Contacts of the helix formed by residues 434 - 451 (chain B) in PDB entry 2HX4
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 THR 434 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432B CYS* 3.5 1.4 - - - -
433B THR* 1.3 95.3 + - - +
435B ALA* 1.3 59.9 + - - +
436B HIS* 3.6 10.4 + - - +
437B GLY* 3.0 19.1 + - - +
438B MET* 2.9 27.9 + - - +
526B ALA* 3.4 9.2 - - - -
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Residues in contact with ALA 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B THR* 1.3 71.1 - - - +
436B HIS* 1.3 59.1 + - - +
438B MET* 3.1 11.0 + - - +
439B PHE* 2.8 27.5 + - - +
524B LEU* 3.6 26.7 - - - +
526B ALA* 3.4 13.9 - - + +
530B ASP 5.8 0.4 - - - +
532B GLU* 3.8 24.5 + - - +
534B PHE* 3.7 18.6 - - + -
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Residues in contact with HIS 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B THR* 3.2 9.5 + - - +
435B ALA* 1.3 75.5 - - - +
437B GLY* 1.3 65.5 + - - +
439B PHE* 3.3 9.0 + + - +
440B ASN* 3.1 21.7 + - - +
532B GLU* 3.9 16.6 + - - -
534B PHE* 3.4 33.0 - + - -
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Residues in contact with GLY 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B CYS* 3.5 14.4 - - - -
433B THR 5.7 0.4 - - - -
434B THR* 3.0 16.6 + - - -
436B HIS* 1.3 80.2 - - - +
438B MET* 1.3 61.9 + - - +
440B ASN* 3.2 7.7 + - - +
441B TYR* 3.0 29.4 + - - -
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Residues in contact with MET 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B CYS* 3.4 12.1 - - - -
434B THR 2.9 14.7 + - - +
435B ALA* 3.1 9.2 + - - +
437B GLY* 1.3 76.4 - - - +
439B PHE* 1.3 62.7 - - - +
441B TYR* 3.2 2.3 + - - +
442B ILE* 2.9 31.0 + - + +
462B PHE* 3.7 31.0 - - + -
472B PHE* 4.0 5.8 - - + -
473B ARG 3.5 27.6 - - - +
474B VAL* 4.0 19.1 - - + -
524B LEU* 4.1 13.7 - - + -
525B GLN 3.2 30.7 - - - +
526B ALA* 3.7 12.3 - - + -
581B ALA* 4.7 1.1 - - + -
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Residues in contact with PHE 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B ALA 2.8 13.1 + - - +
436B HIS* 3.5 12.6 - + - +
437B GLY 3.2 0.2 - - - -
438B MET* 1.3 78.8 - - - +
440B ASN* 1.3 64.0 + - + +
442B ILE* 3.8 2.7 - - - +
443B CYS* 3.0 52.6 + - - -
522B LEU* 3.8 17.3 - - + -
524B LEU* 3.6 12.3 - - + +
534B PHE* 3.3 42.2 - + + -
535B GLN 3.3 30.7 - - - -
536B ILE* 4.3 0.9 - - - -
537B PRO* 4.1 7.4 - - + -
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Residues in contact with ASN 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B HIS 3.1 13.2 + - - +
437B GLY* 3.6 11.4 + - - +
438B MET 3.2 0.2 - - - -
439B PHE* 1.3 84.7 - - + +
441B TYR* 1.3 70.0 + - - +
443B CYS* 3.4 5.9 + - - +
444B ASN* 3.1 46.0 + - - +
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Residues in contact with TYR 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B PHE* 5.5 6.1 - - + -
428B ASP 3.8 12.4 + - - -
429B ALA* 3.6 30.1 - - + -
431B ASP* 2.6 34.2 + - - -
432B CYS* 4.0 13.2 - - + -
437B GLY* 3.0 25.6 + - - -
438B MET 3.2 6.5 + - - +
440B ASN* 1.3 81.5 - - + +
442B ILE* 1.3 56.4 + - - +
444B ASN* 3.1 14.1 + - + +
445B HIS* 2.9 28.3 + - - +
460B THR* 4.1 10.5 + - + -
462B PHE* 3.8 18.8 - + + -
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Residues in contact with ILE 442 (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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438B MET* 2.9 18.1 + - + +
439B PHE 3.8 3.1 - - - +
441B TYR* 1.3 71.3 - - - +
443B CYS* 1.3 60.8 + - - +
445B HIS* 3.1 7.3 + - - +
446B VAL* 2.8 34.4 + - + +
460B THR* 5.4 1.1 - - + -
462B PHE* 3.9 16.8 - - + -
474B VAL* 4.1 17.7 - - + -
479B LEU* 3.8 36.1 - - + -
522B LEU* 3.9 20.0 - - + -
524B LEU* 3.8 31.9 - - + -
536B ILE* 5.4 1.1 - - + -
583B PRO* 4.8 5.2 - - + -
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Residues in contact with CYS 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B PHE* 3.0 60.8 + - - +
