Contacts of the helix formed by residues 457 - 473 (chain A) in PDB entry 6FD3
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 LYS 457 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A GLU* 4.9 0.4 - - - +
455A GLY 3.0 2.7 + - - -
456A PRO* 1.3 76.1 - - + +
458A VAL* 1.3 64.5 + - - +
459A ASP 3.1 0.4 - - - -
460A ILE* 3.1 20.3 + - + +
461A TRP 3.2 4.3 + - - -
519A VAL* 3.0 39.2 + - + +
520A ASP* 3.6 12.5 + - - +
522A ARG* 2.7 58.4 + - + +
523A GLY 4.1 8.5 - - - +
524A SER* 3.9 24.2 - - - +
527A GLU* 4.9 2.4 + - - -
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Residues in contact with VAL 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ILE* 3.7 18.8 - - + -
401A ARG* 4.7 7.4 - - + -
445A ALA* 4.1 12.2 - - + +
447A GLU* 3.4 18.6 + - + +
448A VAL* 3.6 23.3 - - + -
454A TYR* 3.5 32.8 - - + -
455A GLY 3.4 17.7 - - - +
456A PRO 3.0 1.4 + - - -
457A LYS* 1.3 77.3 - - - +
459A ASP* 1.3 63.0 + - - +
461A TRP* 3.4 4.2 + - - +
462A SER* 3.1 30.1 + - - +
522A ARG* 4.1 0.2 - - - +
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Residues in contact with ASP 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A LEU* 3.8 16.7 - - + +
394A HIS* 2.8 28.7 + - + +
399A ILE* 3.5 9.1 - - - +
400A HIS* 2.8 32.5 + - - +
401A ARG* 2.8 29.6 + - - -
403A ILE* 4.0 8.1 - - + +
456A PRO 3.0 9.3 + - - +
458A VAL* 1.3 77.9 - - - +
460A ILE* 1.3 59.6 + - - +
462A SER* 3.4 7.3 + - - -
463A LEU* 2.9 27.9 + - - +
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Residues in contact with ILE 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A LEU* 4.0 15.5 - - + -
390A LEU* 4.2 11.4 - - + -
394A HIS* 4.6 7.9 - - + -
457A LYS* 3.1 19.4 + - + +
459A ASP* 1.3 74.8 - - - +
461A TRP* 1.3 66.0 + - - +
463A LEU* 3.2 6.0 + - + +
464A GLY 2.9 17.7 + - - -
514A CYS* 3.7 23.1 - - + +
522A ARG* 3.9 4.9 - - + -
523A GLY 3.4 25.1 - - - +
524A SER* 4.1 2.0 - - - -
525A ALA* 3.6 37.2 - - + +
528A LEU* 3.5 16.6 - - + -
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Residues in contact with TRP 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A TYR 5.4 0.4 + - - -
443A TRP 3.5 12.3 - - - -
444A MET 3.3 11.3 + - - -
445A ALA* 3.5 23.8 - - + -
446A PRO* 3.5 35.2 - - + -
457A LYS 3.2 4.0 + - - -
458A VAL 3.6 8.3 - - - +
459A ASP 3.4 0.2 - - - -
460A ILE* 1.3 79.1 - - - +
462A SER* 1.3 65.2 + - - +
464A GLY* 2.9 12.1 + - - -
465A ILE* 3.0 26.3 + - + +
489A ILE* 4.6 10.7 - - + +
493A GLY 3.5 25.1 - - - -
495A PRO* 3.9 21.5 - - + -
514A CYS 3.5 10.5 + - - -
515A LEU* 3.3 42.6 - - + +
516A GLU 3.9 5.4 - - - -
517A MET* 4.1 4.5 - - - -
522A ARG* 3.9 18.4 - - - +
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Residues in contact with SER 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A ARG* 5.5 4.2 + - - -
403A ILE* 3.5 36.3 + - - +
443A TRP* 2.7 31.3 + - - +
444A MET* 4.7 2.3 - - - -
445A ALA 4.8 0.3 + - - -
458A VAL* 3.1 18.5 + - - +
459A ASP* 3.7 3.8 + - - -
460A ILE 3.3 0.2 - - - -
461A TRP* 1.3 76.3 - - - +
463A LEU* 1.3 57.6 + - - +
465A ILE* 3.2 5.7 + - - +
466A MET* 2.9 27.2 + - - +
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Residues in contact with LEU 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A CYS* 4.5 18.6 - - - +
386A CYS* 4.0 15.5 - - + -
387A LEU* 3.4 41.1 - - + +
390A LEU* 4.5 10.3 - - + -
403A ILE* 3.9 10.7 - - + +
459A ASP 2.9 19.0 + - - +
460A ILE* 3.5 7.4 - - + +
461A TRP 3.2 0.4 - - - -
462A SER* 1.3 76.6 - - - +
464A GLY* 1.3 58.8 + - - +
466A MET* 3.1 26.1 + - + +
467A ALA* 2.8 27.5 + - - +
470A MET* 5.3 0.4 - - + -
510A PHE* 4.7 4.5 - - + -
514A CYS* 4.6 14.8 - - - -
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Residues in contact with GLY 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A ILE 2.9 7.9 + - - -
461A TRP 2.9 8.9 + - - -
463A LEU* 1.3 76.7 - - - +
465A ILE* 1.3 60.8 + - - +
467A ALA* 3.2 9.5 + - - +
468A ILE* 3.1 23.7 + - - +
511A LEU* 4.0 4.0 - - - +
514A CYS* 3.7 24.2 - - - +
515A LEU* 3.9 13.5 - - - -
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Residues in contact with ILE 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A TYR 3.8 13.9 - - - +
