Contacts of the strand formed by residues 493 - 507 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486E TYR 3.2 11.2 - - - +
487E ILE* 4.2 6.1 - - + -
491E GLY 3.8 2.0 - - - +
492E ARG* 1.4 84.9 - - + +
494E ARG* 1.3 68.1 + - - +
432F GLU* 3.8 11.7 - - - +
446F PHE* 4.2 15.5 - - + -
447F TYR* 4.1 28.0 - - + -
450F ASN* 5.1 6.1 - - + +
451F LEU* 3.7 36.6 - - + -
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Residues in contact with ARG 494 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485E GLN* 3.4 4.3 - - - +
486E TYR* 2.8 56.4 + - + +
488E ASP* 3.5 32.5 - - + +
492E ARG* 4.3 8.5 - - + +
493E PRO* 1.3 81.3 - - - +
495E THR* 1.3 65.4 + - - +
432F GLU* 3.8 7.2 - - - +
447F TYR* 4.6 1.3 + - - -
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Residues in contact with THR 495 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483E LEU* 4.1 16.2 - - + -
484E THR 3.3 13.9 - - - +
485E GLN* 3.9 7.8 - - + +
486E TYR* 4.3 4.1 + - - -
494E ARG* 1.3 76.7 + - - +
496E SER* 1.3 69.5 + - - +
432F GLU* 3.0 34.6 + - - +
434F LEU* 3.8 24.6 - - + +
443F PHE* 4.1 4.9 - - + -
447F TYR* 3.1 20.4 + - - -
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Residues in contact with SER 496 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482E ARG* 3.4 6.8 + - - +
483E LEU* 3.3 4.9 - - - -
484E THR* 2.9 43.1 + - - -
486E TYR* 4.3 15.3 - - - -
495E THR* 1.3 76.6 - - - +
497E GLN* 1.3 63.9 + - - +
498E SER* 5.6 1.2 - - - -
434F LEU* 3.7 6.3 - - - -
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Residues in contact with GLN 497 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481E ILE* 3.8 32.3 - - + +
482E ARG 3.3 3.8 - - - -
483E LEU* 3.8 5.4 - - + -
496E SER* 1.3 78.5 + - - +
498E SER* 1.3 66.7 + - - +
499E GLU* 3.5 24.0 + - - +
520E GLY* 4.0 14.4 - - - -
434F LEU* 3.2 28.8 - - + +
436F ASN* 2.7 34.2 + - - -
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Residues in contact with SER 498 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481E ILE* 3.6 3.6 - - - +
482E ARG* 2.8 65.1 + - - +
496E SER* 5.6 1.3 - - - -
497E GLN* 1.3 78.0 - - - +
499E GLU* 1.3 66.2 + - - +
500E GLU* 3.3 12.3 + - - -
518E CYS* 4.0 12.3 - - - -
519E SER 3.2 15.0 - - - -
520E GLY* 4.4 2.2 - - - -
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Residues in contact with GLU 499 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480E TYR 3.7 4.9 - - - +
481E ILE* 4.6 10.5 - - + +
497E GLN* 3.5 35.6 + - - +
498E SER* 1.3 76.1 - - - +
500E GLU* 1.3 62.0 + - - +
517E HIS 3.7 1.0 - - - +
518E CYS* 3.4 3.3 - - - -
519E SER* 2.8 61.5 + - - +
520E GLY* 4.3 3.7 + - - -
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Residues in contact with GLU 500 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478E ILE 3.8 0.9 - - - +
479E ALA* 3.3 4.9 - - - +
480E TYR* 2.8 66.9 + - + +
482E ARG* 2.8 52.2 + - - +
498E SER* 3.3 10.2 + - - +
499E GLU* 1.3 80.0 - - - +
501E THR* 1.3 61.8 + - - +
502E ARG* 4.0 3.8 + - - -
516E TYR* 2.4 41.2 + - + +
517E HIS 3.3 2.0 - - - +
518E CYS* 3.9 4.9 - - + -
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Residues in contact with THR 501 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477E CYS* 4.2 18.8 - - - -
