Contacts of the helix formed by residues 450 - 460 (chain A) in PDB entry 5KYT
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 ALA 450 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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435A VAL* 4.2 21.5 - - + +
436A ASP* 5.3 0.2 - - - +
441A LEU* 3.8 16.2 - - + -
448A GLN* 4.2 2.8 - - + +
449A VAL* 1.3 78.2 - - - +
451A PRO* 1.3 69.2 - - + +
452A ALA* 3.2 5.4 - - + +
453A GLU* 3.0 39.3 + - + +
454A LEU* 3.7 2.9 + - - +
510A LYS* 6.1 0.8 - - - +
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Residues in contact with PRO 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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436A ASP* 3.8 18.8 - - - +
440A SER* 3.3 27.8 - - - +
441A LEU* 4.1 4.0 - - + -
442A ILE* 3.8 9.2 - - + -
449A VAL* 3.3 10.8 - - + +
450A ALA* 1.3 82.7 - - - +
452A ALA* 1.3 51.1 + - - +
454A LEU* 3.1 4.8 + - + +
455A GLU* 2.7 47.6 + - - +
469A VAL* 3.5 39.4 - - + +
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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
----------------------------------------------------------
318A PRO* 6.1 5.6 - - + -
435A VAL 4.6 14.6 - - - +
436A ASP* 4.3 5.8 + - - +
450A ALA* 3.1 3.9 + - + -
451A PRO* 1.3 78.7 - - - +
453A GLU* 1.3 60.6 + - + +
455A GLU* 3.6 14.0 + - - +
456A SER* 2.8 32.1 + - - -
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Residues in contact with GLU 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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450A ALA* 3.0 27.7 + - + +
452A ALA* 1.3 77.9 - - + +
454A LEU* 1.3 64.1 + - + +
456A SER* 3.7 4.7 + - - -
457A ILE* 3.2 32.7 + - + +
510A LYS* 3.3 34.0 + - + +
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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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449A VAL* 4.0 18.4 - - + -
450A ALA 3.7 2.1 + - - +
451A PRO 3.1 7.9 + - - +
453A GLU* 1.3 77.6 - - + +
455A GLU* 1.3 60.6 + - - +
457A ILE* 3.3 5.0 + - + +
458A LEU* 2.9 35.3 + - + +
469A VAL* 3.8 25.6 - - + -
481A PRO* 3.8 28.5 - - + -
502A VAL* 3.8 25.4 - - + -
506A VAL* 4.0 14.6 - - + -
510A LYS* 3.5 27.4 - - + +
511A LYS 5.2 0.2 - - - -
512A LEU* 4.4 8.7 - - + -
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Residues in contact with GLU 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 PRO* 2.7 32.5 + - - +
452A ALA* 3.6 14.9 + - - +
454A LEU* 1.3 69.9 - - - +
456A SER* 1.3 59.9 + - - +
458A LEU* 3.1 6.9 + - - +
459A LEU* 2.8 38.4 + - + +
467A ALA* 3.8 17.9 - - - +
468A GLY* 3.4 0.4 - - - -
469A VAL* 2.9 37.7 + - + +
530A LEU* 3.2 28.2 - - - +
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Residues in contact with SER 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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320A SER* 4.8 10.2 - - - -
322A GLU* 3.3 31.6 + - - +
452A ALA 2.8 22.5 + - - -
453A GLU* 4.0 5.6 - - - -
455A GLU* 1.3 72.9 - - - +
457A ILE* 1.3 61.5 + - - +
459A LEU* 3.5 12.4 + - - +
460A GLN* 3.4 18.7 + - - +
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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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453A GLU* 3.2 21.7 + - + +
454A LEU* 3.5 7.6 - - + +
455A GLU 3.1 0.8 - - - -
456A SER* 1.3 77.6 - - - +
458A LEU* 1.3 64.1 + - - +
460A GLN* 3.3 19.7 - - - +
501A TYR* 3.4 16.2 + - + -
502A VAL* 4.2 22.0 - - + -
505A GLN* 3.9 31.9 - - + +
506A VAL* 3.0 35.2 - - + -
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Residues in contact with LEU 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 LEU* 2.9 22.8 + - + +
455A GLU* 3.1 4.2 + - - +
457A ILE* 1.3 71.7 - - - +
459A LEU* 1.3 65.6 + - - +
460A GLN 3.1 3.4 + - - -
461A HIS* 3.3 20.5 + - + +
465A PHE 6.0 0.2 + - - -
467A ALA* 4.1 21.8 - - + -
469A VAL* 4.1 11.9 - - + -
483A ALA* 3.6 30.5 - - + -
485A VAL* 5.7 5.6 - - + -
498A ILE* 4.8 13.7 - - + +
501A TYR* 4.9 6.7 - - + -
502A VAL* 3.5 29.6 - - + -
512A LEU* 4.5 10.1 - - + -
516A VAL* 6.0 0.7 - - + -
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Residues in contact with LEU 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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320A SER* 5.7 3.8 - - - +
323A VAL* 5.1 15.7 - - + -
455A GLU* 2.8 25.6 + - + +
456A SER* 3.7 10.8 - - - +
457A ILE 3.3 0.4 - - - -
458A LEU* 1.3 76.5 - - - +
460A GLN* 1.3 63.9 + - - +
461A HIS 3.2 7.3 + - - +
465A PHE 3.9 23.8 - - - +
466A ASP* 4.1 20.4 - - - +
467A ALA* 4.1 12.6 - - + +
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Residues in contact with GLN 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 SER 3.4 9.3 + - - +
457A ILE* 3.3 17.7 + - - +
458A LEU 3.1 0.6 - - - -
459A LEU* 1.3 79.7 - - - +
461A HIS* 1.3 59.2 + - - +
462A PRO* 3.4 8.3 - - - +
501A TYR* 3.4 15.0 + - - +
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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