Contacts of the helix formed by residues 461 - 480 (chain A) in PDB entry 1U1H
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 GLU 461 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462A ASP* 1.3 83.1 + - - +
463A TYR* 3.6 21.0 + - + +
464A VAL* 2.9 29.4 - - + +
465A LYS* 3.1 19.8 + - - +
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Residues in contact with ASP 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A GLU* 1.3 87.3 + - - +
463A TYR* 1.3 67.9 + - - +
464A VAL 3.1 2.0 - - - -
465A LYS* 2.8 22.2 + - - +
466A ALA* 3.0 18.8 + - - +
542A TRP* 5.1 4.5 - - - -
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Residues in contact with TYR 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A GLU* 3.6 16.1 + - + -
462A ASP* 1.3 80.6 + - - +
464A VAL* 1.3 60.6 + - - +
466A ALA* 3.3 4.0 + - - +
467A ILE* 3.0 31.3 + - + +
541A PHE* 3.4 43.1 - + + -
542A TRP* 3.3 33.8 - + - -
545A MSE 5.4 0.7 - - + -
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Residues in contact with VAL 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A GLU* 2.9 36.8 - - + +
463A TYR* 1.3 74.7 - - - +
465A LYS* 1.3 87.7 + - - +
467A ILE* 3.3 16.1 + - + +
468A LYS* 3.2 23.6 + - + +
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Residues in contact with LYS 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A GLU* 5.6 1.7 - - - +
446A LEU* 5.4 17.0 - - + -
461A GLU 3.1 22.7 + - - +
462A ASP* 2.8 14.8 + - - +
464A VAL* 1.3 114.6 - - - +
466A ALA* 1.3 62.3 + - - +
468A LYS* 3.8 9.6 + - - +
469A GLU* 3.7 15.8 + - - +
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Residues in contact with ALA 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A ASP* 3.0 17.1 + - - +
463A TYR 3.6 1.8 - - - +
465A LYS* 1.3 75.2 - - - +
467A ILE* 1.3 65.7 + - - +
469A GLU* 3.2 15.6 + - - +
470A GLU* 3.2 19.1 + - - +
491A PRO* 4.4 6.9 - - + +
492A GLU* 5.0 12.1 - - + -
542A TRP* 3.6 31.2 - - + -
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Residues in contact with ILE 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A TYR* 3.0 22.2 + - + +
464A VAL* 3.6 18.8 - - + +
466A ALA* 1.3 76.5 - - - +
468A LYS* 1.3 65.4 + - - +
470A GLU* 2.9 22.7 + - - +
471A ILE* 2.9 13.4 + - + +
542A TRP* 4.7 0.2 - - + -
545A MSE 3.6 35.9 - - + -
549A MSE 3.5 25.4 - - + -
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Residues in contact with LYS 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A VAL* 3.2 10.2 + - + +
465A LYS* 3.9 12.3 - - - +
466A ALA 3.3 0.2 - - - -
467A ILE* 1.3 79.5 - - - +
469A GLU* 1.3 61.4 + - - +
471A ILE* 2.9 28.1 - - + +
472A LYS* 3.0 38.2 + - - +
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Residues in contact with GLU 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A PRO 4.3 0.7 - - - +
442A GLN* 6.4 0.2 - - - -
443A THR* 3.2 42.7 + - - +
445A GLU* 4.5 13.3 - - - +
465A LYS 3.7 8.5 + - - +
466A ALA* 3.2 10.9 + - - +
467A ILE 3.1 1.0 - - - -
468A LYS* 1.3 79.4 - - - +
470A GLU* 1.3 61.2 + - - +
472A LYS* 3.5 22.1 - - - +
473A LYS* 3.0 57.6 + - - +
491A PRO* 3.8 17.0 - - + -
740A TYR* 3.6 3.8 + - - -
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Residues in contact with GLU 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A ALA 3.2 8.8 + - - +
467A ILE* 2.9 7.3 + - - +
469A GLU* 1.3 73.9 - - - +
471A ILE* 1.3 54.6 + - - +
472A LYS 3.0 1.1 - - - -
473A LYS* 2.8 4.8 + - - +
474A VAL* 2.7 42.8 + - + +
488A HIS* 3.2 45.3 - - + +
491A PRO* 3.4 25.8 - - + -
492A GLU* 4.3 1.3 - - - +
542A TRP* 3.3 43.7 - - - +
545A MSE 3.8 11.7 - - - +
546A ALA* 4.5 4.0 - - + +
549A MSE 4.7 8.1 - - + -
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Residues in contact with ILE 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A ILE* 2.9 9.6 + - + +
468A LYS* 2.9 37.7 - - + +
470A GLU* 1.3 76.4 - - - +
472A LYS* 1.3 56.1 + - + +
