Contacts of the helix formed by residues 415 - 423 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28C TYR* 4.1 3.8 - - - +
413C PHE* 3.5 11.7 - - - +
414C ASP* 1.3 80.9 - - - +
416C PRO* 1.3 87.8 - - + +
417C LEU* 3.4 22.6 + - + +
418C MET* 3.5 23.2 + - + +
419C ALA 3.7 1.0 + - - -
444C ALA* 5.5 1.3 - - + -
485C ALA* 4.1 13.2 - - + -
486C LYS 3.5 20.6 + - - -
487C MET* 3.6 30.9 - - + +
491C GLN* 3.3 34.3 - - + +
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Residues in contact with PRO 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ILE* 5.3 3.8 - - + +
28C TYR* 3.5 37.0 - - + +
415C HIS* 1.3 100.2 - - + +
417C LEU* 1.3 64.9 + - - +
419C ALA* 3.1 17.9 + - + +
420C ILE* 3.1 18.1 + - + +
440C GLU* 4.3 13.9 - - + +
441C ILE* 4.1 24.5 - - + -
444C ALA* 4.1 17.3 - - + -
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Residues in contact with LEU 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415C HIS* 3.4 16.2 + - + +
416C PRO* 1.3 77.4 - - - +
418C MET* 1.3 54.5 + - - +
420C ILE* 2.9 7.5 + - + -
421C LEU* 2.8 58.3 + - + +
444C ALA* 3.6 28.6 - - + +
447C HIS* 3.7 15.0 - - + -
448C ALA* 3.9 18.2 - - + +
451C ILE* 4.4 4.5 - - + -
480C ILE* 5.0 0.4 - - + -
481C LEU* 4.3 11.2 - - + -
485C ALA* 3.7 20.9 - - + -
487C MET* 3.6 22.9 - - + -
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Residues in contact with MET 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413C PHE* 3.7 25.6 - - + -
415C HIS* 3.5 22.3 + - + +
417C LEU* 1.3 78.3 - - - +
419C ALA* 1.3 56.6 + - - +
421C LEU* 3.3 7.3 + - - +
422C TYR* 3.0 32.4 + - - +
487C MET* 4.9 3.2 - - + +
491C GLN* 5.1 3.6 - - + +
494C LYS* 3.7 17.0 - - + +
495C ALA* 3.6 36.6 - - + +
498C LEU* 3.6 18.6 - - + -
545C VAL 3.4 26.9 - - - +
546C VAL* 4.9 4.3 - - - -
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Residues in contact with ALA 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ILE* 4.8 16.2 - - + -
28C TYR* 5.9 3.1 - - + +
30C VAL* 5.0 3.6 - - + -
413C PHE* 3.5 33.8 - - + -
415C HIS 3.7 2.1 + - - +
416C PRO* 3.1 15.9 + - + +
418C MET* 1.3 79.3 - - - +
420C ILE* 1.3 63.4 + - + +
422C TYR* 4.7 0.2 - - - -
423C ILE* 3.0 39.8 + - + +
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Residues in contact with ILE 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ILE* 3.7 34.3 - - + -
416C PRO* 3.1 20.6 - - + +
417C LEU* 2.9 9.5 + - + +
419C ALA* 1.3 74.8 - - - +
421C LEU* 1.3 57.2 + - - +
424C GLY 3.7 7.2 - - - +
425C HIS* 2.7 55.6 + - - +
428C LEU* 3.8 9.2 - - + -
441C ILE* 5.8 4.9 - - + +
444C ALA* 4.4 13.7 - - + +
445C SER* 4.7 11.4 - - - +
448C ALA* 3.7 23.3 - - + +
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Residues in contact with LEU 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365C TYR* 4.1 4.5 - - - -
417C LEU* 2.8 40.7 + - + +
418C MET* 3.7 3.8 - - - +
420C ILE* 1.3 82.9 - - - +
422C TYR* 1.3 54.7 - - - +
423C ILE 3.7 0.2 - - - -
424C GLY* 4.1 1.9 - - - -
448C ALA* 4.7 9.0 - - + +
451C ILE* 4.3 24.7 - - + -
455C GLN* 5.3 2.7 - - - +
481C LEU* 4.7 2.5 - - + -
495C ALA* 4.3 21.8 - - + +
498C LEU* 3.6 18.2 - - + -
499C CYS* 4.0 26.9 - - - -
502C GLN* 2.3 40.9 + - - +
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Residues in contact with TYR 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363C LYS* 4.3 9.6 + - - +
364C VAL* 3.3 25.1 - - - -
365C TYR* 3.6 7.8 + - - -
366C TYR* 2.8 66.3 + + + -
411C GLN* 3.9 19.1 + - - -
413C PHE* 3.8 22.7 - + + -
418C MET* 3.0 18.5 + - - +
419C ALA 4.0 2.0 - - - +
421C LEU* 1.3 79.6 - - - +
423C ILE* 1.3 64.3 + - + +
498C LEU* 4.2 11.7 - - + -
502C GLN* 4.3 0.9 - - - +
542C ILE* 5.1 4.0 - - + +
546C VAL* 3.7 38.7 - - + +
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Residues in contact with ILE 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C SER* 5.9 0.7 - - - -
30C VAL* 4.2 26.2 - - + -
365C TYR* 4.7 6.1 - - - +
366C TYR* 3.5 51.2 + - + +
367C ASN* 5.3 0.2 - - - +
411C GLN* 5.2 4.5 - - + -
413C PHE* 5.1 6.1 - - + -
419C ALA* 3.0 22.2 + - - +
422C TYR* 1.3 84.5 - - + +
424C GLY* 1.3 55.6 + - - +
426C ASP 4.4 3.4 - - - +
427C LYS* 4.4 21.8 - - + +
428C LEU* 3.8 29.4 - - + -
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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