Contacts of the helix formed by residues 422 - 435 (chain C) in PDB entry 3K0J
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 LYS 422 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420C LYS 3.8 2.6 + - - +
421C ILE* 1.3 74.6 - - - +
423C LYS* 1.3 61.2 + - - +
424C ASP* 4.2 8.3 - - + +
425C GLU* 3.0 29.3 + - + +
426C LEU 2.8 26.0 + - - -
124F U 4.9 11.7 + - - -
125F U 5.8 1.6 + - - -
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Residues in contact with LYS 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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418C ASN 3.4 14.3 + - - -
419C GLU* 3.2 24.9 + - - +
421C ILE 3.1 17.7 + - - +
422C LYS* 1.3 71.8 - - - +
424C ASP* 1.3 56.3 + - - +
426C LEU* 3.5 18.5 - - - +
427C LYS* 3.0 28.4 + - - +
445C VAL* 3.9 18.6 - - + +
446C SER 3.5 24.9 - - - +
447C ARG* 5.4 2.9 - - + -
452C ARG* 5.5 3.8 - - - +
453C GLY* 4.7 15.8 - - - +
454C GLN 6.1 0.2 - - - -
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Residues in contact with ASP 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C LYS* 3.0 9.4 + - + +
423C LYS* 1.3 76.5 - - - +
425C GLU* 1.3 81.0 + - - +
427C LYS* 3.4 11.8 + - - +
428C LYS* 3.4 36.1 + - - +
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Residues in contact with GLU 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B ARG* 3.4 14.6 + - - +
421C ILE* 4.7 5.8 - - + -
422C LYS* 3.0 28.3 + - + +
424C ASP* 1.3 92.9 - - - +
426C LEU* 1.3 62.3 + - - +
428C LYS* 2.9 16.2 + - - +
429C SER* 2.8 30.2 + - - -
478C TYR* 4.8 6.5 - - - +
125F U 3.2 65.5 + - + +
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Residues in contact with LEU 426 (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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417C LEU* 4.4 25.1 - - + -
418C ASN 4.5 7.6 - - - +
421C ILE* 3.6 17.7 - - + +
422C LYS 2.8 15.7 + - - +
423C LYS* 3.5 28.3 - - - +
425C GLU* 1.3 77.7 - - - +
427C LYS* 1.3 57.3 + - - +
429C SER* 3.3 2.9 + - - +
430C LEU* 2.8 44.1 + - + +
445C VAL* 4.1 18.6 - - + -
453C GLY 6.0 0.9 - - - -
454C GLN 5.7 0.7 - - - +
477C PHE* 3.4 33.9 - - + -
478C TYR* 4.3 6.7 - - + -
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Residues in contact with LYS 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C LYS 3.0 10.2 + - - +
424C ASP* 3.6 13.9 + - - +
425C GLU 3.2 0.4 - - - -
426C LEU* 1.3 75.8 - - - +
428C LYS* 1.3 59.6 + - + +
430C LEU* 3.1 5.1 + - - +
431C HIS* 2.9 28.7 + - + +
442C ASP* 5.8 1.0 + - - +
443C ILE* 3.8 35.7 + - + +
445C VAL* 3.6 30.7 - - + +
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Residues in contact with LYS 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B ARG* 3.1 31.0 - - - +
424C ASP* 3.4 28.6 + - - +
425C GLU* 2.9 21.9 + - - +
427C LYS* 1.3 77.8 - - + +
429C SER* 1.3 63.2 + - - +
431C HIS* 3.0 18.0 + - - +
432C ALA* 3.1 14.2 + - - +
125F U 3.1 37.8 + - - +
126F G 4.1 6.2 + - - -
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Residues in contact with SER 429 (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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316B ASN* 3.2 27.0 + - - -
374B GLY* 5.8 0.3 - - - -
381B PRO* 3.8 11.6 - - - +
383B ARG* 3.3 15.3 + - - +
