Contacts of the helix formed by residues 441 - 450 (chain A) in PDB entry 2KR6
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 PHE 441 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378A GLY* 4.6 15.9 - - - -
379A VAL* 5.3 0.7 - - - -
380A LYS* 3.9 31.8 - - + +
390A SER* 3.8 46.2 - - - -
391A VAL* 6.3 1.1 - - - -
394A GLY* 4.4 13.7 - - - -
395A LYS* 5.6 4.7 - - - -
440A THR* 1.3 77.9 + - - +
442A GLY* 1.3 64.4 + - - +
443A LEU* 3.0 18.2 + - + +
444A VAL* 3.6 6.2 + - + +
445A PHE* 3.0 21.1 + - - +
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Residues in contact with GLY 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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391A VAL* 5.4 6.6 - - - +
395A LYS* 5.4 1.0 - - - +
411A PHE* 4.3 10.9 - - - -
440A THR 3.4 2.2 + - - -
441A PHE* 1.3 71.6 - - - +
443A LEU* 1.3 58.4 + - - +
445A PHE* 3.8 7.0 - - - -
446A TYR* 2.7 67.9 + - - +
447A PHE* 4.7 0.3 - - - -
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Residues in contact with LEU 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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395A LYS* 3.6 33.2 - - - +
398A ALA* 4.6 12.1 - - + -
411A PHE* 5.6 0.9 - - - -
441A PHE* 3.0 12.2 - - + +
442A GLY* 1.3 81.1 - - - +
444A VAL* 1.3 73.0 + - + +
447A PHE* 3.0 51.5 + - + +
467A ILE* 4.8 16.8 - - + -
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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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440A THR* 5.1 5.6 - - - +
441A PHE* 3.6 7.6 + - + +
443A LEU* 1.3 91.5 - - + +
445A PHE* 1.3 60.4 + - - +
447A PHE* 4.1 4.9 - - + +
448A ALA* 2.9 36.8 + - + +
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Residues in contact with PHE 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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418A LEU* 5.7 3.4 - - + -
422A LEU* 4.2 36.3 - - + -
432A LEU* 4.4 22.2 - - + +
438A SER* 3.1 34.5 - - - -
439A ILE* 6.1 0.4 - - - -
440A THR* 4.0 21.0 + - - +
441A PHE 3.0 21.1 + - - +
442A GLY* 3.8 4.5 - - - -
444A VAL* 1.3 74.9 - - - +
446A TYR* 1.3 83.4 + + - +
448A ALA* 3.0 8.0 + - + +
449A THR* 2.7 34.6 + - - -
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Residues in contact with TYR 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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411A PHE* 3.6 27.0 - + - -
414A ILE* 4.5 18.0 + - + +
415A LEU* 3.3 36.1 + - + +
418A LEU* 4.3 20.1 - - + +
442A GLY* 2.7 42.5 + - - +
443A LEU 4.4 0.2 - - - +
445A PHE* 1.3 94.1 - + - +
447A PHE* 1.3 57.7 + + + +
449A THR* 2.7 23.8 + - - -
450A ASP* 2.8 12.8 + - - +
455A PRO* 3.4 29.2 - - + +
457A MET* 3.9 21.0 - - + +
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Residues in contact with PHE 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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443A LEU* 3.0 43.4 + - + +
444A VAL* 4.1 5.2 - - - +
446A TYR* 1.3 82.1 - + + +
448A ALA* 1.3 60.5 + - - +
450A ASP* 3.4 17.1 - - - +
451A TYR* 3.8 13.7 - - - -
457A MET* 3.5 28.9 - - + -
461A ALA* 5.1 9.4 - - + -
465A PHE* 5.5 2.0 - - + -
466A TYR* 3.8 56.0 - + + -
467A ILE* 4.6 12.8 - - + -
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Residues in contact with ALA 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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432A LEU* 5.2 2.7 - - + -
434A ALA* 5.5 9.6 - - + -
444A VAL* 2.9 27.6 + - + +
445A PHE* 3.0 6.3 + - + +
447A PHE* 1.3 76.7 - - - +
449A THR* 1.3 60.9 + - - +
450A ASP 3.3 0.2 - - - -
451A TYR* 4.0 13.5 + - - +
452A LEU* 3.5 19.1 - - - +
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Residues in contact with THR 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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418A LEU* 6.1 2.7 - - + -
422A LEU* 5.9 3.4 - - + -
432A LEU* 4.1 21.3 - - + +
445A PHE* 2.7 30.4 + - + -
446A TYR* 2.7 9.1 + - - -
448A ALA* 1.3 75.2 - - - +
450A ASP* 1.3 54.1 + - - +
451A TYR 2.9 6.1 - - - -
452A LEU* 2.7 30.6 + - + -
453A VAL* 2.9 30.4 + - + +
454A GLN* 2.8 24.7 + - - +
455A PRO* 3.7 12.7 - - + +
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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 TYR 2.8 9.3 + - - +
447A PHE* 3.4 15.7 - - - +
448A ALA 3.3 0.6 - - - -
449A THR* 1.3 77.7 - - - +
451A TYR* 1.3 68.9 + - + +
452A LEU 3.3 0.2 - - - -
454A GLN* 2.8 32.1 - - - +
457A MET* 3.9 20.8 - - + +
458A ASP* 3.8 10.2 - - - +
464A GLN* 3.3 37.6 + - - +
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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