Contacts of the helix formed by residues 442 - 453 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382A ILE 3.4 3.2 + - - -
383A VAL* 2.7 26.8 + - - +
384A ALA 4.3 8.5 - - - +
386A GLY* 4.3 8.3 - - - +
423B TYR* 3.7 35.7 - - + -
426B GLN* 4.3 2.0 - - - +
441B LYS* 1.3 75.4 - - + +
443B GLY* 1.3 58.6 + - - +
444B THR 3.4 2.2 - - - -
445B ILE* 3.2 10.7 + - + -
446B THR* 2.9 25.1 + - - +
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Residues in contact with GLY 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A VAL* 3.6 4.4 + - - +
353B ARG* 5.0 1.7 + - - -
378B THR* 3.7 6.9 - - - +
380B ALA* 3.9 15.8 - - - +
439B GLY 4.7 9.0 - - - -
440B PRO 4.7 3.0 + - - -
441B LYS 3.4 4.2 - - - -
442B ALA* 1.3 76.3 - - - +
444B THR* 1.3 62.3 + - - +
446B THR* 3.4 9.0 + - - -
447B ALA* 3.2 23.4 + - - +
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Residues in contact with THR 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A VAL 5.1 0.6 + - - -
378B THR* 2.9 9.5 + - - -
380B ALA* 3.1 7.5 + - - +
381B CYS* 2.8 42.3 + - + -
384B ALA* 5.0 1.9 - - - +
391B GLY* 5.5 1.3 - - - -
393B MET* 3.0 30.2 - - + +
417B LEU* 3.7 28.3 - - + -
442B ALA 3.4 0.4 - - - -
443B GLY* 1.3 76.5 - - - +
445B ILE* 1.3 58.2 + - - +
447B ALA* 3.4 3.1 + - - +
448B GLY 3.1 11.3 + - - -
462B HIS* 4.9 0.7 - - - -
464B ASP* 3.6 19.7 - - + +
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Residues in contact with ILE 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A ALA 3.1 26.9 - - - +
385A LEU* 4.4 0.7 - - + -
393B MET* 3.6 7.0 - - - -
417B LEU* 4.1 21.1 - - + -
418B PRO* 3.3 43.5 - - + +
419B LEU* 3.6 2.2 - - + +
423B TYR* 3.5 46.4 - - + +
442B ALA* 3.2 10.1 + - + +
444B THR* 1.3 74.7 - - - +
446B THR* 1.3 60.9 + - - +
448B GLY* 3.1 2.6 + - - -
449B CYS* 2.8 30.6 + - - -
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Residues in contact with THR 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ARG* 4.7 2.5 + - - -
423B TYR* 4.0 17.0 - - + +
426B GLN* 2.6 36.6 - - + +
427B LEU* 3.8 12.5 - - - +
438B GLY* 4.1 21.8 + - - -
439B GLY 5.1 0.2 + - - -
441B LYS 4.1 3.0 + - - +
442B ALA* 2.9 17.3 + - + +
443B GLY* 3.4 13.5 + - - -
445B ILE* 1.3 75.8 - - - +
447B ALA* 1.3 59.8 + - - +
449B CYS* 3.5 7.2 - - - +
450B PHE* 2.8 28.4 + - - +
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Residues in contact with ALA 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B ARG* 3.7 36.2 - - - +
377B LEU* 4.2 13.5 - - + -
378B THR* 3.8 11.2 - - + -
443B GLY 3.2 17.2 + - - +
444B THR 3.7 4.9 - - - +
446B THR* 1.3 76.3 + - - +
448B GLY* 1.3 65.5 + - - +
450B PHE* 3.2 5.5 + - - +
451B LEU* 3.1 27.8 + - - +
462B HIS* 4.9 1.6 - - + -
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Residues in contact with GLY 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393B MET* 3.3 26.4 - - - +
419B LEU* 4.0 8.1 - - - -
444B THR 3.1 12.5 + - - -
445B ILE 3.1 1.3 + - - -
447B ALA* 1.3 77.0 - - - +
449B CYS* 1.3 55.8 + - - +
451B LEU* 3.2 3.1 + - - +
452B SER* 2.8 25.6 + - - -
460B TRP* 3.5 10.2 - - - -
462B HIS* 4.0 9.6 - - - -
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Residues in contact with CYS 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B LEU* 3.9 14.1 - - - +
420B PHE 4.4 2.7 - - - -
423B TYR* 3.8 26.2 - - - +
424B GLN* 2.2 44.1 - - - +
427B LEU* 4.1 4.7 - - + -
445B ILE* 2.8 21.7 + - - +
446B THR* 3.5 10.8 - - - +
447B ALA 3.2 0.2 - - - -
448B GLY* 1.3 75.5 - - - +
450B PHE* 1.3 64.7 + - - +
452B SER* 2.6 23.4 + - - -
453B ARG* 3.5 10.6 + - - +
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Residues in contact with PHE 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343B VAL* 4.0 14.4 - - + -
353B ARG* 3.5 45.3 - - + -
354B LEU* 4.0 20.0 - - + -
357B CYS* 3.9 3.8 - - + -
427B LEU* 3.5 16.5 - - + +
434B MET* 3.5 24.2 - - + -
435B GLY 3.5 24.0 - - - -
436B ASN* 3.7 15.0 - - + -
446B THR 2.8 14.5 + - - +
447B ALA* 3.2 11.6 + - - +
449B CYS* 1.3 80.4 - - - +
451B LEU* 1.3 65.4 + - - +
453B ARG* 3.3 8.6 + - - +
454B PHE* 3.2 39.2 - + - -
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Residues in contact with LEU 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B ARG* 3.7 24.5 - - + +
356B LEU* 3.6 28.7 - - + -
357B CYS* 4.1 3.8 - - - +
360B LEU* 3.8 17.0 - - + +
373B ASP* 3.2 20.2 - - - +
377B LEU* 4.0 11.4 - - + -
447B ALA 3.1 18.9 + - - +
448B GLY 3.7 2.7 - - - +
450B PHE* 1.3 79.6 - - + +
452B SER* 1.3 64.7 + - - +
454B PHE* 2.9 22.0 + - - +
455B ALA* 3.6 4.3 + - - +
460B TRP* 3.7 14.1 - - + -
462B HIS* 3.4 29.4 - - + +
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Residues in contact with SER 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395B ASN* 5.4 4.9 + - - -
419B LEU* 4.2 8.5 - - - -
424B GLN* 4.1 7.1 + - - -
448B GLY 2.8 15.5 + - - -
449B CYS* 2.6 23.0 + - - -
451B LEU* 1.3 77.6 - - - +
453B ARG* 1.3 60.1 + - - +
454B PHE 3.0 1.6 + - - -
455B ALA* 3.2 11.4 + - - +
456B LYS* 3.7 16.7 - - - +
460B TRP* 3.5 28.0 - - - -
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Residues in contact with ARG 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B SER* 6.0 0.2 - - - -
341B GLN* 3.5 29.1 + - - +
424B GLN* 3.1 54.7 + - - +
427B LEU* 3.9 17.8 + - - +
428B ASP* 4.4 9.5 + - - -
433B ASP 3.7 21.4 + - - -
434B MET* 3.8 27.3 - - - +
449B CYS 3.5 10.1 - - - +
450B PHE* 3.5 9.2 - - - +
451B LEU 3.1 1.0 - - - -
452B SER* 1.3 77.6 - - - +
454B PHE* 1.3 63.4 + - + +
455B ALA 3.6 0.4 - - - -
456B LYS* 4.2 25.6 - - - +
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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