425C GLU 2.8 14.9 + - - -
426C LEU 3.8 3.1 - - - -
428C LYS* 1.3 72.4 - - - +
430C LEU* 1.3 61.7 + - - +
432C ALA* 4.0 1.0 - - - +
433C ILE* 3.3 27.0 + - - +
477C PHE* 3.4 23.6 - - - -
478C TYR* 3.5 12.5 + - - -
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Residues in contact with LEU 430 (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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414C ILE* 5.2 4.9 - - + -
417C LEU* 4.3 12.3 - - + -
426C LEU* 2.8 37.0 + - + +
427C LYS* 3.5 5.8 - - - +
428C LYS 3.0 0.2 - - - -
429C SER* 1.3 76.8 - - - +
431C HIS* 1.3 64.1 + - - +
433C ILE* 3.4 2.4 - - + +
434C PHE* 3.2 53.8 + - + +
443C ILE* 3.9 20.9 - - + +
445C VAL* 4.7 1.8 - - + -
455C ALA* 4.0 26.7 - - + -
457C VAL* 5.1 4.7 - - + -
477C PHE* 4.0 20.2 - - + -
482C MET* 4.6 6.7 - - - -
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Residues in contact with HIS 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C LYS 2.9 12.9 + - - +
428C LYS* 3.0 11.6 + - - +
430C LEU* 1.3 78.1 - - - +
432C ALA* 1.3 54.2 + - - +
434C PHE 3.6 0.2 - - - -
435C SER* 2.7 50.0 + - - -
440C ILE* 4.1 25.6 - - + +
443C ILE* 3.5 17.6 - - + +
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Residues in contact with ALA 432 (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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373B GLN* 3.4 38.5 - - - +
374B GLY* 5.4 0.9 - - - +
383B ARG* 3.7 24.2 - - + -
384B ILE 5.6 0.2 - - - +
428C LYS 3.1 6.4 + - - +
429C SER 4.0 2.5 - - - +
431C HIS* 1.3 82.2 - - - +
433C ILE* 1.3 65.9 + - - +
434C PHE 2.9 1.6 + - - -
435C SER* 3.0 19.5 + - - -
436C ARG* 4.1 2.3 - - - +
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Residues in contact with ILE 433 (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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373B GLN* 4.2 8.9 - - - +
374B GLY* 3.9 19.9 - - - -
429C SER 3.3 14.1 + - - +
430C LEU* 3.4 12.8 - - + +
432C ALA* 1.3 79.9 - - - +
434C PHE* 1.3 88.6 + - + +
436C ARG* 3.1 34.4 + - - +
437C PHE* 4.1 4.2 - - - -
472C MET* 3.2 35.0 - - + -
475C PHE* 4.4 13.7 - - + -
477C PHE* 4.2 16.2 - - + -
482C MET* 4.6 3.1 - - + -
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Residues in contact with PHE 434 (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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412C ILE* 3.9 16.6 - - + -
414C ILE* 4.3 10.5 - - + -
430C LEU* 3.2 30.6 + - + +
432C ALA 3.1 1.0 - - - -
433C ILE* 1.3 100.9 - - + +
435C SER* 1.3 57.9 + - - +
436C ARG 2.8 12.6 + - - -
437C PHE* 3.2 31.9 + + - -
440C ILE* 3.8 11.9 - - + -
457C VAL* 4.4 12.1 - - + -
459C PHE* 3.8 17.8 - + + -
468C ALA* 4.0 16.6 - - + -
472C MET* 3.4 22.0 - - + -
482C MET* 3.5 28.9 - - + -
484C ILE* 4.0 10.8 - - + -
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Residues in contact with SER 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B GLN* 5.3 1.7 - - - +
431C HIS* 2.7 40.2 + - - -
432C ALA* 3.0 16.2 + - - -
434C PHE* 1.3 71.6 - - - +
436C ARG* 1.3 59.8 + - - +
437C PHE 3.4 0.7 - - - -
438C GLY 3.8 14.5 + - - +
440C ILE* 3.8 9.2 - - - -
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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