443A TRP* 3.4 24.2 - - + -
461A TRP* 3.0 35.4 + - + +
462A SER 3.2 7.2 + - - +
464A GLY* 1.3 74.2 - - - +
466A MET* 1.3 58.1 + - - +
468A ILE* 3.0 12.5 + - + +
469A GLU* 2.9 24.3 + - - +
475A PRO* 3.5 24.2 - - + +
476A PRO* 4.1 9.9 - - + -
495A PRO* 3.8 21.8 - - + -
515A LEU* 3.7 16.4 - - + -
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Residues in contact with MET 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A LEU* 4.1 15.0 - - + -
386A CYS* 3.7 23.1 - - - -
403A ILE* 4.0 10.5 - - + -
404A LYS* 3.4 32.5 - - - -
405A SER* 3.5 7.4 - - - +
408A ILE* 3.5 17.7 - - + -
443A TRP* 4.1 0.2 - - - -
462A SER 2.9 14.0 + - - +
463A LEU* 3.1 31.8 + - + +
465A ILE* 1.3 78.3 - - - +
467A ALA* 1.3 55.5 + - - +
469A GLU* 3.1 27.2 + - - +
470A MET* 3.0 30.6 + - + +
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Residues in contact with ALA 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ILE* 4.9 0.2 - - + -
383A CYS* 4.4 13.7 - - - -
463A LEU 2.8 12.5 + - - +
464A GLY* 3.2 10.7 + - - +
466A MET* 1.3 73.9 - - - +
468A ILE* 1.3 64.6 + - - +
470A MET* 3.1 29.1 + - + +
471A VAL* 3.2 18.7 + - - +
507A PHE* 4.5 8.4 - - + -
510A PHE* 5.0 3.8 - - + -
511A LEU* 3.6 20.6 - - + -
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Residues in contact with ILE 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A GLY 3.1 9.7 + - - +
465A ILE* 3.0 16.4 + - + +
467A ALA* 1.3 72.9 - - - +
469A GLU* 1.3 60.1 + - - +
471A VAL* 3.0 7.6 + - - +
472A GLU* 2.8 53.9 + - - +
474A GLU 4.0 10.5 - - - +
476A PRO* 4.4 14.6 - - + -
495A PRO* 3.8 35.7 - - + +
496A GLU 5.6 2.0 - - - +
497A LEU* 3.9 19.3 - - + -
511A LEU* 4.6 7.4 - - + -
515A LEU* 3.9 16.2 - - + -
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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
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366A THR* 5.4 1.4 - - - +
369A VAL* 3.6 18.8 - - + +
405A SER* 2.6 44.2 + - - -
443A TRP* 2.8 38.5 + - - +
465A ILE 2.9 16.0 + - - +
466A MET* 3.1 14.1 + - - +
468A ILE* 1.3 75.5 - - - +
470A MET* 1.3 60.4 + - - +
473A GLY* 2.8 27.9 + - - +
474A GLU* 3.8 14.9 + - - +
475A PRO* 3.8 23.1 - - + +
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Residues in contact with MET 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A LEU* 4.1 13.0 - - + -
369A VAL* 3.8 18.4 - - + +
373A CYS* 5.7 0.5 - - - -
374A MET* 3.7 48.5 + - - +
379A ILE* 3.8 29.4 - - + +
382A VAL* 4.0 24.2 - - + -
383A CYS* 3.9 22.9 - - - -
463A LEU* 5.3 0.4 - - + -
466A MET* 3.0 20.8 + - + +
467A ALA* 3.1 31.3 + - - +
469A GLU* 1.3 77.3 - - + +
471A VAL* 1.3 60.1 + - - +
605A EDO 4.7 0.9 + - - -
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Residues in contact with VAL 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ILE* 4.1 0.9 - - + -
467A ALA 3.4 13.5 - - - +
468A ILE* 3.0 10.2 + - - +
470A MET* 1.3 81.2 - - - +
472A GLU* 1.3 73.6 + - + +
473A GLY 3.7 0.7 - - - -
497A LEU* 4.6 7.6 - - + -
499A ASN 6.1 0.4 - - - +
503A LEU* 4.2 21.3 - - + -
507A PHE* 3.6 32.5 - - + -
511A LEU* 5.3 0.9 - - + -
605A EDO 4.0 26.1 + - - +
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Residues in contact with GLU 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A ILE* 2.8 27.4 + - + +
471A VAL* 1.3 89.7 - - + +
473A GLY* 1.3 59.9 + - - +
474A GLU* 3.3 21.2 + - + +
475A PRO 6.0 0.2 - - - -
476A PRO* 5.7 2.8 - - - +
496A GLU 4.9 2.1 - - - +
497A LEU* 3.4 20.2 - - - +
498A GLN* 2.7 49.9 + - + +
499A ASN 4.4 1.2 + - - -
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Residues in contact with GLY 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A VAL* 3.7 24.2 - - - +
370A THR* 3.9 21.6 - - - +
469A GLU* 2.8 21.4 + - - +
471A VAL 3.7 1.0 - - - -
472A GLU* 1.3 76.3 - - - +
474A GLU* 1.3 63.2 + - - +
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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
------------------------------------------------------------
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