440B ASN* 3.7 7.9 - - - +
442B ILE* 1.3 75.4 - - - +
444B ASN* 1.3 61.8 + - - +
446B VAL* 3.1 6.6 + - - +
447B LYS* 2.9 29.9 + - - +
522B LEU* 5.6 0.7 - - - -
536B ILE* 5.1 5.2 - - - -
537B PRO* 3.7 21.3 - - - -
540B LEU* 3.9 16.4 - - + +
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Residues in contact with ASN 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B PHE* 5.0 2.5 - - + -
440B ASN* 3.1 36.9 + - - +
441B TYR* 3.1 15.0 + - + +
443B CYS* 1.3 76.6 - - - +
445B HIS* 1.3 66.1 + - - +
447B LYS* 4.1 5.8 - - - +
448B TYR* 3.0 26.2 + - - +
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Residues in contact with HIS 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B PHE* 4.6 14.1 - + + -
441B TYR 2.9 9.5 + - - +
442B ILE* 3.4 12.1 - - - +
444B ASN* 1.3 79.4 - - - +
446B VAL* 1.3 61.6 + - + +
448B TYR* 3.7 1.0 - - - +
449B ALA* 2.8 32.9 + - + +
458B ALA* 3.4 28.7 + - + +
459B ILE* 3.6 1.9 - - - -
460B THR* 2.7 31.6 + - - +
479B LEU* 4.7 13.3 - - + +
564B LEU* 5.1 1.1 - - + -
583B PRO* 3.3 26.4 + - - +
584B PHE* 4.0 3.4 - - - -
585B SER* 2.9 28.2 + - - -
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Residues in contact with VAL 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B ILE* 2.8 24.8 + - + +
443B CYS* 3.7 6.5 - - - +
445B HIS* 1.3 76.8 - - - +
447B LYS* 1.3 56.8 + - - +
450B THR* 2.6 41.8 + - - +
479B LEU* 4.1 24.5 - - + -
480B ILE* 4.4 17.7 - - + -
536B ILE* 5.2 10.5 - - + -
540B LEU* 3.4 33.0 - - + +
564B LEU* 4.2 19.1 - - + -
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Residues in contact with LYS 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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443B CYS 2.9 15.4 + - - +
444B ASN* 4.1 7.4 - - - +
446B VAL* 1.3 75.6 - - - +
448B TYR* 1.3 66.3 + - - +
450B THR* 4.0 2.9 - - - -
451B ASN* 3.1 21.1 + - - -
456B ARG* 4.8 0.5 + - - -
540B LEU* 4.1 31.0 - - + +
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Residues in contact with TYR 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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425B GLN* 3.3 46.0 + - + +
427B PHE* 3.5 31.4 - + + -
444B ASN 3.0 18.6 + - - +
445B HIS 3.7 2.0 - - - +
447B LYS* 1.3 78.4 - - - +
449B ALA* 1.3 68.4 + - - +
451B ASN 3.5 3.1 + - - -
456B ARG* 2.8 86.7 + - + +
457B SER 4.3 2.2 - - - -
458B ALA* 4.1 4.0 - - + -
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Residues in contact with ALA 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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445B HIS* 2.8 24.0 + - + +
446B VAL 4.3 1.1 - - - +
448B TYR* 1.3 78.6 - - - +
450B THR* 1.3 63.6 + - - +
451B ASN* 3.5 0.5 + - - +
455B LEU* 3.2 7.3 - - - +
456B ARG 2.9 44.7 + - - +
458B ALA* 4.6 4.0 - - + -
564B LEU* 3.9 12.8 - - + -
585B SER* 3.7 20.4 - - - +
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Residues in contact with THR 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B VAL* 2.6 34.0 + - - +
447B LYS* 4.1 3.6 - - - -
449B ALA* 1.3 78.2 - - - +
451B ASN* 1.3 71.4 + - - +
452B LYS* 4.1 7.2 - - - +
453B GLY 2.9 13.2 + - - -
454B ASN 3.5 1.2 + - - -
455B LEU* 3.4 17.6 - - + +
540B LEU 4.2 7.0 + - - +
542B LEU* 3.7 41.2 + - + +
564B LEU* 4.0 15.7 - - + +
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Residues in contact with ASN 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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447B LYS 3.1 16.5 + - - -
448B TYR 3.5 12.8 - - - +
449B ALA 4.1 0.7 - - - +
450B THR* 1.3 74.9 - - - +
452B LYS* 1.3 68.9 + - - +
453B GLY 3.1 1.6 + - - -
454B ASN* 3.0 47.8 + - - +
456B ARG* 3.5 37.4 + - - +
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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
------------------------------------------------------------
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