Contacts of the strand formed by residues 493 - 507 (chain D) in PDB entry 2UX0
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 PRO 493 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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486D TYR 3.2 12.8 - - - +
487D ILE* 4.2 6.5 - - + -
491D GLY 4.0 1.1 - - - +
492D ARG* 1.4 89.5 - - + +
494D ARG* 1.3 67.6 + - - +
432E GLU* 4.0 10.1 - - - +
446E PHE* 4.1 19.1 - - + -
447E TYR* 4.6 15.9 - - + -
450E ASN* 5.3 3.1 - - + +
451E LEU* 3.8 42.4 - - + -
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Residues in contact with ARG 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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485D GLN* 3.4 5.2 - - - +
486D TYR* 2.9 65.2 + - + +
488D ASP* 4.0 26.2 + - + +
492D ARG* 4.5 8.3 - - + +
493D PRO* 1.3 81.4 - - - +
495D THR* 1.3 68.7 + - - +
432E GLU* 4.1 5.6 - - - -
447E TYR* 5.2 1.5 + - - -
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Residues in contact with THR 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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483D LEU* 4.1 13.9 - - + -
484D THR 3.3 14.1 - - - +
485D GLN* 4.3 2.8 - - + +
486D TYR* 4.2 4.7 + - - -
494D ARG* 1.3 82.9 + - - +
496D SER* 1.3 69.1 + - - +
432E GLU* 2.7 38.5 + - - +
434E LEU* 3.6 27.3 - - + +
443E PHE* 4.2 7.1 - - + -
447E TYR* 3.4 18.4 + - - -
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Residues in contact with SER 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482D ARG* 3.4 6.1 + - - +
483D LEU* 3.3 5.5 - - - +
484D THR* 2.9 41.8 + - - -
486D TYR* 4.2 15.7 - - - -
495D THR* 1.3 75.5 - - - +
497D GLN* 1.3 63.2 + - - +
498D SER* 5.0 1.9 + - - -
434E LEU* 3.6 5.8 - - - -
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Residues in contact with GLN 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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481D ILE* 3.7 35.0 - - + +
482D ARG 3.3 3.6 - - - -
483D LEU* 3.8 3.6 - - + -
496D SER* 1.3 78.4 + - - +
498D SER* 1.3 64.6 + - - +
499D GLU* 2.9 28.2 + - - +
520D GLY* 4.0 13.0 - - - -
521D ALA 4.3 5.0 + - - -
434E LEU* 3.4 30.7 - - + +
436E ASN* 2.8 28.6 + - - +
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Residues in contact with SER 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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481D ILE* 3.5 4.7 - - - +
482D ARG* 2.8 49.1 + - - +
496D SER* 5.5 2.5 - - - -
497D GLN* 1.3 75.8 - - - +
499D GLU* 1.3 65.0 + - - +
500D GLU* 3.2 27.5 + - - +
518D CYS* 3.9 12.6 - - - -
519D SER 3.3 14.4 - - - -
520D GLY* 4.6 2.0 - - - -
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Residues in contact with GLU 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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480D TYR 3.7 6.5 - - - +
481D ILE* 4.5 11.2 - - + +
497D GLN* 2.9 41.5 + - - +
498D SER* 1.3 74.0 - - - +
500D GLU* 1.3 61.9 + - - +
517D HIS 3.7 1.2 - - - +
518D CYS* 3.4 2.9 - - - -
519D SER* 2.9 61.9 + - - +
520D GLY* 4.4 3.5 + - - -
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Residues in contact with GLU 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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407D ILE* 5.0 0.2 - - - +
479D ALA* 3.3 4.3 - - - +
480D TYR* 2.8 79.5 + - + +
482D ARG* 2.9 39.5 + - - -
498D SER* 3.2 19.6 + - - +
499D GLU* 1.3 77.6 - - - +
501D THR* 1.3 62.0 + - - +
502D ARG* 4.4 2.7 + - - -
516D TYR* 2.2 36.7 + - + +
517D HIS 3.4 3.4 - - - +
518D CYS* 3.5 4.6 - - - -
