Contacts of the helix formed by residues 466 - 479 (chain B) in PDB entry 4HXG
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 466 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B GLY* 4.4 9.0 - - - -
387B GLY 5.1 1.6 - - - +
465B ILE* 1.3 78.1 - - + +
467B TYR* 1.3 58.1 - - - +
469B GLY* 2.7 22.0 + - - -
470B TYR* 2.9 10.2 + - - +
488B GLU 2.8 13.1 + - - -
489B ASN 3.0 16.8 + - - -
490B GLY* 3.3 7.4 - - - -
491B ILE* 4.5 4.5 - - - -
549B CYS* 4.3 3.4 - - - -
578B HIS* 3.3 29.2 - - + +
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Residues in contact with TYR 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B VAL* 5.2 2.5 - - + -
385B HIS* 4.5 10.3 - + - -
386B GLY* 4.2 0.2 - - - -
387B GLY* 3.4 29.4 - - - +
388B PRO* 4.1 32.5 - - + -
415B PRO* 6.4 2.0 - - + -
429B VAL* 4.2 1.0 - - - +
433B THR* 3.2 38.0 - - + +
437B ASP* 2.7 28.6 + - - -
465B ILE 3.2 0.2 + - - -
466B ALA* 1.3 81.4 - - - +
468B GLY* 1.3 57.6 + - - +
470B TYR* 3.2 30.2 + + - +
471B MET* 2.9 39.4 + - + +
491B ILE* 4.8 4.1 - - + +
494B TRP* 4.1 15.9 - + - -
507B PHE* 6.4 0.2 - + - -
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Residues in contact with GLY 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B VAL* 3.2 38.9 - - - +
385B HIS 3.5 3.8 + - - -
464B GLY* 3.5 8.4 - - - -
465B ILE 2.8 9.6 + - - -
467B TYR* 1.3 79.5 - - - +
469B GLY* 1.3 57.2 + - - +
471B MET* 3.7 2.3 + - - +
472B THR* 2.8 30.0 + - - -
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Residues in contact with GLY 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B GLY 3.5 18.7 - - - -
466B ALA 2.7 10.8 + - - -
468B GLY* 1.3 77.1 - - - +
470B TYR* 1.3 57.7 + - - -
472B THR* 3.6 3.3 - - - -
473B ASN* 2.9 35.7 + - - -
487B SER* 3.3 14.8 + - - -
488B GLU 4.1 7.0 - - - -
490B GLY* 4.2 3.6 - - - -
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Residues in contact with TYR 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B THR* 3.3 21.3 + - - -
434B GLY* 3.8 13.0 + - - -
466B ALA 2.9 5.9 + - - +
467B TYR* 3.3 52.0 - + + +
469B GLY* 1.3 75.9 - - - +
471B MET* 1.3 60.4 + - + +
473B ASN* 3.2 4.0 + - - +
474B TRP* 2.8 43.7 + + + +
491B ILE* 3.3 41.1 - - + +
494B TRP* 3.3 27.8 + + - -
525B LEU* 2.7 30.6 + - - -
527B PRO* 3.3 14.1 - - + -
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Residues in contact with MET 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B VAL* 3.8 16.2 - - + -
415B PRO* 5.9 1.1 - - + -
434B GLY* 4.8 3.1 - - - -
437B ASP* 3.3 35.2 - - + +
438B PHE* 3.9 33.2 - - + +
441B ILE* 3.5 31.4 - - + -
462B ILE* 5.0 4.0 - - + -
467B TYR* 2.9 32.6 + - + +
468B GLY 3.8 5.2 - - - +
470B TYR* 1.3 78.0 - - + +
472B THR* 1.3 53.7 + - - +
474B TRP* 3.3 12.5 - - - +
475B ALA* 2.6 37.9 + - - +
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Residues in contact with THR 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B VAL* 5.3 0.2 - - - +
462B ILE* 3.8 30.0 - - + +
463B THR* 3.5 23.6 + - - -
464B GLY 3.5 0.7 + - - -
468B GLY 2.8 21.9 + - - -
469B GLY* 3.6 8.5 - - - -
471B MET* 1.3 72.9 - - - +
473B ASN* 1.3 67.6 + - - +
475B ALA* 3.2 7.3 + - - +
476B LEU* 3.1 24.7 + - + +
485B GLY* 4.5 4.5 - - - -
486B ILE 4.0 9.9 - - - +
487B SER* 3.9 18.2 - - - -
538B LEU* 4.5 5.2 - - + -
