Contacts of the helix formed by residues 480 - 500 (chain A) in PDB entry 4U7C
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 480 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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443A ALA* 3.7 4.3 - - - -
479A SER* 1.3 82.7 - - - +
481A ALA* 1.3 64.6 + - - +
482A GLU* 3.1 26.1 + - - +
483A GLU* 2.9 30.9 + - - +
484A ILE* 3.3 23.7 + - - +
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Residues in contact with ALA 481 (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 GLN 5.3 0.4 - - - +
439A CYS* 4.1 7.1 - - + +
440A SER* 3.8 36.6 - - - +
443A ALA* 3.3 14.6 - - + +
480A THR* 1.3 75.0 - - - +
482A GLU* 1.3 67.5 + - - +
484A ILE* 4.8 1.1 - - - -
485A PHE* 2.9 33.1 + - - +
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Residues in contact with GLU 482 (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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480A THR* 3.1 25.0 + - - +
481A ALA* 1.3 87.9 + - - +
483A GLU* 1.3 59.5 + - + +
485A PHE* 3.8 5.6 - - - +
486A ALA* 2.9 27.4 + - - +
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Residues in contact with GLU 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A VAL 5.4 1.0 - - - +
478A VAL* 3.4 26.1 - - + -
479A SER* 2.5 33.8 + - - -
480A THR* 2.9 29.3 + - - +
482A GLU* 1.3 75.5 - - + +
484A ILE* 1.3 59.5 + - - +
486A ALA* 2.8 26.8 + - - +
487A ILE* 3.0 17.9 + - - +
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Residues in contact with ILE 484 (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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439A CYS* 3.7 26.0 - - + +
442A LEU* 4.4 9.6 - - + -
443A ALA 4.3 14.1 - - - +
446A LEU* 3.9 20.2 - - + -
456A VAL* 4.2 18.8 - - + +
478A VAL* 3.6 20.9 - - + -
479A SER 3.9 13.7 - - - +
480A THR 3.3 17.5 + - - +
481A ALA 4.2 2.5 - - - +
483A GLU* 1.3 74.8 - - - +
485A PHE* 1.3 59.4 + - - +
487A ILE* 3.3 2.3 + - - +
488A ALA* 2.9 27.2 + - - +
511A VAL* 3.9 18.6 - - + -
513A ILE* 4.8 2.9 - - + -
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Residues in contact with PHE 485 (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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432A TYR* 3.4 35.4 - - + -
435A CYS* 3.9 10.8 - - + -
436A GLN* 3.5 48.7 - - + -
439A CYS* 3.7 16.5 - - + -
481A ALA 2.9 22.0 + - - +
482A GLU* 3.9 4.9 - - - +
484A ILE* 1.3 75.3 - - - +
486A ALA* 1.3 65.9 + - - +
488A ALA 4.5 0.2 - - - +
489A LYS* 2.8 71.0 + - + +
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Residues in contact with ALA 486 (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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482A GLU 2.9 15.4 + - - +
483A GLU* 2.8 17.3 + - - +
485A PHE* 1.3 79.6 - - - +
487A ILE* 1.3 61.9 + - + +
489A LYS* 3.9 8.3 - - - +
490A GLU* 3.7 21.3 + - - +
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Residues in contact with ILE 487 (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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454A ARG 5.7 0.4 - - - +
456A VAL* 3.7 29.6 - - + +
472A SER* 3.6 31.2 - - - +
474A VAL* 3.8 34.3 - - + -
478A VAL* 4.6 12.3 - - + -
483A GLU 3.0 13.9 + - - +
484A ILE 3.8 3.8 - - - +
486A ALA* 1.3 74.8 - - + +
488A ALA* 1.3 66.5 + - - +
489A LYS 3.1 1.6 - - - -
490A GLU* 3.0 18.9 + - + +
491A LEU* 3.0 28.2 + - + +
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Residues in contact with ALA 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A CYS* 3.5 24.0 - - - -
439A CYS* 4.0 9.9 - - - -
456A VAL* 4.3 7.6 - - + +
458A ILE* 3.6 23.4 - - + +
484A ILE 2.9 20.3 + - - +
485A PHE 4.3 0.2 - - - +
487A ILE* 1.3 73.7 - - - +
489A LYS* 1.3 63.5 - - - +
491A LEU* 3.3 6.6 + - - +
492A LEU* 2.9 25.8 + - - +
511A VAL* 4.5 2.2 - - + -
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Residues in contact with LYS 489 (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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432A TYR* 3.6 23.8 - - + -
435A CYS* 4.4 1.9 - - - -
485A PHE* 2.8 54.4 + - + +
486A ALA* 3.9 9.0 - - - +
488A ALA* 1.3 79.2 - - - +
490A GLU* 1.3 58.8 + - + +
492A LEU* 3.5 5.6 + - - +
493A LYS* 2.9 27.3 + - + +
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Residues in contact with GLU 490 (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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486A ALA 3.7 13.9 + - - +
487A ILE* 3.0 21.4 + - + +
489A LYS* 1.3 78.9 - - + +
491A LEU* 1.3 65.0 + - + +
493A LYS* 3.4 11.1 - - + +
