Contacts of the helix formed by residues 415 - 424 (chain E) in PDB entry 4KYI
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 HIS 415 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28E TYR* 4.3 2.0 - + - -
413E PHE* 4.0 5.6 - - - +
414E ASP* 1.3 79.5 - - - +
416E PRO* 1.3 81.7 - - + +
417E LEU* 3.1 36.5 + - + +
418E MET* 3.0 25.4 + - + +
419E ALA 3.6 2.6 + - - -
444E ALA* 5.2 4.3 - - + -
447E HIS* 5.5 1.6 - + - -
485E ALA* 2.7 39.0 + - + -
486E LYS 4.7 1.8 - - - -
487E MET* 3.7 21.0 - - + +
491E GLN* 3.6 31.4 - - + +
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Residues in contact with PRO 416 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ILE* 4.3 5.3 - - + +
28E TYR* 3.5 47.1 - - + +
415E HIS* 1.3 101.8 - - + +
417E LEU* 1.3 60.4 + - - +
418E MET 3.3 0.2 - - - -
419E ALA* 3.2 11.0 + - + +
420E ILE* 3.1 28.0 + - + +
440E GLU* 4.6 13.9 - - + +
441E ILE* 4.6 13.7 - - + -
444E ALA* 4.2 17.7 - - + -
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Residues in contact with LEU 417 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415E HIS* 3.1 19.9 + - + +
416E PRO* 1.3 75.3 - - - +
418E MET* 1.3 65.3 + - - +
420E ILE* 3.3 2.5 + - + +
421E LEU* 2.9 43.7 + - + +
444E ALA* 3.8 25.7 - - + +
447E HIS* 4.0 16.6 - - + +
448E ALA* 4.2 10.8 - - + +
451E ILE* 4.1 10.3 - - + -
480E ILE* 5.3 0.4 - - + +
481E LEU* 3.7 24.2 - - + -
485E ALA* 3.6 27.8 - - + -
487E MET* 3.6 5.4 - - + -
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Residues in contact with MET 418 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413E PHE* 3.7 23.1 - - + -
414E ASP* 5.9 1.3 - - + +
415E HIS* 3.0 19.5 + - + +
417E LEU* 1.3 79.5 - - - +
419E ALA* 1.3 61.2 + - - +
421E LEU* 3.4 5.6 + - - -
422E TYR* 3.0 28.3 + - + +
487E MET* 4.5 4.4 - - + +
491E GLN* 4.8 5.8 - - + +
494E LYS* 3.7 8.7 - - + -
495E ALA* 3.5 37.2 - - + +
498E LEU* 3.7 27.6 - - - -
545E VAL 3.3 29.8 - - - +
546E VAL* 4.8 6.1 - - - -
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Residues in contact with ALA 419 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ILE* 3.6 23.1 - - + -
28E TYR* 5.9 0.7 - - + -
30E VAL* 5.0 1.3 - - + -
413E PHE* 3.8 35.8 - - + -
415E HIS 3.6 2.0 + - - -
416E PRO* 3.2 15.7 + - + +
417E LEU 3.2 0.2 - - - -
418E MET* 1.3 80.2 - - - +
420E ILE* 1.3 62.2 + - - +
422E TYR* 3.2 0.7 + - - -
423E ILE* 3.1 36.4 + - + +
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Residues in contact with ILE 420 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ILE* 3.6 19.1 - - + -
416E PRO* 3.1 18.0 + - + +
417E LEU* 3.3 4.4 + - - +
419E ALA* 1.3 75.7 - - - +
421E LEU* 1.3 58.2 + - - +
422E TYR 3.4 0.2 - - - -
424E GLY* 3.1 21.6 - - - -
425E HIS* 3.7 16.6 + - + +
428E LEU* 4.0 17.0 - - + -
441E ILE* 4.3 11.0 - - + +
444E ALA* 3.9 11.7 - - + +
445E SER* 3.8 38.8 - - - +
448E ALA* 3.6 24.5 - - + +
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Residues in contact with LEU 421 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365E TYR* 4.2 5.9 - - - -
417E LEU* 2.9 40.9 + - + +
418E MET* 3.9 5.8 - - - +
420E ILE* 1.3 78.2 - - - +
422E TYR* 1.3 57.9 + - - +
424E GLY* 4.5 1.6 - - - -
448E ALA* 4.6 11.9 - - + +
451E ILE* 4.1 31.2 - - + -
452E LEU* 5.5 2.9 - - + +
455E GLN* 4.8 3.4 - - - +
481E LEU* 4.5 7.0 - - + -
495E ALA* 4.8 7.9 - - + +
498E LEU* 4.0 11.9 - - + -
499E CYS* 3.6 26.9 - - - -
502E GLN* 2.5 40.4 + - - +
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Residues in contact with TYR 422 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363E LYS* 4.1 13.3 + - - +
364E VAL 3.5 21.8 - - - -
365E TYR* 3.5 6.5 + - - -
366E TYR* 2.6 78.4 + + + +
411E GLN* 4.4 4.0 - - - -
413E PHE* 3.9 24.9 - + + -
418E MET* 3.0 19.1 + - - +
419E ALA 4.0 2.5 - - - +
421E LEU* 1.3 78.9 - - - +
423E ILE* 1.3 55.1 - - + +
498E LEU* 4.0 13.5 - - + -
502E GLN* 4.5 0.9 - - - +
542E ILE* 5.5 1.8 - - + -
546E VAL* 3.8 37.7 - - + +
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Residues in contact with ILE 423 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E SER* 5.6 2.5 - - - +
20E ILE* 5.0 0.2 - - + -
30E VAL* 3.8 30.1 - - + -
365E TYR* 4.7 5.7 - - - +
366E TYR* 3.3 36.7 + - + +
411E GLN* 4.2 14.6 - - - +
413E PHE* 5.2 1.3 - - + -
419E ALA* 3.1 22.4 + - + +
422E TYR* 1.3 83.2 - - + +
424E GLY* 1.3 68.1 + - - +
427E LYS* 3.6 38.0 + - + +
428E LEU* 4.0 22.2 - - + -
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Residues in contact with GLY 424 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365E TYR* 4.8 8.3 - - - -
420E ILE 3.1 17.9 - - - -
421E LEU 4.5 3.6 - - - -
422E TYR 4.0 1.1 - - - -
423E ILE* 1.3 83.2 + - - +
425E HIS* 1.3 61.2 + - - +
426E ASP* 3.4 7.7 + - - +
427E LYS* 4.8 3.0 - - - +
428E LEU* 3.2 27.4 + - - +
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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