Contacts of the helix formed by residues 448 - 460 (chain A) in PDB entry 3DYQ
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 448 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421A LEU* 4.0 8.1 - - - -
447A VAL* 1.3 79.4 - - - +
449A LYS* 1.3 67.2 + - - +
450A ALA* 3.7 6.1 + - - +
451A THR* 2.9 31.9 + - + +
452A ALA* 2.8 23.0 + - - +
494A LYS* 5.9 0.2 - - - +
497A ASP* 4.1 14.9 + - + +
501A LYS* 3.6 30.1 - - - +
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Residues in contact with LYS 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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414A GLU* 3.0 40.1 + - - +
417A VAL* 3.9 25.6 - - + +
418A ASP* 3.0 43.6 + - - +
421A LEU* 3.8 12.4 - - + +
448A THR* 1.3 73.5 - - - +
450A ALA* 1.3 62.6 - - - +
452A ALA* 3.3 2.8 + - - +
453A GLN* 2.9 28.3 + - - +
490A TYR* 4.5 12.2 + - + -
493A LEU* 4.8 10.1 - - + -
497A ASP* 5.4 0.2 + - - -
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Residues in contact with ALA 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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448A THR* 3.2 7.3 - - - +
449A LYS* 1.3 79.5 - - - +
451A THR* 1.3 57.4 + - - +
453A GLN* 3.3 0.9 + - - +
454A ILE* 3.0 37.4 + - - +
490A TYR* 3.7 33.7 - - - +
493A LEU* 4.3 8.5 - - + +
494A LYS* 3.9 24.9 - - + +
497A ASP* 4.2 9.2 + - - +
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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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446A LYS 4.2 6.0 + - - +
447A VAL* 3.7 8.8 - - - +
448A THR* 2.9 37.1 + - + +
450A ALA* 1.3 76.0 - - - +
452A ALA* 1.3 67.7 + - - +
453A GLN 3.3 0.3 + - - -
454A ILE* 3.7 9.8 + - - +
455A GLY* 3.8 8.5 + - - -
494A LYS* 3.9 31.4 - - + -
498A ASP* 5.8 0.9 - - - +
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Residues in contact with ALA 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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417A VAL* 4.9 1.8 - - + -
420A LEU* 6.1 0.2 - - + -
421A LEU* 4.3 22.9 - - + -
424A TYR* 6.1 1.6 - - + -
441A PHE 6.0 0.9 - - - +
447A VAL* 4.5 9.5 - - + +
448A THR 2.8 18.6 + - - +
449A LYS* 3.3 7.2 - - - +
451A THR* 1.3 79.5 + - - +
453A GLN* 1.3 70.1 + - - +
455A GLY* 4.8 0.2 - - - -
456A PHE* 3.4 11.6 + - - +
900A PCG 3.3 20.0 + - - +
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Residues in contact with GLN 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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406A GLU* 2.9 24.9 + - - +
417A VAL* 3.4 24.8 - - + +
420A LEU* 4.9 0.2 - - - +
449A LYS 2.9 22.1 + - - +
452A ALA* 1.3 78.0 - - - +
454A ILE* 1.3 60.8 + - - +
456A PHE* 4.3 2.4 - - - -
457A ILE* 2.8 40.6 + - + +
490A TYR* 3.6 35.9 - - + -
900A PCG 2.6 54.6 + - - -
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Residues in contact with ILE 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 ALA 3.0 29.7 + - - +
451A THR* 4.4 4.0 - - - +
452A ALA 3.5 0.2 - - - -
453A GLN* 1.3 76.3 - - - +
455A GLY* 1.3 64.1 + - - +
457A ILE* 3.8 4.4 - - - +
458A LYS* 3.0 50.4 + - + +
487A ARG* 4.4 4.9 - - + +
490A TYR* 3.6 38.8 - - + +
491A GLU* 3.8 25.1 - - + +
494A LYS* 4.1 21.5 - - + -
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Residues in contact with GLY 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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451A THR 3.8 9.8 + - - -
452A ALA 4.8 0.2 - - - -
453A GLN 3.4 0.2 - - - -
454A ILE* 1.3 78.8 - - - +
456A PHE* 1.3 63.4 + - - +
459A PHE* 2.9 48.8 + - - +
460A VAL* 4.9 0.2 - - - +
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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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365A MET* 4.7 6.7 - - + -
403A ILE* 4.0 19.7 - - + -
452A ALA 3.4 20.6 + - - +
453A GLN* 3.3 5.6 + - - +
454A ILE 3.3 0.4 - - - -
455A GLY* 1.3 77.4 - - - +
457A ILE* 1.3 57.8 + - + +
460A VAL* 3.0 40.4 + - + +
461A LEU* 3.0 49.5 + - + -
900A PCG 3.2 78.7 - + - +
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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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406A GLU* 4.2 13.2 - - + -
453A GLN* 2.8 29.5 + - + +
454A ILE* 3.8 3.1 - - - +
456A PHE* 1.3 75.4 - - + +
458A LYS* 1.3 60.4 + - - +
459A PHE 3.5 0.2 + - - -
461A LEU* 4.1 19.5 - - + -
462A ILE* 2.9 43.6 + - + +
483A LEU* 3.7 25.1 - - + +
486A SER* 3.7 27.6 - - - +
487A ARG* 3.7 28.9 - - + +
490A TYR* 4.1 11.9 - - + -
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Residues in contact with LYS 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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454A ILE* 3.0 40.1 + - + +
457A ILE* 1.3 77.3 - - - +
459A PHE* 1.3 91.7 + - + +
462A ILE* 4.1 9.6 - - + +
463A PRO* 3.3 18.8 - - - +
487A ARG* 4.0 27.1 - - + +
491A GLU* 3.4 20.0 + - - +
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Residues in contact with PHE 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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368A HIS* 5.3 2.4 + - - -
454A ILE* 6.1 0.2 - - + -
455A GLY* 2.9 34.8 + - - +
458A LYS* 1.3 112.1 - - + +
460A VAL* 1.3 64.0 + - + +
463A PRO* 3.5 15.2 - - - +
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Residues in contact with VAL 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A MET* 4.2 12.6 - - + -
368A HIS* 3.7 27.7 + - + +
403A ILE* 3.7 26.0 - - + -
455A GLY 4.9 0.4 - - - +
456A PHE* 3.0 40.7 + - + +
459A PHE* 1.3 83.7 - - + +
461A LEU* 1.3 65.4 + - - +
462A ILE 3.7 0.2 - - - -
463A PRO* 3.6 2.5 - - - +
464A MET* 3.3 23.2 + - - +
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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
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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