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Residues in contact with ASN 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B GLY 2.9 20.0 + - - -
470B TYR 3.4 5.6 - - - +
472B THR* 1.3 76.8 - - - +
474B TRP* 1.3 63.9 + - - +
476B LEU* 3.3 6.5 + - - +
477B THR* 3.2 24.1 + - - +
487B SER* 2.9 27.2 + - - -
490B GLY 4.9 1.4 - - - -
491B ILE 3.5 25.9 + - - +
492B SER* 3.9 3.8 - - - +
527B PRO* 3.6 14.6 - - + -
538B LEU* 4.3 3.5 - - - +
540B LEU* 4.0 3.0 - - - +
553B GLN 5.0 2.4 + - - -
557B PHE* 3.3 39.7 - - + -
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Residues in contact with TRP 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B GLY* 2.6 44.5 + - - -
435B LEU* 5.0 4.5 - - + -
438B PHE* 3.6 30.3 - + + -
470B TYR* 2.8 25.1 + + + +
471B MET* 3.3 15.7 - - - +
473B ASN* 1.3 71.4 - - - +
475B ALA* 1.3 66.4 + - - +
477B THR* 2.7 26.1 + - - -
478B GLN* 2.8 42.8 + - + +
524B LYS 3.5 17.7 - - - -
525B LEU* 3.8 29.6 - - + -
527B PRO* 3.6 21.1 - - + +
530B TYR* 3.8 16.2 - + - -
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Residues in contact with ALA 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B PHE* 3.8 21.1 - - + -
462B ILE* 4.0 16.8 - - + -
471B MET 2.6 20.3 + - - +
472B THR 3.2 4.9 + - - +
474B TRP* 1.3 71.8 - - - +
476B LEU* 1.3 60.2 + - - +
479B SER* 2.9 35.3 + - - +
482B PHE* 3.7 28.5 - - + -
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Residues in contact with LEU 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B ILE* 4.7 5.6 - - + -
472B THR* 3.1 16.3 + - + +
473B ASN* 3.8 7.6 - - - +
475B ALA* 1.3 78.2 - - - +
477B THR* 1.3 58.9 + - - +
479B SER 3.9 12.3 - - - +
482B PHE* 4.1 25.6 - - + +
484B ALA 4.6 7.0 - - - +
485B GLY* 4.5 6.7 - - - +
533B ASN 3.8 3.6 - - - +
534B VAL* 3.5 46.1 - - + +
535B LYS 4.6 1.2 + - - -
536B ALA* 3.8 26.2 - - + +
538B LEU* 3.9 38.8 - - + -
557B PHE* 6.2 0.4 - - + -
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Residues in contact with THR 477 (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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473B ASN 3.2 11.6 + - - +
474B TRP* 2.7 27.9 + - - -
476B LEU* 1.3 79.0 - - - +
478B GLN* 1.3 73.1 + - - +
479B SER 3.5 0.8 + - - -
527B PRO* 3.6 25.8 - - + +
530B TYR* 3.4 28.2 - - + +
531B ALA 4.3 0.4 - - - +
533B ASN* 3.1 32.4 + - - +
534B VAL* 3.8 15.0 - - + -
557B PHE* 4.4 3.8 - - + -
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Residues in contact with GLN 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B PHE* 3.6 22.5 - - + -
474B TRP* 2.8 58.8 + - + +
477B THR* 1.3 86.5 + - - +
479B SER* 1.3 60.9 + - - +
530B TYR* 3.2 38.6 - - - +
533B ASN* 5.1 1.8 + - - -
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Residues in contact with SER 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B PHE* 4.3 15.3 - - - -
442B LEU* 4.6 7.6 - - - +
475B ALA 2.9 17.5 + - - +
476B LEU* 3.9 12.3 - - - +
477B THR 3.5 2.2 + - - -
478B GLN* 1.3 81.9 - - - +
480B ASP* 1.3 68.0 + - - +
481B LEU* 2.9 25.5 + - - +
482B PHE* 4.1 13.0 + - - +
533B ASN 5.7 0.5 - - - +
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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
------------------------------------------------------------
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