Contacts of the helix formed by residues 450 - 461 (chain D) 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 GLN 450 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322D PHE* 4.6 12.6 - - - -
325D LEU 4.5 1.6 + - - -
326D GLU* 3.0 35.0 + - - +
327D ASP 3.7 11.5 + - - -
328D CYS 5.1 1.2 + - - -
329D ASP* 4.3 10.9 + - - +
448D THR 3.6 0.6 + - - -
449D THR* 1.3 76.6 - - - +
451D LEU* 1.3 60.3 + - - +
452D ILE 4.7 0.2 - - - +
453D PRO* 3.1 18.2 - - + +
454D ALA* 2.8 27.4 + - - +
474D SER* 3.4 4.9 - - - -
476D THR* 3.5 22.6 + - + +
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Residues in contact with LEU 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330D GLN* 3.4 24.5 + - + +
331D ILE 3.7 14.8 - - - +
332D HIS* 3.7 7.0 - - - +
333D VAL* 3.7 29.8 - - + +
384D TYR* 3.6 29.8 - - + +
450D GLN* 1.3 71.7 - - - +
452D ILE* 1.3 63.2 + - + +
454D ALA* 3.3 4.7 + - - +
455D LEU* 3.0 38.1 + - + +
472D ILE* 4.1 29.6 - - + +
474D SER* 3.1 13.9 + - - -
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Residues in contact with ILE 452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316D ALA* 4.0 10.1 - - + -
320D LEU* 3.8 32.5 - - + +
322D PHE* 3.8 20.9 - - + -
325D LEU* 3.7 40.8 - - + +
384D TYR* 4.2 17.5 - - + +
387D VAL* 4.2 23.3 - - + -
450D GLN* 4.7 0.2 - - - +
451D LEU* 1.3 72.3 - - - +
453D PRO* 1.3 77.1 - - + +
455D LEU* 3.1 11.5 + - + +
456D ALA* 3.0 18.9 + - - +
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Residues in contact with PRO 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312D ILE* 4.1 4.6 - - + +
313D PHE* 4.1 24.2 - - + -
316D ALA* 4.9 3.1 - - + -
322D PHE* 3.5 29.8 - - + -
449D THR* 3.7 15.9 - - + -
450D GLN* 3.1 26.7 - - + +
452D ILE* 1.3 94.4 - - + +
454D ALA* 1.3 55.5 + - - +
456D ALA* 2.9 11.5 + - + +
457D LYS* 2.8 32.4 + - - +
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Residues in contact with ALA 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D LEU* 4.9 3.4 - - + -
445D LEU* 5.8 0.4 - - + -
447D THR* 3.9 22.7 - - + -
449D THR* 3.3 14.5 - - + +
450D GLN 2.8 20.0 + - - +
451D LEU* 3.3 7.6 - - - +
453D PRO* 1.3 77.1 - - - +
455D LEU* 1.3 57.8 + - - +
457D LYS* 3.2 7.6 + - - +
458D VAL* 2.9 36.4 + - + +
472D ILE* 4.9 11.0 - - + -
474D SER* 5.7 0.4 - - - -
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Residues in contact with LEU 455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320D LEU* 4.6 7.0 - - + -
333D VAL* 4.1 17.3 - - + -
387D VAL* 3.5 30.1 - - + -
391D TYR* 4.2 16.5 - - + -
451D LEU* 3.0 25.4 + - + +
452D ILE* 3.1 15.5 + - + +
454D ALA* 1.3 75.3 - - - +
456D ALA* 1.3 61.9 + - - +
458D VAL* 3.6 4.9 + - - +
459D LEU* 3.1 31.2 + - + +
469D ILE* 4.2 14.8 - - + -
472D ILE* 3.7 37.5 - - + -
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Residues in contact with ALA 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312D ILE* 3.6 32.8 - - + +
