Contacts of the helix formed by residues 429 - 447 (chain A) in PDB entry 5F0L
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 ASP 429 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387A HIS* 6.4 1.1 - - - -
388A ILE 3.2 15.6 + - - +
389A ALA* 3.5 11.4 - - - +
390A THR* 3.4 37.1 + - - +
428A PHE* 1.3 79.9 - - - +
430A TYR* 1.3 85.3 + - - +
431A GLU* 3.2 12.3 + - - +
432A SER* 4.1 4.0 - - - +
433A ARG* 3.2 24.9 + - - +
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Residues in contact with TYR 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ASP* 1.3 84.7 + - - +
431A GLU* 1.3 64.1 + - + +
433A ARG* 3.5 28.0 + - + +
434A LYS* 3.5 53.6 + - + +
466A THR 5.7 2.5 - - - -
467A LEU 5.9 0.4 - - - -
468A ILE 4.5 5.0 + - - -
469A GLN 3.3 31.1 + - - -
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Residues in contact with GLU 431 (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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390A THR* 3.5 32.2 + - - +
429A ASP* 3.2 8.6 + - - +
430A TYR* 1.3 84.9 - - + +
432A SER* 1.3 57.1 + - - +
434A LYS* 3.7 7.5 + - - +
435A SER* 3.1 26.9 + - - -
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Residues in contact with SER 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A THR* 2.6 37.4 + - - +
395A SER* 3.6 7.4 + - - -
399A THR* 5.1 1.8 + - - -
428A PHE* 3.3 35.8 - - - -
429A ASP* 3.5 3.6 + - - +
430A TYR 3.4 0.4 - - - -
431A GLU* 1.3 74.5 - - - +
433A ARG* 1.3 57.4 + - - +
434A LYS 3.3 0.2 - - - -
435A SER* 3.7 6.9 - - - -
436A MET* 2.8 38.1 + - - +
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Residues in contact with ARG 433 (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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387A HIS* 6.1 2.2 + - - -
425A PHE* 3.5 39.3 - - + +
426A GLU* 4.5 11.7 + - - +
428A PHE* 4.0 12.3 + - + +
429A ASP 3.2 19.3 + - - +
430A TYR* 3.5 40.0 - - + +
432A SER* 1.3 74.6 - - - +
434A LYS* 1.3 56.3 + - - +
437A SER* 2.7 41.7 + - - -
466A THR* 4.1 28.9 - - - +
469A GLN 6.6 0.2 - - - -
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Residues in contact with LYS 434 (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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430A TYR* 3.5 41.8 + - + +
431A GLU* 3.7 10.8 - - - +
433A ARG* 1.3 78.9 - - - +
435A SER* 1.3 61.1 + - - +
438A CYS* 3.2 24.3 + - - +
466A THR 4.4 6.0 + - - +
467A LEU* 3.1 47.4 + - + +
468A ILE* 4.4 7.1 + - - +
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Residues in contact with SER 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A THR* 6.6 0.2 - - - -
431A GLU* 3.1 20.4 + - - -
432A SER* 3.7 7.6 - - - -
433A ARG 3.3 0.4 - - - -
434A LYS* 1.3 76.4 - - - +
436A MET* 1.3 58.8 + - - +
438A CYS* 3.6 5.2 - - - +
439A TYR* 3.0 27.1 + - - +
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Residues in contact with MET 436 (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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399A THR* 4.2 29.2 - - - +
402A LEU* 3.9 25.8 - - + +
403A LYS* 3.8 29.4 - - + +
406A VAL* 5.0 1.1 - - + -
421A PHE* 4.8 1.6 - - + -
425A PHE* 3.3 28.7 - - + -
428A PHE* 4.2 14.1 - - + -
432A SER 2.8 22.4 + - - +
435A SER* 1.3 71.3 - - - +
437A SER* 1.3 65.8 + - - +
439A TYR* 3.1 18.9 + - + +
440A VAL* 3.1 37.6 + - + +
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Residues in contact with SER 437 (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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425A PHE* 3.8 12.5 - - - -
433A ARG 2.7 27.2 + - - -
434A LYS 4.4 0.2 - - - -
436A MET* 1.3 72.8 - - - +
438A CYS* 1.3 62.4 + - - +
440A VAL* 3.5 1.4 + - - +
441A LEU* 3.1 31.6 + - - +
463A LEU* 3.4 25.8 - - - +
466A THR* 2.8 25.1 + - - -
467A LEU* 3.8 15.5 - - - -
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Residues in contact with CYS 438 (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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434A LYS 3.2 20.3 + - - +
