Contacts of the helix formed by residues 423 - 438 (chain A) in PDB entry 3HB0
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 LEU 423 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A GLU* 2.9 48.0 + - + +
419A ALA* 5.1 3.1 - - - -
422A ASP* 1.3 81.5 - - - +
424A TRP* 1.3 68.4 + - - +
425A LEU 3.3 2.5 - - - -
426A THR* 3.1 24.1 + - + +
427A HIS* 3.1 23.7 + - + +
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Residues in contact with TRP 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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277A GLU 4.1 12.6 - - - -
278A THR 3.1 28.3 + - - -
279A ILE 3.6 17.5 + - - -
280A ILE* 4.4 1.3 - - - -
281A ILE* 3.4 42.7 - - + +
290A PHE* 4.1 6.1 - + - -
294A TYR* 3.9 8.7 - - - -
421A THR* 3.3 20.2 + - - +
422A ASP 3.3 0.2 - - - -
423A LEU* 1.3 74.8 - - - +
425A LEU* 1.3 58.6 + - - +
427A HIS* 2.8 21.3 + - - +
428A SER 3.0 10.6 + - - -
520A ILE* 4.0 13.2 - - + -
521A SER 4.1 5.6 - - - -
522A CYS* 3.5 29.2 - - - -
523A HIS* 3.4 49.8 - + - -
526A LEU* 3.7 10.4 - - + +
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Residues in contact with LEU 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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279A ILE 3.9 10.8 - - - +
280A ILE* 4.3 15.3 - - + -
414A ARG* 3.2 38.4 - - - +
417A LEU* 5.4 4.9 - - + -
418A GLU* 3.1 21.4 + - + +
421A THR* 5.0 0.2 + - - -
423A LEU 3.3 0.4 - - - -
424A TRP* 1.3 75.5 - - - +
426A THR* 1.3 63.0 + - - +
428A SER* 3.2 14.8 + - - +
429A LEU* 2.9 43.8 + - + +
461A TYR* 3.5 28.9 - - + +
463A LEU* 4.3 7.6 - - + -
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Residues in contact with THR 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A GLU* 2.7 22.3 + - - -
423A LEU* 3.1 27.0 + - + +
425A LEU* 1.3 80.0 - - - +
427A HIS* 1.3 65.3 + - + +
429A LEU* 3.6 8.7 + - - +
430A LYS* 3.2 44.9 + - - +
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Residues in contact with HIS 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A ASP 4.0 5.9 + - - -
423A LEU* 3.1 28.0 + - + +
424A TRP 2.8 7.5 + - - +
426A THR* 1.3 77.6 - - + +
428A SER* 1.3 66.4 + - - +
430A LYS* 3.2 38.8 + - - +
431A ALA* 3.6 4.5 + - - +
523A HIS* 3.3 39.9 - + + +
526A LEU* 4.0 27.2 - - + +
527A GLU* 5.5 8.3 + - + +
530A ARG* 5.5 0.7 - - - +
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Residues in contact with SER 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A TRP* 4.5 1.6 - - - -
279A ILE* 2.7 50.4 + - - +
424A TRP 3.0 5.0 + - - -
425A LEU* 3.2 14.2 + - - +
427A HIS* 1.3 75.8 - - - +
429A LEU* 1.3 65.0 + - - +
431A ALA* 3.0 7.5 + - - +
432A LEU* 3.0 25.5 + - - +
526A LEU* 3.8 27.7 - - - +
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Residues in contact with LEU 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ARG* 5.6 2.5 - - - +
425A LEU* 2.9 43.7 + - + +
426A THR* 3.8 7.2 - - - +
428A SER* 1.3 78.8 + - - +
430A LYS* 1.3 53.7 + - - +
432A LEU* 4.0 9.6 - - + -
433A ASN* 2.7 58.7 + - - +
461A TYR 5.2 1.3 - - - +
462A GLY 4.4 13.5 - - - +
463A LEU* 3.7 25.6 - - + -
466A VAL* 4.9 5.6 - - + -
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Residues in contact with LYS 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A THR* 3.2 31.4 + - + +
427A HIS* 3.2 28.0 + - - +
429A LEU* 1.3 78.5 - - - +
431A ALA* 1.3 59.8 + - - +
433A ASN* 4.4 4.9 - - - +
434A LEU* 3.5 22.0 + - - +
527A GLU* 5.9 0.7 - - - +
530A ARG* 3.8 30.9 - - - +
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Residues in contact with ALA 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A TRP* 3.9 19.3 - - + -