315D LEU* 4.4 11.0 - - + -
316D ALA* 4.5 3.4 - - + +
320D LEU* 4.3 15.9 - - + +
452D ILE 3.0 10.2 + - - +
453D PRO* 2.9 13.7 + - + +
455D LEU* 1.3 77.0 - - - +
457D LYS* 1.3 65.4 + - - +
459D LEU* 3.3 3.3 + - - +
460D LEU* 3.0 30.2 + - - +
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Residues in contact with LYS 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D LEU* 3.9 14.8 - - + -
276D ASP* 3.0 24.5 + - - +
280D ILE* 4.2 12.3 - - + -
282D PHE* 3.8 20.5 - - + -
283D HIS* 3.4 21.2 + - - -
312D ILE* 3.5 26.7 - - + -
449D THR* 2.8 44.4 + - - +
453D PRO* 2.8 14.0 + - - +
454D ALA 3.2 6.7 + - - +
456D ALA* 1.3 76.3 - - - +
458D VAL* 1.3 57.8 + - - +
460D LEU* 3.2 1.3 + - - -
461D TYR* 2.8 41.2 + - + +
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Residues in contact with VAL 458 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D LEU* 4.5 11.2 - - + -
391D TYR* 3.6 21.8 - - + +
445D LEU* 3.7 30.1 - - + -
454D ALA* 2.9 21.7 + - + +
455D LEU* 3.9 7.0 - - - +
457D LYS* 1.3 76.6 - - - +
459D LEU* 1.3 59.3 + - - +
461D TYR 3.5 0.2 + - - -
462D GLY 3.4 1.7 + - - -
463D LEU* 2.8 51.1 + - + +
464D GLY* 3.1 20.0 + - - +
467D PHE* 4.7 3.4 - - + -
472D ILE* 4.4 7.9 - - + -
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Residues in contact with LEU 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315D LEU* 4.4 26.0 - - + -
320D LEU* 4.7 8.7 - - + -
390D MET* 5.9 0.4 - - + -
391D TYR* 3.9 38.8 - - + +
394D TYR* 4.4 6.5 - - + +
395D LYS* 3.9 31.0 - - + +
398D VAL* 3.5 26.1 - - + +
401D LEU* 4.6 13.7 - - + -
410D TRP* 4.3 1.2 - - - -
455D LEU* 3.1 25.7 + - + +
456D ALA 3.8 3.1 - - - +
458D VAL* 1.3 75.7 - - - +
460D LEU* 1.3 63.3 + - - +
462D GLY* 3.1 14.2 + - - -
464D GLY* 4.5 4.7 + - - +
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Residues in contact with LEU 460 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308D MET* 4.5 13.7 - - + +
311D MET* 3.3 43.1 - - + +
312D ILE* 3.7 15.5 - - + +
315D LEU* 3.7 22.9 - - + -
398D VAL* 3.9 14.8 - - + -
402D ILE* 4.6 7.0 - - + -
410D TRP* 3.0 46.1 + - + +
414D ARG* 3.1 14.7 + - - +
456D ALA 3.0 18.8 + - - +
457D LYS 3.9 2.7 - - - +
459D LEU* 1.3 75.4 - - - +
461D TYR* 1.3 60.0 + - - +
462D GLY 3.3 1.1 - - - -
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Residues in contact with TYR 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D ILE* 3.4 49.1 - - + -
281D ILE 3.0 25.1 + - - -
282D PHE* 3.3 17.5 - - + +
285D LEU* 5.1 0.5 - - - +
308D MET* 3.3 37.3 - - + +
312D ILE* 4.8 3.1 - - + -
414D ARG* 3.6 12.7 + - - +
417D LEU* 3.6 24.9 - - + +
425D LEU* 3.3 41.1 - - + +
429D LEU* 4.7 1.9 - - - +
457D LYS* 2.8 27.6 + - - +
458D VAL 3.5 0.4 + - - +
459D LEU 3.2 0.4 - - - -
460D LEU* 1.3 78.9 - - - +
462D GLY* 1.3 62.5 - - - +
463D LEU* 3.2 10.9 + - + +
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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