2 0.2 - - - -
442A LEU* 1.3 79.7 - - - +
444A ILE* 1.3 55.9 + - - +
446A LEU* 3.2 17.0 + - + +
447A ASN* 2.8 36.3 + - - +
465A VAL* 3.6 27.9 - - + +
467A LEU* 3.8 32.8 - - + +
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Residues in contact with ILE 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A LEU* 3.1 28.6 + - + +
441A ASP* 3.4 14.1 - - - +
442A LEU 3.2 0.2 - - - -
443A HIS* 1.3 73.8 - - + +
445A GLU* 1.3 68.8 + - + +
447A ASN* 3.1 23.2 + - + +
448A GLY* 3.0 19.4 + - - -
467A LEU* 6.0 3.8 - - + -
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Residues in contact with GLU 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LYS* 3.3 33.5 + - - +
434A GLU* 3.7 5.7 - - - +
437A ARG* 2.5 46.0 + - - +
441A ASP 3.2 12.8 - - - +
442A LEU* 3.2 8.2 + - - +
444A ILE* 1.3 77.0 - - + +
446A LEU* 1.3 62.2 + - - +
448A GLY* 3.2 2.9 + - - +
449A TYR* 2.8 29.3 + - - +
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Residues in contact with LEU 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A TYR* 4.0 28.9 - - + +
426A CYS* 3.7 23.3 - - + -
427A LEU* 3.9 45.5 - - + +
430A LYS* 4.5 3.7 - - + +
442A LEU 2.9 13.9 + - - +
443A HIS* 3.2 18.6 + - + +
445A GLU* 1.3 76.6 - - - +
447A ASN* 1.3 52.1 + - - +
449A TYR* 3.1 2.4 + - - +
450A MET* 2.8 50.1 + - + +
465A VAL* 4.1 16.8 - - + -
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Residues in contact with ASN 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A HIS* 2.8 39.4 + - - +
444A ILE* 3.1 28.0 - - + +
446A LEU* 1.3 78.1 - - - +
448A GLY* 1.3 57.3 + - - +
450A MET* 3.2 5.4 + - - +
451A TYR* 2.9 49.9 + - + -
465A VAL* 4.3 14.7 - - - +
467A LEU* 5.6 5.0 - - - +
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Residues in contact with GLY 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ILE 3.0 8.9 + - - -
445A GLU* 3.2 4.0 + - - -
447A ASN* 1.3 79.7 - - - +
449A TYR* 1.3 62.2 + - - +
451A TYR* 3.4 9.2 + - - +
452A ASP* 3.1 24.8 + - - +
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Residues in contact with TYR 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A LEU* 3.7 35.4 - - + +
426A CYS* 3.8 24.4 - - + -
429A GLN* 4.9 16.4 + - - -
430A LYS* 5.4 7.4 - - - -
445A GLU 2.8 14.3 + - - +
446A LEU 3.1 9.2 + - - +
448A GLY* 1.3 76.2 - - - +
450A MET* 1.3 86.0 + - + +
452A ASP* 3.4 7.5 + - - +
453A TRP* 3.1 19.9 + - + +
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Residues in contact with MET 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A LEU* 3.7 31.9 - - + +
423A TYR* 3.9 14.4 - - - -
426A CYS* 3.8 11.4 - - + -
446A LEU* 2.8 26.7 + - + +
447A ASN* 3.8 4.7 - - - +
449A TYR* 1.3 103.3 - - + +
451A TYR* 1.3 60.0 + - + +
453A TRP* 3.4 3.9 + - - +
454A ASN* 2.9 36.3 + - - +
463A TYR* 4.1 30.7 - - + +
465A VAL* 3.8 27.6 - - + -
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Residues in contact with TYR 451 (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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447A ASN* 2.9 41.8 + - + +
448A GLY* 3.7 8.1 - - - +
450A MET* 1.3 77.1 - - + +
452A ASP* 1.3 62.9 + - - +
454A ASN* 3.4 11.9 + - + +
455A SER* 3.1 24.1 + - - -
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Residues in contact with ASP 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A GLY 3.1 17.0 + - - +
449A TYR* 3.7 6.7 - - - +
450A MET 3.3 0.2 - - - -
451A TYR* 1.3 74.9 - - - +
453A TRP* 1.3 65.0 + - - +
455A SER* 2.7 24.8 + - - -
456A ARG* 2.9 48.5 + - - +
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Residues in contact with TRP 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A LEU* 3.4 33.9 - - + -
449A TYR* 3.1 15.4 + - + +
450A MET* 3.7 8.3 - - - +
452A ASP* 1.3 79.1 + - - +
454A ASN* 1.3 81.0 + - - +
456A ARG* 3.0 20.1 + - - +
457A VAL* 3.5 41.5 + - + +
461A GLU* 2.9 40.9 + - + -
463A TYR* 3.6 22.7 - + + -
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Residues in contact with ASN 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A MET* 2.9 20.3 + - - +
451A TYR* 3.7 13.4 - - + +
452A ASP 3.3 0.2 - - - -
453A TRP* 1.3 84.3 - - - +
455A SER* 1.3 62.2 + - - +
456A ARG 3.3 0.9 + - - -
457A VAL* 3.6 6.5 + - - +
462A LYS* 3.1 50.8 + - + +
463A TYR* 2.8 45.3 + - - +
464A TYR* 4.3 12.5 - - - -
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Residues in contact with SER 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A TYR 3.1 13.0 + - - -
452A ASP* 2.7 26.6 + - - -
453A TRP 3.2 0.2 - - - -
454A ASN* 1.3 77.3 - - - +
456A ARG* 1.3 65.5 + - - +
457A VAL 3.6 0.8 - - - +
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Residues in contact with ARG 456 (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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452A ASP* 2.9 48.9 + - - +
453A TRP* 3.0 12.9 + - + +
455A SER* 1.3 85.2 - - - +
457A VAL* 1.3 64.9 + - + +
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Residues in contact with VAL 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A TRP* 3.6 55.9 - - + +
454A ASN 3.6 1.9 + - - +
455A SER 3.6 1.1 - - - +
456A ARG* 1.3 88.6 - - + +
458A SER* 1.3 73.9 + - - +
461A GLU* 3.7 25.1 - - + +
462A LYS* 3.5 27.1 + - + -
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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