Contacts of the helix formed by residues 422 - 431 (chain B) in PDB entry 3K5N
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 SER 422 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420B TYR 3.3 3.2 + - - -
421B LYS* 1.3 89.1 - - - +
423B LEU* 1.3 65.8 + - - +
424B TYR 3.3 2.4 + - - -
425B PRO* 3.6 17.1 - - - -
426B SER* 3.2 14.2 + - - -
474B TRP* 3.7 19.5 - - - -
496B MET* 4.2 12.9 - - - -
497B ASN* 4.7 10.1 + - - -
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Residues in contact with LEU 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420B TYR* 3.6 42.4 + - + +
421B LYS 2.7 8.0 + - - -
422B SER* 1.3 74.5 - - - +
424B TYR* 1.3 81.9 - - + +
426B SER* 2.1 28.5 + - - -
427B ILE* 2.8 22.4 + - + +
523B GLY* 4.8 8.3 - - - -
526B ILE* 5.1 6.5 - - + -
527B MET* 5.7 2.0 - - - -
546B THR 4.1 11.0 - - - +
547B ASP* 3.9 26.2 + - + +
590B LEU* 4.2 17.5 - - + -
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Residues in contact with TYR 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B LEU* 1.3 91.2 - - + +
425B PRO* 1.3 65.7 - - + +
427B ILE* 2.6 16.8 + - + +
428B ILE* 2.5 38.2 + - + +
500B TYR* 3.5 34.4 + + + -
519B ILE* 3.0 43.7 - - + -
520B THR* 2.9 26.5 + - + +
523B GLY* 5.0 4.7 - - - -
524B HIS* 5.5 1.2 - - - -
546B THR* 5.0 19.5 + - - +
547B ASP* 6.1 1.3 - - + -
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Residues in contact with PRO 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422B SER* 3.6 23.8 - - - +
424B TYR* 1.3 94.5 - - + +
426B SER* 1.3 56.0 + - - +
428B ILE* 2.5 32.8 + - + +
429B ARG* 2.8 20.2 + - - +
470B VAL* 3.6 22.7 - - + -
474B TRP* 4.2 0.9 - - + -
496B MET* 4.0 35.9 - - + +
497B ASN* 5.0 6.3 - - - +
499B PHE* 6.3 0.2 - - + -
500B TYR* 5.7 2.9 - - + -
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Residues in contact with SER 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B LYS 4.2 3.4 - - - -
422B SER 3.2 10.3 + - - -
423B LEU* 2.1 27.5 + - - -
425B PRO* 1.3 78.7 - - - +
427B ILE* 1.3 67.5 + - - +
429B ARG* 4.0 1.3 - - - +
430B THR* 2.8 22.6 + - - -
474B TRP* 3.8 21.2 - - - -
589B ALA* 2.9 31.7 - - - +
590B LEU* 3.4 21.9 - - - +
591B GLU 5.3 0.4 - - - -
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Residues in contact with ILE 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B LEU* 3.5 24.9 - - + +
424B TYR* 2.6 23.0 + - + +
426B SER* 1.3 82.1 + - - +
428B ILE* 1.3 63.0 + - - +
430B THR* 4.5 0.2 - - - -
431B PHE* 2.9 51.5 + - + +
433B ILE* 4.3 3.9 - - + +
519B ILE* 3.7 35.7 - - + +
522B ARG* 3.7 12.8 - - + +
523B GLY* 3.9 23.8 - - - +
526B ILE* 4.6 9.4 - - + -
590B LEU* 4.7 1.6 - - + -
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Residues in contact with ILE 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B TYR* 2.5 26.2 + - + +
425B PRO* 2.5 18.7 + - + +
427B ILE* 1.3 71.6 - - - +
429B ARG* 1.3 62.3 + - - +
432B LEU* 3.0 17.2 + - - -
433B ILE* 3.0 39.6 + - + +
466B LEU* 4.0 22.7 - - + -
467B PRO* 3.7 2.9 - - - +
470B VAL* 4.1 11.4 - - + -
499B PHE* 6.0 6.7 - - + -
500B TYR* 5.8 2.5 - - + -
503B LEU* 4.9 9.9 - - + -
519B ILE* 2.5 43.1 - - + -
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Residues in contact with ARG 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425B PRO 2.8 17.0 + - - +
426B SER* 4.0 11.2 - - - +
428B ILE* 1.3 71.6 - - - +
430B THR* 1.3 64.8 + - - +
432B LEU* 2.8 28.1 + - - +
467B PRO* 3.6 11.4 - - + -
470B VAL* 4.0 14.1 - - + -
471B THR* 2.9 49.7 + - + +
474B TRP* 3.0 45.7 - - - +
475B HIS* 4.1 19.8 + - - -
589B ALA* 4.0 17.1 + - + +
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Residues in contact with THR 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426B SER 2.8 9.8 + - - -
429B ARG* 1.3 81.9 - - - +
431B PHE* 1.3 94.2 + - + +
432B LEU* 3.4 7.8 + - - +
581B LEU* 4.5 14.6 - - + -
586B LEU* 4.1 20.8 - - + +
587B THR 4.1 10.4 - - - +
588B SER* 3.3 0.7 - - - -
589B ALA* 2.2 50.4 + - - +
590B LEU* 3.8 4.3 + - + -
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Residues in contact with PHE 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427B ILE* 2.9 34.9 + - + +
430B THR* 1.3 95.0 - - + +
432B LEU* 1.3 73.1 - - - +
433B ILE* 3.3 17.2 + - + +
451B THR* 4.5 12.3 + - + -
459B PHE* 4.4 9.0 - - - +
522B ARG* 2.4 70.7 - - + +
525B GLN* 5.4 1.3 - - - -
526B ILE* 4.2 17.5 - - + -
577B TRP* 6.0 1.8 - + - -
581B LEU* 4.8 21.5 - - + -
586B LEU* 4.8 13.2 - - + -
590B LEU* 4.7 3.4 - - + -
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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