478E ILE 3.3 9.0 - - - +
479E ALA* 4.4 9.8 - - + +
500E GLU* 1.3 75.4 + - - +
502E ARG* 1.3 68.1 + - - +
503E VAL* 4.4 9.6 - - + -
515E HIS* 5.3 4.0 - - + -
516E TYR* 3.3 10.0 - - - -
517E HIS* 2.8 48.8 + - + +
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Residues in contact with ARG 502 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403E THR* 4.4 8.1 - - - +
406E LEU* 3.8 24.2 - - - +
407E ILE* 5.0 4.0 - - - +
410E ILE* 3.7 24.7 - - - +
418E TYR* 5.1 7.3 + - - -
426E LEU* 5.5 0.6 - - - +
444E HIS* 6.0 0.2 - - - -
477E CYS* 3.5 2.3 - - - -
478E ILE* 2.9 38.9 + - + +
480E TYR* 3.2 29.0 + - + +
500E GLU* 4.0 4.0 + - - -
501E THR* 1.3 80.4 - - - +
503E VAL* 1.3 62.4 + - - +
504E TRP* 3.5 24.8 - - - +
513E ASN* 3.1 30.3 + - - +
515E HIS 3.4 3.6 - - - -
516E TYR* 3.4 44.8 + - + +
1521E GLY* 4.9 1.6 + - - -
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Residues in contact with VAL 503 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471E ILE* 6.1 2.7 - - + -
475E ALA* 6.4 0.7 - - + -
476E ALA 3.7 10.3 - - - +
477E CYS* 4.5 10.5 - - + +
501E THR* 4.4 10.5 - - + -
502E ARG* 1.3 75.1 - - - +
504E TRP* 1.3 66.4 + - - +
513E ASN* 2.7 23.6 + - - -
514E VAL* 2.9 32.6 + - + -
515E HIS* 3.0 34.1 + - + -
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Residues in contact with TRP 504 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399E ILE* 3.6 20.0 - - + -
402E ILE* 3.8 22.7 - - + -
403E THR* 3.3 37.1 + - - -
406E LEU* 4.0 4.9 - - + -
421E ILE* 3.6 29.4 - - + -
475E ALA* 3.4 6.4 - - - +
476E ALA* 2.8 41.7 + - + +
478E ILE* 3.6 10.5 - - + +
502E ARG* 3.5 33.6 - - + +
503E VAL* 1.3 77.9 - - - +
505E HIS* 1.3 60.2 + - - +
511E TRP* 3.7 29.4 - - + -
512E LEU 3.4 25.4 - - - -
513E ASN* 3.5 24.2 - - + -
514E VAL* 5.0 0.7 - - - -
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Residues in contact with HIS 505 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423E ASP* 5.2 4.0 + - - -
474E ASP* 3.4 22.3 - - + +
475E ALA* 5.4 3.6 - - + -
504E TRP* 1.3 75.3 - - - +
506E ARG* 1.3 67.9 + - - +
507E ARG* 3.6 30.2 + - + +
510E LYS 3.6 0.2 - - - +
511E TRP* 3.7 3.6 - - - -
512E LEU* 2.8 36.3 + - + +
514E VAL* 3.9 26.7 - - + +
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Residues in contact with ARG 506 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395E ARG* 3.8 14.8 - - - +
398E GLU* 3.1 26.3 + - - -
473E GLU* 2.7 28.1 + - - +
474E ASP* 2.9 38.7 + - - +
505E HIS* 1.3 83.6 + - - +
507E ARG* 1.3 59.7 + - - +
508E ASP 4.4 0.6 + - - +
509E GLY* 4.1 35.2 + - - +
510E LYS 3.4 5.8 - - - +
511E TRP* 3.5 37.2 - - + +
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Residues in contact with ARG 507 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423E ASP* 2.8 31.1 + - - -
424E PRO* 4.2 10.9 - - - +
505E HIS* 3.6 21.6 + - + +
506E ARG* 1.3 73.7 - - - +
508E ASP* 1.3 91.8 + - - +
509E GLY 3.2 0.7 - - - -
510E LYS* 3.0 26.1 + - - +
512E LEU* 3.8 24.1 - - + +
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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