Contacts of the helix formed by residues 442 - 453 (chain A) in PDB entry 3H8E
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 ALA 442 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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423A TYR* 3.7 35.9 - - + -
426A GLN* 4.3 2.2 - - - +
441A LYS* 1.3 74.3 - - + +
443A GLY* 1.3 58.2 + - - +
444A THR 3.3 2.7 - - - -
445A ILE* 3.2 7.9 + - + -
446A THR* 2.8 26.0 + - - +
382B ILE 3.3 3.0 + - - -
383B VAL 2.6 23.4 + - - -
384B ALA 3.9 14.1 - - - +
386B GLY* 4.2 7.6 - - - +
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Residues in contact with GLY 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ARG* 5.1 1.6 + - - -
378A THR* 3.7 6.5 - - - +
380A ALA* 4.0 14.8 - - - +
439A GLY 4.7 8.7 - - - -
440A PRO 4.6 3.5 + - - -
441A LYS 3.3 4.4 - - - -
442A ALA* 1.3 75.8 - - - +
444A THR* 1.4 62.1 + - - +
446A THR* 3.4 9.2 + - - -
447A ALA* 3.1 23.6 + - - +
383B VAL* 3.4 5.5 + - - +
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Residues in contact with THR 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A THR* 2.9 9.3 + - - -
380A ALA* 3.2 9.1 + - - +
381A CYS* 2.8 41.2 + - + -
384A ALA* 5.0 2.0 - - - +
391A GLY* 5.4 1.3 - - - -
393A MET* 3.0 28.1 - - + +
417A LEU* 3.7 28.5 - - + -
442A ALA 3.3 0.8 - - - -
443A GLY* 1.4 77.5 - - - +
445A ILE* 1.4 62.2 + - - +
447A ALA* 3.4 2.9 + - - +
448A GLY 3.1 9.0 + - - -
462A HIS* 4.9 0.5 + - - -
464A ASP* 3.6 20.9 - - + +
383B VAL 5.2 0.2 + - - -
384B ALA 6.1 0.2 - - - -
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Residues in contact with ILE 445 (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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393A MET* 3.6 7.2 - - - -
417A LEU* 4.0 22.0 - - + -
418A PRO* 3.3 43.3 - - + +
419A LEU* 3.6 2.1 - - + +
423A TYR* 3.6 46.9 - - + -
442A ALA* 3.2 9.2 + - + +
444A THR* 1.4 75.2 - - - +
446A THR* 1.4 60.6 + - - +
448A GLY* 3.1 2.6 + - - -
449A CYS* 2.7 31.6 + - - -
384B ALA 3.4 24.9 - - - +
385B LEU* 4.1 4.5 - - + -
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Residues in contact with THR 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ARG* 4.7 4.4 + - - -
423A TYR* 4.1 15.0 - - + +
426A GLN* 2.6 37.5 - - + +
427A LEU* 3.9 12.1 - - - +
438A GLY* 4.1 22.7 + - - -
439A GLY 5.1 0.3 + - - -
441A LYS 4.1 3.5 + - - +
442A ALA* 2.8 19.2 + - + +
443A GLY* 3.4 13.7 + - - -
445A ILE* 1.4 76.5 - - - +
447A ALA* 1.4 59.3 + - - +
449A CYS* 3.2 7.5 + - - +
450A PHE* 2.9 28.9 + - - +
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Residues in contact with ALA 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ARG* 3.7 35.0 - - - +
377A LEU* 4.1 14.6 - - + -
378A THR* 3.7 11.9 - - + -
443A GLY 3.1 16.9 + - - +
444A THR 3.7 4.7 - - - +
446A THR* 1.4 78.1 + - - +
448A GLY* 1.4 61.4 + - - +
450A PHE* 3.3 6.5 + - - +
451A LEU* 3.1 28.8 + - - +
462A HIS* 5.1 0.9 - - - +
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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
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393A MET* 3.4 25.4 - - - +
419A LEU* 3.9 7.6 - - - -
444A THR 3.1 8.5 + - - -
445A ILE 3.1 4.3 + - - -
447A ALA* 1.4 76.4 - - - +
449A CYS* 1.3 57.1 + - - +
451A LEU* 3.2 2.9 + - - +
452A SER* 2.9 29.3 + - - -
460A TRP* 3.5 7.7 - - - -
462A HIS* 3.9 11.2 - - - -
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Residues in contact with CYS 449 (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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419A LEU* 3.8 15.5 - - - +
420A PHE 4.3 4.5 - - - -
423A TYR* 3.8 24.9 - - - -
424A GLN* 2.4 48.6 - - - +
427A LEU* 4.1 6.1 - - + -
445A ILE* 2.7 22.2 + - - +
446A THR* 3.2 11.9 + - - +
448A GLY* 1.3 71.1 - - - +
450A PHE* 1.4 66.9 + - - +
452A SER* 2.6 22.0 + - - -
453A ARG* 3.5 5.4 + - - +
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Residues in contact with PHE 450 (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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343A VAL* 4.0 15.0 - - + -
353A ARG* 3.5 45.5 - - + -
354A LEU* 4.0 20.0 - - + -
357A CYS* 3.8 14.8 - - + -
427A LEU* 3.6 15.7 - - + +
434A MET* 3.5 24.2 - - + -
435A GLY 3.5 24.2 - - - -
436A ASN* 3.7 15.9 - - - -
446A THR 2.9 13.1 + - - +
447A ALA* 3.3 11.9 + - - +
449A CYS* 1.4 75.7 - - - +
451A LEU* 1.3 67.4 + - - +
453A ARG* 3.2 15.5 + - - +
454A PHE* 3.2 23.5 - + - -
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Residues in contact with LEU 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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353A ARG* 3.7 24.7 - - + +
356A LEU* 3.7 29.4 - - + -
357A CYS* 4.1 3.4 - - - +
360A LEU* 3.9 16.8 - - + +
373A ASP* 3.2 19.7 - - - +
377A LEU* 4.0 9.9 - - + -
447A ALA 3.1 18.5 + - - +
448A GLY 3.2 3.3 + - - +
450A PHE* 1.3 80.2 - - + +
452A SER* 1.3 58.5 + - - +
454A PHE* 2.9 29.5 + - - +
455A ALA* 3.6 4.7 + - - +
460A TRP* 3.6 14.6 - - + -
462A HIS* 3.5 29.6 - - + +
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Residues in contact with SER 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A ASN* 5.3 4.6 + - - -
419A LEU* 4.2 8.9 - - - +
424A GLN* 4.0 9.9 + - - -
448A GLY 2.9 14.5 + - - -
449A CYS* 2.6 22.3 + - - -
451A LEU* 1.3 75.9 - - - +
453A ARG* 1.3 58.9 + - - +
454A PHE 3.0 5.0 + - - -
455A ALA* 3.2 13.0 + - - +
456A LYS* 3.7 16.6 + - - +
460A TRP* 3.5 26.9 - - - -
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Residues in contact with ARG 453 (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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341A GLN* 3.4 29.3 + - - +
424A GLN* 3.1 51.9 + - - +
427A LEU* 3.8 18.5 - - - +
428A ASP* 4.4 9.9 + - - -
433A ASP 3.8 9.9 + - - -
434A MET* 3.8 40.0 - - - +
449A CYS 3.5 11.0 - - - +
450A PHE* 3.5 8.7 - - - +
451A LEU 3.0 1.2 + - - -
452A SER* 1.3 77.9 - - - +
454A PHE* 1.3 63.1 + - + +
455A ALA 3.5 0.4 - - - -
456A LYS* 4.4 28.2 - - - +
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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