Contacts of the helix formed by residues 415 - 424 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28G TYR* 4.1 4.5 - + - -
413G PHE* 3.7 7.5 - - - +
414G ASP* 1.3 80.4 - - - +
416G PRO* 1.3 81.2 - - + +
417G LEU* 3.0 40.5 + - + +
418G MET* 3.2 22.0 + - + +
419G ALA 3.4 3.6 + - - -
444G ALA* 5.0 4.0 - - + -
447G HIS* 5.6 1.1 - + - -
485G ALA* 3.9 15.0 - - + -
486G LYS* 3.9 22.1 + - - +
487G MET* 3.6 32.3 - - + +
491G GLN* 3.5 23.1 - - + +
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Residues in contact with PRO 416 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G ILE* 4.3 3.8 - - + +
28G TYR* 3.5 37.6 - - + +
415G HIS* 1.3 98.5 - - + +
417G LEU* 1.3 59.7 + - - +
419G ALA* 3.0 11.4 + - + +
420G ILE* 2.8 34.2 + - + +
440G GLU* 4.7 8.1 - - + +
441G ILE* 3.8 27.4 - - + -
444G ALA* 3.9 18.4 - - + -
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Residues in contact with LEU 417 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415G HIS* 3.0 17.9 + - + +
416G PRO* 1.3 79.1 - - - +
418G MET* 1.3 63.5 + - - +
420G ILE* 3.2 3.3 + - - +
421G LEU* 2.9 52.2 + - + +
444G ALA* 3.9 15.8 - - + +
447G HIS* 3.7 20.6 - - + -
448G ALA* 3.9 26.0 - - + +
451G ILE* 4.2 4.5 - - + -
480G ILE 5.0 1.1 - - - +
481G LEU* 3.7 20.9 - - + -
485G ALA* 3.7 28.0 - - + -
487G MET* 3.7 4.5 - - + -
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Residues in contact with MET 418 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413G PHE* 3.4 25.4 - - + -
414G ASP 5.6 0.9 - - - +
415G HIS* 3.2 21.3 + - + +
416G PRO 3.2 0.6 - - - -
417G LEU* 1.3 79.2 - - - +
419G ALA* 1.3 60.5 + - - +
421G LEU* 3.4 6.3 + - - +
422G TYR* 3.1 22.5 + - - +
487G MET* 4.4 5.6 - - + +
491G GLN 4.7 3.1 - - - +
494G LYS* 3.6 9.0 - - + +
495G ALA* 3.5 35.0 - - + +
498G LEU* 3.6 18.4 - - + -
545G VAL 3.3 27.1 - - - +
546G VAL* 4.6 11.7 - - - -
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Residues in contact with ALA 419 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G ILE* 3.6 24.2 - - + -
28G TYR* 5.7 1.3 - - + -
30G VAL* 5.0 3.6 - - + -
413G PHE* 3.5 36.1 - - + -
415G HIS 3.4 2.0 + - - -
416G PRO* 3.0 16.0 + - + +
418G MET* 1.3 81.9 - - - +
420G ILE* 1.3 63.2 + - - +
421G LEU 3.4 0.7 + - - -
422G TYR* 3.4 1.0 + - - +
423G ILE* 3.1 30.1 + - - +
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Residues in contact with ILE 420 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G ILE* 3.6 20.2 - - + -
416G PRO* 2.8 27.5 + - + +
417G LEU* 3.2 6.3 + - - +
419G ALA* 1.3 72.9 - - - +
421G LEU* 1.3 58.6 + - - +
424G GLY* 3.1 27.0 - - - -
425G HIS* 3.5 14.9 + - + -
428G LEU* 3.9 17.5 - - + -
429G LYS* 4.5 9.4 - - - +
441G ILE* 4.7 7.4 - - + -
444G ALA* 4.2 15.0 - - + +
445G SER* 4.4 22.9 - - - +
448G ALA* 3.6 26.5 - - + -
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Residues in contact with LEU 421 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365G TYR* 3.9 10.4 - - - -
417G LEU* 2.9 37.1 + - + +
418G MET* 3.9 2.7 - - - +
419G ALA 3.2 0.2 - - - -
420G ILE* 1.3 79.0 - - - +
422G TYR* 1.3 60.2 + - - +
423G ILE 3.7 0.2 + - - -
424G GLY* 4.2 1.7 - - - -
448G ALA* 3.8 27.6 - - + +
451G ILE* 4.2 20.0 - - + -
452G LEU* 5.7 2.2 - - + +
455G GLN* 5.0 6.5 - - - +
481G LEU* 4.9 6.1 - - + -
495G ALA* 4.8 5.4 - - + +
498G LEU* 3.6 19.3 - - + -
499G CYS* 3.5 27.4 - - - -
502G GLN* 3.0 25.8 + - - +
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Residues in contact with TYR 422 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363G LYS* 3.7 29.4 + - - +
364G VAL 3.6 14.6 - - - -
365G TYR* 3.7 3.6 + - - -
366G TYR* 2.8 71.0 + + + +
411G GLN* 4.2 5.8 - - - -
413G PHE* 3.9 21.3 - + + -
418G MET* 3.1 21.2 + - - +
419G ALA 3.4 2.4 + - - +
420G ILE 3.4 0.2 - - - -
421G LEU* 1.3 77.6 - - - +
423G ILE* 1.3 60.9 + - + +
424G GLY 3.9 0.2 - - - -
498G LEU* 4.0 13.9 - - + -
502G GLN* 4.4 2.0 - - - +
542G ILE* 5.3 3.2 - - + +
546G VAL* 4.0 35.8 - - + +
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Residues in contact with ILE 423 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G SER* 5.5 2.7 - - - +
30G VAL* 4.7 10.5 - - + -
365G TYR* 4.8 4.2 - - - +
366G TYR* 3.4 38.6 + - + +
411G GLN* 3.4 33.2 - - - +
413G PHE* 5.2 2.2 - - + -
419G ALA* 3.1 20.8 + - + +
422G TYR* 1.3 81.4 - - + +
424G GLY* 1.3 69.6 + - - +
427G LYS* 3.6 29.6 + - + +
428G LEU* 3.7 25.4 - - + -
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Residues in contact with GLY 424 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365G TYR* 4.5 11.6 - - - -
420G ILE 3.1 18.2 - - - -
421G LEU 4.2 5.2 - - - -
422G TYR 4.1 1.1 - - - -
423G ILE* 1.3 90.2 + - - +
425G HIS* 1.3 64.8 + - - -
426G ASP* 3.2 4.0 + - - +
427G LYS* 3.3 8.5 + - - +
428G LEU* 3.2 8.7 - - - +
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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