Contacts of the helix formed by residues 444 - 457 (chain A) in PDB entry 4YCV
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 444 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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425A ILE* 3.7 3.6 - - - -
442A PRO* 2.8 31.2 + - + +
443A PRO* 1.3 78.5 - - - +
445A ALA* 1.3 65.1 + - - +
446A ALA* 4.1 5.3 + - - +
447A LYS* 3.6 19.1 + - - +
448A LEU* 3.1 18.9 + - - +
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Residues in contact with ALA 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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419A PHE* 5.1 0.4 - - + -
420A ASP* 3.4 41.2 - - + +
425A ILE* 3.5 13.1 - - + +
428A MET* 3.7 17.6 - - + +
444A THR* 1.3 72.5 - - - +
446A ALA* 1.3 62.4 - - - +
448A LEU* 3.1 3.7 + - - +
449A LEU* 2.8 38.0 + - + +
474A ILE* 5.2 4.7 - - + -
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Residues in contact with ALA 446 (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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444A THR* 4.1 5.1 + - - +
445A ALA* 1.3 78.8 - - - +
447A LYS* 1.3 57.3 + - - +
449A LEU* 3.3 5.5 + - - +
450A ASP* 2.9 29.3 + - - +
474A ILE* 4.1 30.4 - - + +
475A MET* 4.1 21.8 - - + +
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Residues in contact with LYS 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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440A PRO* 4.2 17.1 - - + +
442A PRO* 4.0 13.9 - - + +
444A THR* 3.6 19.9 + - - +
445A ALA 3.2 0.2 - - - -
446A ALA* 1.3 79.0 - - - +
448A LEU* 1.3 63.5 + - + +
450A ASP* 3.1 8.6 + - - +
451A GLN* 2.9 24.3 + - - +
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Residues in contact with LEU 448 (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 ILE* 3.4 29.4 - - + +
428A MET* 3.9 23.3 - - + -
429A ILE* 3.9 28.7 - - + -
432A ILE* 3.5 28.4 - - + +
439A LEU* 5.3 3.4 - - + -
440A PRO* 4.4 9.9 - - + +
443A PRO* 3.9 18.8 - - + +
444A THR 3.1 17.2 + - - +
445A ALA 3.1 3.7 + - - +
447A LYS* 1.3 75.7 - - - +
449A LEU* 1.3 58.1 + - - +
451A GLN* 3.4 3.5 + - - +
452A LEU* 2.9 36.3 + - - +
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Residues in contact with LEU 449 (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 ILE* 4.4 1.9 - - + +
404A VAL* 5.0 4.5 - - + -
407A ILE* 4.3 19.6 - - + +
415A LEU* 5.0 3.6 - - + -
419A PHE* 3.6 38.6 - - + -
428A MET* 3.9 13.2 - - + -
445A ALA* 2.8 20.1 + - + +
446A ALA 3.6 1.3 - - - +
448A LEU* 1.3 74.0 - - - +
450A ASP* 1.3 59.9 + - - +
452A LEU* 3.8 4.2 - - + +
453A ALA* 2.9 33.7 + - - +
472A PRO* 3.6 33.7 - - + -
474A ILE* 4.1 13.0 - - + -
475A MET* 3.5 20.2 - - + -
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Residues in contact with ASP 450 (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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446A ALA 2.9 13.4 + - - +
447A LYS* 3.1 11.6 + - - +
449A LEU* 1.3 78.4 - - - +
451A GLN* 1.3 49.9 + - - +
453A ALA* 3.8 4.2 - - - +
454A SER* 2.3 48.2 + - - -
458A GLU* 4.6 6.0 - - - +
475A MET* 4.5 14.5 - - + +
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Residues in contact with GLN 451 (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 ILE* 4.4 8.1 - - + -
437A ILE* 3.7 31.6 - - + +
438A GLU* 4.0 15.6 - - + +
440A PRO* 4.0 33.0 - - + +
447A LYS 2.9 13.0 + - - +
448A LEU 3.6 8.1 - - - +
450A ASP* 1.3 74.0 + - - +
452A LEU* 1.3 66.5 - - - +
454A SER* 3.3 8.3 + - - -
455A HIS* 2.9 28.3 + - - +
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Residues in contact with LEU 452 (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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407A ILE* 3.9 17.0 - - + -
415A LEU* 4.5 11.9 - - + -
428A MET* 4.0 41.3 - - + +
431A ILE* 3.5 32.1 - - + -
432A ILE* 4.1 17.0 - - + +
437A ILE* 4.7 4.5 - - + -
448A LEU 2.9 25.3 + - - +
449A LEU* 3.8 4.9 - - + +
451A GLN* 1.3 73.9 - - - +
453A ALA* 1.3 63.5 + - - +
455A HIS* 3.2 2.1 + - - -
456A PHE* 2.9 48.6 + - + +
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Residues in contact with ALA 453 (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 ILE* 3.6 32.5 - - + -
407A ILE* 3.7 9.1 - - + +
449A LEU 2.9 22.6 + - - +
450A ASP* 3.8 4.7 - - - +
452A LEU* 1.3 73.1 - - - +
454A SER* 1.3 54.1 + - - +
457A ILE* 2.6 43.7 + - + +
458A GLU* 3.0 4.8 + - + +
468A ILE* 5.4 5.6 - - + -
475A MET* 5.7 0.2 - - + -
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Residues in contact with SER 454 (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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450A ASP* 2.3 37.4 + - - -
451A GLN* 3.3 12.4 + - - -
453A ALA* 1.3 74.5 - - - +
455A HIS* 1.3 64.1 + - - +
456A PHE 3.2 0.7 + - - -
458A GLU* 3.4 50.8 + - - +
459A ASN* 4.5 2.9 + - - +
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Residues in contact with HIS 455 (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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435A HIS* 4.7 11.5 + - + +
437A ILE* 3.4 47.1 - - + +
451A GLN* 2.9 24.0 + - - +
452A LEU 4.0 1.8 - - - +
454A SER* 1.3 73.0 - - - +
456A PHE* 1.3 83.5 + + - +
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Residues in contact with PHE 456 (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 GLU 5.7 0.2 - - - +
407A ILE* 4.8 12.6 - - + -
410A VAL* 3.6 40.2 - - + -
411A THR* 4.8 7.6 - - - -
431A ILE* 4.1 9.4 - - + -
435A HIS* 3.9 34.1 - + - -
437A ILE* 4.4 5.8 - - + -
452A LEU* 2.9 52.1 + - + +
455A HIS* 1.3 100.9 - + - +
457A ILE* 1.3 70.7 + - + +
459A ASN 4.8 0.7 + - - -
460A LYS* 4.2 13.0 + - - +
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Residues in contact with ILE 457 (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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401A VAL* 3.9 20.6 - - + -
402A SER 4.3 3.8 - - - +
403A ILE* 3.2 48.5 - - + +
406A GLU* 4.7 12.3 - - + +
407A ILE* 3.8 14.1 - - + +
410A VAL* 6.6 0.2 - - + -
453A ALA* 2.6 24.9 + - + +
456A PHE* 1.3 77.1 - - + +
458A GLU* 1.3 54.6 + - - +
459A ASN 3.3 2.2 - - - -
460A LYS* 2.7 33.7 + - + +
466A PHE* 3.5 8.7 - - + -
468A ILE* 3.6 27.6 - - + -
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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
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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