427A HIS 3.6 4.8 + - - +
428A SER* 3.0 9.7 + - - +
430A LYS* 1.3 77.9 - - - +
432A LEU* 1.3 66.3 + - - +
433A ASN 3.2 0.2 - - - -
434A LEU 3.2 1.0 + - - -
435A ILE* 3.0 30.0 + - - +
526A LEU* 4.6 7.0 - - + +
529A LEU* 4.1 9.2 - - + -
530A ARG* 4.3 10.7 - - - +
533A LEU* 3.5 21.8 - - + +
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Residues in contact with LEU 432 (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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273A TRP* 3.5 35.7 - - + +
279A ILE* 3.8 31.9 - - + -
428A SER 3.0 23.7 + - - +
429A LEU* 3.6 10.8 - - + +
431A ALA* 1.3 76.9 - - - +
433A ASN* 1.3 56.5 + - - +
435A ILE* 4.4 1.8 - - - -
436A ASN 3.0 21.0 + - - -
443A ASN* 3.0 20.9 + - - +
463A LEU* 3.8 18.6 - - + -
466A VAL* 3.4 17.5 - - + +
467A PHE* 3.5 24.7 - - + -
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Residues in contact with ASN 433 (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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429A LEU* 2.7 48.0 + - - +
430A LYS* 4.5 4.6 - - - +
432A LEU* 1.3 71.2 - - - +
434A LEU* 1.3 61.6 + - - +
436A ASN* 3.8 7.7 - - - +
437A SER* 3.0 29.8 + - - -
465A SER* 5.7 0.7 + - - -
466A VAL* 4.3 13.2 - - - +
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Residues in contact with LEU 434 (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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430A LYS 3.5 14.5 + - - +
431A ALA 3.2 4.8 + - - +
433A ASN* 1.3 75.5 - - - +
435A ILE* 1.3 66.0 + - - +
437A SER* 3.2 11.1 + - - +
438A ARG* 3.0 35.1 + - + +
530A ARG* 3.8 17.3 - - + +
533A LEU* 3.7 33.4 - - + +
534A GLU* 3.8 28.3 - - + +
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Residues in contact with ILE 435 (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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271A PHE* 3.4 34.5 - - + -
273A TRP* 3.6 25.6 - - + +
431A ALA 3.0 17.2 + - - +
432A LEU 3.5 4.0 - - - +
434A LEU* 1.3 77.4 - - - +
436A ASN* 1.3 61.6 + - - +
438A ARG* 3.2 17.4 + - - +
441A CYS* 3.5 15.4 - - + +
442A VAL* 3.7 23.1 - - - +
443A ASN* 3.2 31.9 - - - +
529A LEU* 5.1 0.2 - - + -
533A LEU* 3.6 25.8 - - + -
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Residues in contact with ASN 436 (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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432A LEU 3.0 18.9 + - - +
433A ASN* 3.8 10.6 - - - +
435A ILE* 1.3 79.9 - - - +
437A SER* 1.3 62.2 + - - +
438A ARG 3.3 6.2 + - - +
441A CYS 4.9 2.2 - - - +
442A VAL* 6.2 0.2 - - - +
443A ASN* 4.2 8.5 - - - +
465A SER 4.0 15.3 - - - +
466A VAL* 4.3 13.8 + - + +
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Residues in contact with SER 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A ASN 3.0 19.2 + - - -
434A LEU* 3.2 17.0 + - - +
436A ASN* 1.3 77.4 - - - +
438A ARG* 1.3 65.0 + - - +
439A PRO* 3.3 7.4 - - - +
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Residues in contact with ARG 438 (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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434A LEU* 3.0 29.3 + - + +
435A ILE 3.2 15.1 - - - +
436A ASN 3.2 5.2 - - - +
437A SER* 1.3 80.3 - - - +
439A PRO* 1.4 72.1 - - + +
440A ASN 3.4 1.3 - - - +
441A CYS* 3.4 32.9 + - - +
532A ALA 4.5 0.2 + - - -
533A LEU* 2.7 56.2 + - - +
536A GLU* 2.8 50.0 + - - +
537A TYR* 5.5 0.2 - - - +
538A LEU* 3.2 30.5 - - - +
537D TYR* 4.8 1.0 + - - -
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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