Contacts of the helix formed by residues 485 - 507 (chain D) in PDB entry 4XH9
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 ASP 485 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464D ASN* 3.4 17.7 - - - +
483D ALA* 3.3 1.3 - - - +
484D ASN* 1.3 87.7 - - - +
486D VAL* 1.3 62.3 + - + +
487D PHE* 3.2 6.7 + - + +
488D HIS* 2.7 35.7 + - - +
489D LYS* 3.0 28.4 + - - +
104E LYS* 3.4 35.6 + - - +
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Residues in contact with VAL 486 (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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443D ASP* 5.9 0.9 - - - +
464D ASN* 3.3 22.9 + - - +
485D ASP* 1.3 76.3 - - + +
487D PHE* 1.3 70.8 + - + +
489D LYS* 3.4 10.8 + - + +
490D GLN* 3.2 28.0 + - - +
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Residues in contact with PHE 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485D ASP* 3.2 7.6 + - - +
486D VAL* 1.3 85.6 - - + +
488D HIS* 1.3 65.9 + - - +
490D GLN* 3.2 9.4 + - + +
491D GLN 3.1 16.1 + - - -
96E PRO* 3.4 47.3 - - + -
100E THR* 3.6 27.6 - - + -
101E PRO* 3.3 21.6 - - + +
104E LYS* 4.0 7.0 - - + -
147E MET* 5.6 0.2 - - - -
150E ARG* 3.3 36.1 - - + -
151E ILE* 4.0 12.1 - - + -
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Residues in contact with HIS 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392D GLU 4.2 7.0 - - - -
393D LEU* 4.0 10.5 - - + -
483D ALA* 3.5 2.6 - - - +
484D ASN* 3.0 45.1 + - - -
485D ASP* 2.7 35.3 + - - +
487D PHE* 1.3 71.2 - - - +
489D LYS* 1.3 64.5 + - - +
491D GLN* 3.1 11.6 + - + +
492D TRP* 3.3 28.4 + + - -
104E LYS* 4.0 9.8 - - + +
105E HIS* 3.1 50.9 + - + -
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Residues in contact with LYS 489 (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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440D ASP* 2.6 30.7 + - - -
441D LEU 3.2 7.9 + - - -
443D ASP* 5.3 1.8 + - - -
464D ASN* 3.8 22.7 - - + +
465D ILE 2.9 27.3 + - - +
466D PHE* 4.1 21.0 - - + -
483D ALA* 3.5 15.8 - - + +
485D ASP 3.0 12.3 + - - +
486D VAL* 3.5 13.2 - - + +
488D HIS* 1.3 76.2 - - - +
490D GLN* 1.3 56.9 + - - +
492D TRP* 3.2 6.1 + - - +
493D PHE* 2.7 45.2 + - + +
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Residues in contact with GLN 490 (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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486D VAL* 3.2 14.5 + - - +
487D PHE* 3.3 18.6 - - + +
488D HIS 3.2 0.2 - - - -
489D LYS* 1.3 86.3 - - - +
491D GLN* 1.3 56.2 + - - +
493D PHE* 4.4 8.0 - - - +
494D ASN* 2.9 61.4 + - - +
96E PRO 5.3 3.4 - - - +
97E GLU* 5.3 8.0 + - - +
101E PRO* 4.2 12.6 - - + -
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Residues in contact with GLN 491 (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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389D CYS* 3.4 28.5 - - - -
487D PHE 3.1 4.8 + - - -
488D HIS* 3.1 11.0 + - + +
490D GLN* 1.3 76.5 - - - +
492D TRP* 1.3 61.6 + - - +
494D ASN* 4.3 2.5 - - - +
495D CYS* 3.2 40.2 + - - +
101E PRO* 3.1 42.6 - - + +
102E GLU* 3.7 15.1 + - - +
105E HIS* 3.6 19.1 + - + -
106E PHE* 4.3 14.6 - - - -
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Residues in contact with TRP 492 (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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389D CYS* 3.8 24.5 - - + -
390D HIS* 3.7 13.2 - - - -
391D GLY* 3.5 28.7 - - - -
392D GLU 4.6 1.2 + - - -
393D LEU* 3.6 33.4 - - + +
403D ILE* 3.5 46.0 - - + -
405D LEU* 4.4 7.0 - - + -
466D PHE* 4.0 17.0 - - + -
483D ALA* 5.0 0.7 - - + -
488D HIS* 3.3 37.3 + + - +
489D LYS* 3.2 6.6 + - - +
491D GLN* 1.3 78.7 - - - +
493D PHE* 1.3 66.1 + - - +
495D CYS* 3.3 3.6 + - - +
496D ILE* 3.0 48.7 + - + +
105E HIS* 3.6 9.9 - + - -
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Residues in contact with PHE 493 (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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438D LEU* 3.6 44.3 - - + +
439D GLU 4.0 0.9 - - - -
440D ASP* 3.6 44.9 - - + -
466D PHE* 4.0 17.2 - + + -
489D LYS* 2.7 34.1 + - + +
490D GLN* 4.1 9.0 - - - +
492D TRP* 1.3 75.1 - - - +
494D ASN* 1.3 62.1 + - - +
496D ILE* 4.9 2.2 - - - -
497D ARG* 2.9 49.6 + - + +
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Residues in contact with ASN 494 (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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490D GLN* 2.9 50.6 + - - +
491D GLN* 4.3 2.6 - - - +
493D PHE* 1.3 83.3 - - - +
495D CYS* 1.3 57.6 + - - +
497D ARG* 3.9 14.1 + - - +
498D ALA* 2.9 33.4 + - - +
97E GLU* 4.6 20.6 + - - -
101E PRO* 5.5 1.4 - - - +
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Residues in contact with CYS 495 (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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388D LEU* 4.3 15.6 - - + +
389D CYS* 3.8 22.9 - - + -
405D LEU* 3.7 16.8 - - + +
491D GLN* 3.2 36.6 + - - +
492D TRP* 3.6 4.3 - - + +
493D PHE 3.3 0.2 - - - -
494D ASN* 1.3 81.0 - - - +
496D ILE* 1.3 57.3 + - - +
498D ALA* 3.5 4.3 + - - +