435A SER* 3.6 5.8 - - - +
436A MET 3.2 0.2 - - - -
437A SER* 1.3 78.2 - - - +
439A TYR* 1.3 54.6 + - - +
441A LEU* 4.0 2.4 - - - +
442A SER* 2.7 44.2 + - - -
467A LEU* 4.3 18.0 - - + +
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Residues in contact with TYR 439 (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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403A LYS* 3.8 46.5 - - + +
406A VAL* 4.0 19.1 - - + -
407A ASP* 2.6 32.7 + - - -
435A SER 3.0 17.9 + - - +
436A MET* 3.1 18.6 + - + +
438A CYS* 1.3 78.1 - - - +
440A VAL* 1.3 60.8 + - - +
442A SER* 3.8 6.6 - - - -
443A ASN* 3.5 25.2 + - - +
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Residues in contact with VAL 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A VAL* 4.2 15.5 - - + -
412A ILE* 5.1 7.1 - - + +
415A VAL* 5.5 4.0 - - + -
416A LEU* 4.9 4.5 - - + -
421A PHE* 4.2 29.2 - - + -
425A PHE* 4.5 4.9 - - + -
436A MET* 3.1 29.5 + - + +
437A SER 4.0 3.1 - - - +
439A TYR* 1.3 73.5 - - + +
441A LEU* 1.3 68.5 + - - +
443A ASN* 3.0 17.8 + - - +
444A VAL* 3.2 20.3 + - + +
463A LEU* 3.7 29.4 - - + -
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Residues in contact with LEU 441 (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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437A SER 3.1 18.5 + - - +
438A CYS* 4.0 2.7 - - - +
440A VAL* 1.3 78.5 - - - +
442A SER* 1.3 61.7 + - - +
444A VAL* 3.2 21.9 + - + +
445A LEU* 3.5 21.7 + - + +
460A ILE* 3.9 27.1 - - + +
463A LEU* 3.9 39.5 - - + +
464A VAL* 3.9 21.8 - - + -
467A LEU* 4.0 21.3 - - + -
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Residues in contact with SER 442 (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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438A CYS* 2.7 31.9 + - - -
439A TYR* 3.8 9.2 - - - -
441A LEU* 1.3 71.9 - - - +
443A ASN* 1.3 57.3 + - - +
445A LEU* 3.4 11.3 + - - +
446A ASP* 2.9 43.4 + - - +
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Residues in contact with ASN 443 (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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406A VAL* 3.8 25.0 + - + +
407A ASP* 4.6 8.5 + - - +
412A ILE* 3.1 26.7 - - + +
439A TYR* 3.5 16.3 + - - +
440A VAL 3.0 10.9 + - - +
442A SER* 1.3 76.6 - - - +
444A VAL* 1.3 63.8 + - - +
446A ASP* 3.9 9.0 - - - +
447A TYR* 3.1 52.0 + - - +
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Residues in contact with VAL 444 (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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412A ILE* 4.0 23.6 - - + -
416A LEU* 4.7 20.4 - - + -
440A VAL* 3.2 20.8 + - + +
441A LEU* 3.2 17.9 + - + +
443A ASN* 1.3 76.2 - - - +
445A LEU* 1.3 58.8 + - + +
447A TYR 2.6 20.3 - - - +
448A ASN 4.2 6.8 - - - -
449A THR* 4.2 19.3 + - - +
460A ILE* 5.7 11.0 - - + -
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Residues in contact with LEU 445 (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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441A LEU* 3.5 16.1 + - + +
442A SER* 3.4 9.3 + - - +
443A ASN 3.2 0.2 - - - -
444A VAL* 1.3 81.7 - - + +
446A ASP* 1.3 66.2 + - - +
447A TYR 3.1 9.3 + - - -
448A ASN* 4.0 9.2 + - - +
449A THR* 5.9 6.1 - - + -
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Residues in contact with ASP 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A SER* 2.9 38.1 + - - +
443A ASN* 3.5 14.8 + - - +
445A LEU* 1.3 75.5 - - - +
447A TYR* 1.3 73.0 - - + +
448A ASN* 4.4 3.3 + - - +
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Residues in contact with TYR 447 (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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410A ASN 5.3 6.3 - - - -
412A ILE* 3.8 19.5 - - + -
443A ASN* 3.1 31.2 + - - +
444A VAL* 2.6 30.5 - - - +
445A LEU 3.6 2.0 - - - -
446A ASP* 1.3 87.9 - - + +
448A ASN* 1.3 61.8 - - - +
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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