474A VAL* 4.2 2.0 - - + -
475A VAL* 2.6 58.3 + - + +
549A MSE 3.4 55.3 - - + +
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Residues in contact with LYS 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A THR* 5.8 3.8 - - + -
468A LYS* 3.0 53.8 + - - +
469A GLU* 3.5 29.4 - - - +
470A GLU 3.0 0.4 - - - -
471A ILE* 1.3 84.2 - - + +
473A LYS* 1.3 57.5 + - + +
475A VAL* 4.0 5.2 - - - +
476A ASP* 3.0 27.2 + - - +
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Residues in contact with LYS 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A PHE* 3.7 28.4 + - + -
441A PRO 4.2 3.5 + - - -
442A GLN* 5.1 4.4 - - - +
445A GLU* 5.8 0.2 + - - -
469A GLU* 3.0 33.2 + - + +
470A GLU 2.8 7.0 + - - +
472A LYS* 1.3 76.7 - - + +
474A VAL* 1.3 57.1 + - + +
476A ASP* 3.4 5.5 - - - +
477A LEU* 2.7 47.1 + - + +
488A HIS 3.6 23.6 - - - +
489A GLY* 3.4 28.3 + - - -
491A PRO* 3.4 22.0 - - + +
740A TYR* 3.2 28.3 - - + +
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Residues in contact with VAL 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A GLU* 2.7 29.0 + - + +
471A ILE* 3.7 7.2 - - + +
473A LYS* 1.3 70.1 - - + +
475A VAL* 1.3 61.0 + - + +
476A ASP 3.0 1.3 - - - -
477A LEU* 3.2 8.9 + - + +
478A GLN* 2.9 36.9 + - - +
486A LEU* 4.0 5.6 - - + -
487A VAL 4.7 11.4 - - - +
488A HIS* 5.2 1.6 - - - -
546A ALA* 4.6 16.6 - - + +
549A MSE 4.1 27.4 - - + +
550A THR* 3.8 34.5 - - + -
554A MSE 5.4 1.8 - - - -
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Residues in contact with VAL 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A ILE* 2.6 52.9 + - + +
472A LYS* 4.3 5.4 - - - +
474A VAL* 1.3 73.9 - - + +
476A ASP* 1.3 60.9 + - - +
478A GLN* 4.0 14.2 - - - +
479A GLU* 3.2 34.8 + - + +
549A MSE 6.0 0.7 - - - +
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Residues in contact with ASP 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440A PHE* 5.2 11.3 - - + -
472A LYS 3.0 22.3 + - - +
473A LYS* 3.4 8.3 - - - +
475A VAL* 1.3 74.9 - - - +
477A LEU* 1.3 55.3 + - - +
478A GLN 3.1 0.2 + - - -
479A GLU* 3.1 13.8 - - - +
480A GLU* 2.4 63.6 + - - +
740A TYR* 4.5 12.6 - - + -
744A LYS* 3.5 30.0 + - - +
747A LEU* 6.0 0.2 - - - +
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Residues in contact with LEU 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A THR* 4.7 4.9 - - - +
440A PHE* 4.2 26.5 - - + -
473A LYS* 2.7 34.2 + - + +
474A VAL* 3.6 6.7 - - - +
476A ASP* 1.3 72.4 - - - +
478A GLN* 1.3 57.5 + - - +
480A GLU* 2.6 31.2 - - - +
482A ASP 2.8 11.9 - - - +
483A ILE* 3.4 32.5 - - + +
485A VAL 4.5 0.7 - - - +
486A LEU* 3.4 33.9 - - + -
487A VAL 3.0 33.7 - - - +
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Residues in contact with GLN 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474A VAL* 2.9 21.8 + - - +
475A VAL* 4.0 17.0 - - - +
477A LEU* 1.3 72.2 - - - +
479A GLU* 1.3 66.0 + - - +
482A ASP* 3.0 23.4 + - - +
486A LEU* 3.9 3.6 - - + +
549A MSE 3.9 7.9 + - - +
550A THR* 2.6 41.0 + - - +
551A SER* 4.1 3.4 + - - +
552A ARG* 3.8 35.2 + - - +
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Residues in contact with GLU 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475A VAL* 3.2 25.0 + - + +
476A ASP* 3.1 19.8 + - - +
478A GLN* 1.3 80.5 - - - +
480A GLU* 1.3 64.7 + - + +
481A LEU* 2.9 9.5 + - - -
482A ASP* 3.9 1.9 + - - +
744A LYS* 5.2 7.6 + - - -
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Residues in contact with GLU 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A PHE* 6.3 0.4 - - + -
476A ASP* 2.4 49.5 + - - +
477A LEU* 2.6 16.8 - - - +
479A GLU* 1.3 69.9 - - + +
481A LEU* 1.3 98.8 + - + +
482A ASP 2.4 16.8 + - - -
483A ILE* 3.3 9.5 - - + +
744A LYS* 3.1 35.1 - - - +
747A LEU* 4.3 9.4 - - + -
748A LYS* 3.7 22.6 + - - +
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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