499D ALA* 3.0 27.9 + - - +
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Residues in contact with ILE 496 (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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403D ILE* 6.2 0.4 - - + -
405D LEU* 3.8 21.1 - - + -
410D LEU* 4.3 11.9 - - + -
436D LEU* 3.7 27.8 - - + -
438D LEU* 4.0 17.5 - - + -
466D PHE* 3.9 27.4 - - + -
468D ILE* 4.3 11.2 - - + -
481D LEU* 6.0 0.7 - - + -
492D TRP* 3.0 34.3 + - + +
493D PHE 3.9 2.7 - - - +
495D CYS* 1.3 73.9 - - - +
497D ARG* 1.3 66.0 - - - +
499D ALA* 3.2 2.8 + - - +
500D ILE* 3.0 32.6 + - + +
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Residues in contact with ARG 497 (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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438D LEU* 3.8 13.2 - - + +
493D PHE* 2.9 36.8 + - - +
494D ASN* 3.9 13.0 + - - +
496D ILE* 1.3 78.3 - - - +
498D ALA* 1.3 57.8 + - - +
500D ILE* 3.4 6.7 + - - +
501D ALA* 2.9 29.8 + - + +
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Residues in contact with ALA 498 (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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494D ASN 2.9 18.8 + - - +
495D CYS* 3.8 5.4 - - - +
497D ARG* 1.3 73.9 - - - +
499D ALA* 1.3 62.1 + - - +
501D ALA* 3.7 6.4 - - - +
502D HIS* 2.8 32.7 + - - +
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Residues in contact with ALA 499 (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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388D LEU* 3.7 26.0 - - + +
405D LEU* 4.4 14.6 - - + -
407D GLN* 4.4 9.2 - - - +
433D VAL* 3.5 18.3 - - + +
436D LEU* 6.1 0.2 - - + -
495D CYS 3.0 18.8 + - - +
496D ILE* 3.5 5.8 - - + +
498D ALA* 1.3 77.0 - - - +
500D ILE* 1.3 62.4 + - + +
502D HIS* 3.3 7.0 + - - +
503D HIS* 3.1 18.5 + - - +
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Residues in contact with ILE 500 (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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433D VAL* 3.8 14.1 - - + +
436D LEU* 3.7 40.4 - - + +
438D LEU* 3.8 31.2 - - + +
496D ILE* 3.0 27.7 + - + +
497D ARG* 3.7 6.5 - - - +
499D ALA* 1.3 75.2 - - - +
501D ALA* 1.3 65.0 + - - +
503D HIS* 3.3 2.6 + - - +
504D HIS* 3.1 50.1 + - + +
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Residues in contact with ALA 501 (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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497D ARG* 2.9 20.6 + - + +
498D ALA* 3.7 7.4 - - - +
500D ILE* 1.3 77.0 - - - +
502D HIS* 1.3 58.0 + - - +
504D HIS* 3.3 5.8 + - - +
505D HIS* 2.9 31.5 + - - +
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Residues in contact with HIS 502 (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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407D GLN* 3.5 35.1 + - + +
498D ALA 2.8 21.9 + - - +
499D ALA* 3.6 5.4 + - - +
500D ILE 3.3 0.2 - - - -
501D ALA* 1.3 73.5 - - - +
503D HIS* 1.3 66.0 + - - +
505D HIS* 3.4 4.4 + - - -
506D HIS* 2.8 68.0 + + + -
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Residues in contact with HIS 503 (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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407D GLN 5.7 1.8 - - - +
408D ASP* 5.8 2.6 + - - -
433D VAL* 3.7 13.1 - - + +
434D GLN* 3.3 64.1 + - + +
499D ALA 3.1 13.6 + - - +
500D ILE 3.6 6.5 - - - +
501D ALA 3.3 0.4 - - - -
502D HIS* 1.3 81.0 + - - +
504D HIS* 1.3 76.0 + + - +
506D HIS* 3.2 3.3 + - - +
507D HIS* 2.7 50.5 + - - +
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Residues in contact with HIS 504 (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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433D VAL 4.8 2.4 + - - -
434D GLN* 4.3 13.9 + - + -
436D LEU 5.3 2.4 + - - -
500D ILE* 3.1 43.6 + - + +
501D ALA* 3.7 6.1 - - - +
503D HIS* 1.3 92.5 + + - +
505D HIS* 1.3 59.9 + - - +
507D HIS* 2.8 37.1 + - + +
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Residues in contact with HIS 505 (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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501D ALA 2.9 18.6 + - - +
502D HIS* 3.8 6.5 - - - +
503D HIS 3.2 0.2 - - - -
504D HIS* 1.3 78.4 - - - +
506D HIS* 1.3 82.4 + + + +
507D HIS* 3.8 12.0 + - - -
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Residues in contact with HIS 506 (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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502D HIS* 2.8 59.6 + + + +
503D HIS* 3.2 3.8 + - - +
505D HIS* 1.3 97.2 - + + +
507D HIS* 1.3 76.2 + - - +
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Residues in contact with HIS 507 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434D GLN* 5.7 2.7 - - - -
503D HIS* 2.7 40.1 + - - +
504D HIS* 2.8 32.0 + - + +
505D HIS* 3.8 10.1 + - - -
506D HIS* 1.3 84.9 + - - +
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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
------------------------------------------------------------
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