494A THR* 2.8 32.5 + - - +
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Residues in contact with LEU 491 (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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456A VAL 3.7 18.2 - - - +
458A ILE* 3.9 26.5 - - + -
470A ARG* 3.6 29.7 - - + +
471A ALA 3.6 12.1 - - - +
472A SER* 3.3 24.9 - - - +
487A ILE* 3.0 26.2 + - + +
488A ALA* 3.3 6.7 + - - +
490A GLU* 1.3 80.1 - - + +
492A LEU* 1.3 62.2 + - - +
494A THR* 3.2 10.9 + - - +
495A GLU* 3.0 24.9 + - - +
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Residues in contact with LEU 492 (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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431A GLN* 3.8 30.1 - - + +
432A TYR* 4.2 13.2 - - + +
435A CYS* 4.2 7.2 - - + -
458A ILE* 3.7 10.2 - - + +
460A LEU* 4.2 24.2 - - + -
488A ALA 2.9 17.3 + - - +
489A LYS* 3.6 4.5 - - - +
491A LEU* 1.3 72.6 - - - +
493A LYS* 1.3 66.7 + - - +
495A GLU* 2.9 3.1 + - - +
496A ILE* 2.9 37.4 + - + +
504A LEU* 3.9 24.2 - - + -
506A LEU* 5.1 0.9 - - + -
509A MET* 3.6 24.0 - - + -
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Residues in contact with LYS 493 (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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432A TYR* 3.2 31.4 + - + +
489A LYS* 2.9 19.8 + - + +
490A GLU* 3.4 14.1 - - + +
492A LEU* 1.3 75.2 - - - +
494A THR* 1.3 59.3 + - - +
496A ILE* 3.3 1.1 + - - +
497A ASP* 2.8 68.3 + - - +
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Residues in contact with THR 494 (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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490A GLU* 2.8 19.7 + - - +
491A LEU* 3.2 13.8 - - - +
493A LYS* 1.3 78.5 - - - +
495A GLU* 1.3 67.8 + - - +
497A ASP* 4.0 4.8 - - - +
498A ALA* 2.9 32.9 + - + +
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Residues in contact with GLU 495 (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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458A ILE* 4.7 0.4 - - + -
460A LEU* 3.8 29.6 - - + -
468A LYS* 3.8 15.9 + - + +
470A ARG* 2.9 51.4 + - + +
491A LEU 3.0 13.0 + - - +
492A LEU 2.9 8.2 + - - +
494A THR* 1.3 84.6 - - - +
496A ILE* 1.3 66.4 + - - +
498A ALA* 3.3 9.6 + - - +
499A ASP* 3.0 24.6 + - - +
504A LEU* 4.3 13.8 - - + +
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Residues in contact with ILE 496 (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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428A ALA* 3.8 24.9 - - + +
431A GLN* 3.2 27.1 - - + +
432A TYR* 4.2 17.9 - - + +
492A LEU* 2.9 30.7 + - + +
493A LYS* 3.6 5.6 - - - +
495A GLU* 1.3 74.9 - - - +
497A ASP* 1.3 67.7 + - - +
499A ASP* 3.3 4.5 + - - +
500A PHE* 3.1 19.6 + - - +
502A HIS 4.3 8.1 - - - +
503A PRO* 6.3 0.9 - - + -
504A LEU* 3.6 23.1 - - + +
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Residues in contact with ASP 497 (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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493A LYS* 2.8 59.1 + - - +
494A THR* 4.0 5.3 + - - +
496A ILE* 1.3 77.3 - - - +
498A ALA* 1.3 66.4 + - - +
499A ASP 3.0 2.0 - - - -
500A PHE* 2.9 26.6 + - - +
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Residues in contact with ALA 498 (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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494A THR* 2.9 23.8 + - + +
495A GLU* 3.4 15.3 - - - +
497A ASP* 1.3 76.5 - - - +
499A ASP* 1.3 58.5 + - - +
500A PHE 4.8 1.2 - - - +
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Residues in contact with ASP 499 (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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495A GLU 3.0 15.0 + - - +
496A ILE* 3.9 4.0 - - - +
497A ASP 3.0 0.4 - - - -
498A ALA* 1.3 75.1 - - - +
500A PHE* 1.3 69.6 + - - +
501A PRO* 4.3 0.2 - - - +
502A HIS* 3.1 36.1 + - + +
503A PRO 5.6 0.7 - - - +
504A LEU* 4.4 17.5 - - + +
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Residues in contact with PHE 500 (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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496A ILE* 3.1 12.6 + - + +
497A ASP* 2.9 22.7 + - - +
498A ALA 4.8 1.4 - - - +
499A ASP* 1.3 78.5 - - - +
501A PRO* 1.3 68.5 - - + +
502A HIS 3.3 3.4 - - - +
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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
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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