Contacts of the helix formed by residues 450 - 463 (chain A) in PDB entry 3Q0F
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 VAL 450 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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448A GLN* 2.7 35.1 + - + +
449A LEU* 1.3 80.2 - - - +
451A THR* 1.3 96.8 + - + +
453A ASN* 3.1 15.1 + - - +
454A LEU* 3.7 8.8 - - + +
5B G 6.1 0.9 - - - +
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Residues in contact with THR 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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397A TYR* 3.6 28.0 - - - +
405A LEU* 3.6 19.6 - - - +
431A GLN* 3.5 14.3 + - - +
450A VAL* 1.3 96.7 + - + +
452A GLY* 1.3 58.1 + - - -
453A ASN* 5.4 0.2 - - - -
454A LEU* 3.1 2.3 + - - +
455A ALA* 2.8 33.6 + - - +
5B G 4.9 4.6 + - - +
10C G 5.0 14.8 - - - +
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Residues in contact with GLY 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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395A ILE* 3.6 26.7 - - - +
397A TYR* 3.5 14.2 - - - -
431A GLN* 3.4 14.4 - - - +
451A THR* 1.3 81.7 + - - +
453A ASN* 1.3 62.4 + - - -
455A ALA* 2.9 3.3 + - - +
456A LEU* 2.8 24.4 + - - +
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Residues in contact with ASN 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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395A ILE* 3.7 4.3 - - - +
430A GLY* 3.3 10.8 - - - -
431A GLN* 2.8 55.3 + - - +
447A GLN* 4.2 0.6 - - - +
448A GLN 3.1 27.3 + - - +
449A LEU* 4.2 11.6 - - + +
450A VAL* 3.1 4.3 + - - +
452A GLY* 1.3 75.5 - - - +
454A LEU* 1.3 63.1 + - - +
456A LEU* 3.3 3.6 + - - +
457A LYS* 3.1 18.0 + - - +
509A PHE* 3.6 19.8 - - + -
511A PHE* 3.6 15.1 - - + -
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Residues in contact with LEU 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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404A GLU* 6.4 0.4 - - + -
405A LEU* 3.8 20.0 - - + -
449A LEU* 3.6 39.9 - - + +
450A VAL* 3.3 9.8 + - + +
451A THR 3.1 8.1 + - - +
453A ASN* 1.3 75.8 - - - +
455A ALA* 1.3 68.7 + - - +
457A LYS* 3.1 9.8 + - + +
458A ASN* 2.9 53.4 + - - +
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Residues in contact with ALA 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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395A ILE* 4.9 0.2 - - + -
397A TYR* 3.4 36.6 - - + -
405A LEU* 3.8 18.1 - - + +
406A VAL* 3.7 1.5 - - - -
407A ALA* 3.4 20.3 + - + +
451A THR 2.8 17.1 + - - +
452A GLY* 3.2 10.3 - - - +
454A LEU* 1.3 73.6 - - - +
456A LEU* 1.3 63.0 - - - +
458A ASN* 3.2 3.8 + - - +
459A SER 3.0 16.5 + - - -
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Residues in contact with LEU 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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395A ILE* 3.8 27.1 - - + -
407A ALA* 3.7 21.1 - - + -
410A ILE* 4.2 13.7 - - + -
428A TYR* 4.0 16.8 - - + -
452A GLY 2.8 13.4 + - - +
453A ASN 3.6 7.4 - - - +
455A ALA* 1.3 73.5 - - - +
457A LYS* 1.3 59.6 + - - +
459A SER* 2.8 24.6 + - - -
460A ILE 3.4 3.3 + - - -
466A VAL* 5.0 2.0 - - + -
494A VAL* 3.7 32.5 - - + +
511A PHE* 3.7 38.8 - - + -
513A LEU* 4.8 7.2 - - + -
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Residues in contact with LYS 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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449A LEU* 3.8 25.6 - - + +
453A ASN 3.1 8.7 + - - +
454A LEU* 3.1 14.4 + - + +
456A LEU* 1.3 79.5 - - - +
458A ASN* 1.3 72.3 + - - +
460A ILE* 3.0 32.7 + - + +
461A ASN* 3.8 10.6 + - - +
497A TYR* 2.8 47.4 + - + +
511A PHE* 3.9 9.7 - - + -
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Residues in contact with ASN 458 (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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404A GLU* 3.4 31.1 + - - +
405A LEU 2.9 37.1 + - - +
406A VAL* 4.5 3.5 - - + +
454A LEU* 2.9 45.2 + - - +
455A ALA 3.6 1.6 - - - +
457A LYS* 1.3 83.2 - - - +
459A SER* 1.3 57.1 + - - +
460A ILE 3.1 0.2 - - - -
461A ASN* 3.6 8.2 + - - +
462A LYS* 3.1 27.5 + - - +
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Residues in contact with SER 459 (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* 3.9 2.3 - - - +
407A ALA* 3.2 29.3 + - - +
455A ALA 3.0 5.4 + - - -
456A LEU* 2.8 14.6 + - - -
458A ASN* 1.3 74.6 - - - +
460A ILE* 1.3 59.4 - - - +
462A LYS* 4.3 1.6 - - - -
463A LYS* 2.9 26.5 + - - -
464A ASN* 2.5 32.0 + - - +
466A VAL* 4.6 2.7 - - - -
494A VAL* 4.0 21.1 + - - +
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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
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456A LEU 3.4 0.9 + - - +
457A LYS* 3.0 22.2 + - + +
459A SER* 1.3 82.4 - - - +
461A ASN* 1.3 72.4 + - - +
463A LYS* 3.2 24.0 + - - +
494A VAL* 3.4 36.2 - - + +
495A GLU 3.8 16.2 - - - +
496A GLU* 3.7 24.0 - - - +
497A TYR* 3.7 27.4 - - + -
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Residues in contact with ASN 461 (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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457A LYS* 3.8 20.4 + - - +
458A ASN* 3.6 6.6 + - - +
460A ILE* 1.3 81.0 - - - +
462A LYS* 1.3 66.9 + - - +
463A LYS* 3.0 17.8 + - - +
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Residues in contact with LYS 462 (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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400A ASP* 4.7 22.0 - - + +
401A ASP 5.7 2.2 - - - -
406A VAL* 4.4 20.2 - - + -
458A ASN 3.1 19.2 + - - +
459A SER* 4.3 0.4 - - - -
461A ASN* 1.3 76.7 - - - +
463A LYS* 1.3 68.3 + - - +
464A ASN* 3.2 21.7 + - + +
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Residues in contact with LYS 463 (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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459A SER 2.9 13.9 + - - -
460A ILE* 3.3 19.0 + - - +
461A ASN* 3.5 13.6 + - - +
462A LYS* 1.3 77.6 - - - +
464A ASN* 1.3 63.8 + - - +
465A PRO* 4.0 2.6 - - - +
493A LEU* 3.7 22.7 - - + +
494A VAL 6.0 0.4 - - - +
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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
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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