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Residues in contact with THR 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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477D CYS* 4.5 11.4 - - - -
478D ILE 3.3 9.6 - - - +
479D ALA* 4.5 9.6 - - + +
500D GLU* 1.3 75.0 + - - +
502D ARG* 1.3 70.4 + - - +
503D VAL* 4.4 12.8 - - + -
515D HIS* 5.5 3.8 - - + -
516D TYR* 3.3 8.5 - - - -
517D HIS* 2.8 49.1 + - + +
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Residues in contact with ARG 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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403D THR* 4.7 4.4 - - + +
406D LEU* 3.6 24.1 - - - +
407D ILE* 4.6 8.1 - - - +
410D ILE* 3.8 24.5 - - - +
418D TYR* 5.1 8.3 + - - -
426D LEU* 5.9 1.0 - - - +
444D HIS* 5.9 0.6 - - - -
477D CYS* 3.5 2.3 - - - -
478D ILE* 2.9 38.1 + - + +
480D TYR* 3.2 33.5 + - + +
482D ARG* 5.7 0.6 - - - +
500D GLU* 4.4 2.8 + - - -
501D THR* 1.3 78.3 - - - +
503D VAL* 1.3 63.2 + - - +
504D TRP* 3.6 23.0 - - - +
513D ASN* 3.3 28.2 + - - +
515D HIS 3.5 4.9 - - - -
516D TYR* 3.4 44.8 + - + +
1521D GLY* 5.0 1.4 + - - -
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Residues in contact with VAL 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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471D ILE* 6.1 2.5 - - + -
475D ALA* 6.5 0.4 - - + -
476D ALA 3.8 9.9 - - - +
477D CYS* 4.5 10.5 - - + +
501D THR* 4.4 12.1 - - + -
502D ARG* 1.3 75.7 - - - +
504D TRP* 1.3 67.6 + - - +
513D ASN* 2.8 18.5 + - - -
514D VAL* 2.9 35.5 + - + -
515D HIS* 3.0 31.8 + - + +
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Residues in contact with TRP 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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399D ILE* 3.8 22.2 - - + -
402D ILE* 3.9 26.7 - - + -
403D THR* 3.3 35.6 + - - -
406D LEU* 4.1 9.9 - - + -
421D ILE* 3.6 28.5 - - + -
475D ALA* 3.4 6.1 - - - +
476D ALA 2.9 34.4 + - - +
478D ILE* 3.7 3.7 - - + +
502D ARG* 3.6 31.4 - - + +
503D VAL* 1.3 78.8 - - - +
505D HIS* 1.3 61.6 + - - +
511D TRP* 3.7 28.0 - - + -
512D LEU 3.3 26.2 - - - -
513D ASN* 3.4 26.2 - - + -
514D VAL* 4.9 0.2 - - - -
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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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423D ASP* 5.3 4.0 + - - -
474D ASP* 3.4 26.5 + - + +
475D ALA* 5.2 4.0 - - + -
504D TRP* 1.3 75.8 - - - +
506D ARG* 1.3 73.2 + - - +
507D ARG* 3.6 17.0 + - + +
510D LYS 3.7 0.2 - - - +
511D TRP* 3.8 3.6 - - - -
512D LEU* 2.8 33.2 + - + +
514D VAL* 3.8 26.3 - - + +
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Residues in contact with ARG 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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395D ARG* 3.7 16.2 - - - +
398D GLU* 3.7 10.9 + - - -
473D GLU* 2.7 34.2 + - - +
474D ASP* 2.9 29.0 + - + +
505D HIS* 1.3 82.6 + - - +
507D ARG* 1.3 59.2 + - - +
508D ASP 5.2 0.2 - - - +
509D GLY* 4.2 28.2 + - - +
510D LYS 3.4 9.2 - - - +
511D TRP* 3.3 55.0 - - + +
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Residues in contact with ARG 507 (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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423D ASP* 5.8 0.7 - - - +
505D HIS* 3.6 16.9 + - + +
506D ARG* 1.3 73.0 - - - +
508D ASP* 1.3 71.0 + - + +
509D GLY 3.3 0.4 - - - -
510D LYS* 3.0 26.0 + - + +
512D LEU* 3.6 27.1 - - + -
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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