Contacts of the helix formed by residues 409 - 425 (chain B) in PDB entry 3RC0
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 409 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407B LYS 3.7 0.6 + - - -
408B LEU* 1.3 76.5 - - - +
410B ALA* 1.3 74.4 + - + +
411B SER* 3.1 49.0 - - - +
412B TRP* 3.1 32.4 + - + +
413B ARG* 3.3 9.5 + - - +
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Residues in contact with ALA 410 (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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408B LEU 3.5 1.4 + - - -
409B LYS* 1.3 84.7 - - + +
411B SER* 1.3 64.6 + - - +
412B TRP 3.1 0.3 + - - -
413B ARG* 3.2 31.2 + - - +
414B GLN* 3.0 23.7 + - - +
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Residues in contact with SER 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B CYS* 3.5 26.8 + - - +
409B LYS* 3.1 37.7 - - - +
410B ALA* 1.3 75.2 - - - +
412B TRP* 1.3 72.7 + - - +
414B GLN* 3.5 7.9 + - - +
415B LEU* 3.3 17.3 + - - +
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Residues in contact with TRP 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B THR* 4.4 19.3 - - + -
371B LEU* 3.9 33.6 + - + +
372B LYS* 3.5 48.0 + - + +
375B CYS* 3.6 26.5 - - + +
376B MET 5.3 0.2 - - - +
400B LEU* 6.1 0.2 - - + -
408B LEU* 4.4 29.4 - - + -
409B LYS* 3.1 26.0 + - + +
410B ALA 3.1 0.4 - - - -
411B SER* 1.3 93.7 + - - +
413B ARG* 1.3 67.1 + - - +
414B GLN 3.2 0.3 + - - -
415B LEU* 3.2 4.0 + - - +
416B LEU* 2.9 24.3 + - - +
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Residues in contact with ARG 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B ILE* 3.6 22.7 - - + +
406B PRO* 3.3 17.2 + - - -
407B LYS 5.3 0.2 - - - -
408B LEU* 3.1 30.4 + - + +
409B LYS 3.3 4.2 + - - +
410B ALA* 3.2 32.3 + - - +
412B TRP* 1.3 78.7 - - - +
414B GLN* 1.3 53.9 + - - +
416B LEU* 3.3 4.6 + - - -
417B GLN* 2.7 36.8 + - - +
471B LEU 4.3 3.6 - - - -
472B THR* 3.6 38.7 + - + +
473B SER 4.2 14.7 + - - -
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Residues in contact with GLN 414 (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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410B ALA 3.0 13.1 + - - +
411B SER* 3.6 12.1 - - - +
412B TRP 3.2 0.6 - - - -
413B ARG* 1.3 75.6 - - - +
415B LEU* 1.3 58.8 + - - +
417B GLN* 3.2 23.2 + - - +
418B ASN* 3.0 65.7 + - - +
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Residues in contact with LEU 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B VAL* 3.9 7.2 - - + +
321B ALA* 3.8 13.5 - - + +
322B ALA* 3.7 32.5 - - + +
371B LEU* 4.1 16.2 - - + -
374B LEU* 3.8 39.0 - - + +
375B CYS* 3.9 16.2 - - - -
411B SER 3.3 9.6 + - - +
412B TRP 3.2 7.9 + - - +
414B GLN* 1.3 78.1 - - - +
416B LEU* 1.3 58.4 + - - +
418B ASN* 3.5 5.6 + - + +
419B SER* 2.8 34.6 + - - +
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Residues in contact with LEU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ILE* 4.2 23.3 - - + -
318B VAL* 5.7 2.0 - - + -
361B VAL* 6.1 0.7 - - + -
367B LEU* 4.5 27.4 - - + -
371B LEU* 4.3 21.9 - - + +
400B LEU* 5.1 7.6 - - + -
405B ILE* 4.9 7.4 - - + -
408B LEU* 5.2 2.9 - - + -
412B TRP 2.9 17.4 + - - +
413B ARG* 3.7 5.2 - - - +
415B LEU* 1.3 75.6 - - - +
417B GLN* 1.3 60.7 + - - +
419B SER* 3.2 9.3 + - - -
420B VAL* 2.9 33.9 + - - +
468B LEU* 4.3 21.5 - - + -
472B THR* 4.0 20.4 - - + -
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Residues in contact with GLN 417 (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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413B ARG 2.7 17.7 + - - +
414B GLN* 3.2 28.3 + - - +
416B LEU* 1.3 72.8 - - - +
418B ASN* 1.3 63.3 + - - +
420B VAL* 3.3 2.7 + - - -
421B LEU* 3.0 37.6 + - + +
469B LEU* 3.6 23.2 - - + +
472B THR* 3.3 29.6 + - - +
473B SER* 3.5 21.8 + - - +
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Residues in contact with ASN 418 (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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321B ALA* 4.1 14.6 + - + -
324B GLN* 3.9 24.2 + - - +
414B GLN* 3.0 43.1 + - - +
415B LEU* 4.0 5.6 - - - +
417B GLN* 1.3 80.2 + - - +
419B SER* 1.3 65.9 + - - +
421B LEU* 3.3 15.2 + - - +
422B LEU* 3.1 28.8 + - - +
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Residues in contact with SER 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ILE* 4.4 7.9 - - - -
317B THR* 3.6 10.0 - - - +
318B VAL* 3.3 44.7 - - - +
321B ALA* 3.6 10.5 - - - +
371B LEU* 6.0 0.2 - - - +
415B LEU* 2.8 23.5 + - - +
416B LEU* 3.4 12.3 - - - -
418B ASN* 1.3 77.4 - - - +
420B VAL* 1.3 56.4 + - - +
422B LEU 3.5 0.7 + - - -
423B THR* 3.0 30.9 + - - -
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Residues in contact with VAL 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ILE* 3.9 11.4 - - + -
416B LEU* 2.9 23.0 + - + +
417B GLN* 3.7 6.3 - - - +
419B SER* 1.3 75.6 - - - +
421B LEU* 1.3 58.1 + - - +
423B THR* 3.2 6.5 + - - -
424B LEU* 2.9 33.3 + - + +
465B LEU* 3.4 39.9 - - + +
468B LEU* 3.5 36.1 - - + -
469B LEU* 3.8 16.2 - - + +
472B THR* 5.6 0.2 - - - +
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Residues in contact with LEU 421 (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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417B GLN* 3.0 32.2 + - + +
418B ASN* 3.6 20.0 - - - +
420B VAL* 1.3 75.8 - - - +
422B LEU* 1.3 62.7 + - + +
424B LEU* 3.4 7.9 + - + +
425B GLN* 3.1 39.3 + - - +
469B LEU* 3.9 27.4 - - + -
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Residues in contact with LEU 422 (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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317B THR* 3.6 25.6 - - + +
320B GLU* 4.0 28.3 - - + +
321B ALA* 3.8 31.2 - - + +
324B GLN* 4.3 20.6 - - - +
418B ASN 3.1 21.0 + - - +
419B SER 3.7 0.2 - - - +
421B LEU* 1.3 74.5 - - + +
423B THR* 1.3 65.1 + - - +
425B GLN* 3.2 31.5 + - - +
426B THR* 3.4 14.8 - - - +
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Residues in contact with THR 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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312B ASP 3.6 22.9 - - - +
313B ILE* 3.5 22.0 - - - +
314B GLN 4.8 0.8 + - - +
317B THR* 3.8 8.5 + - - +
419B SER 3.0 15.6 + - - -
420B VAL* 3.2 11.0 + - - -
422B LEU* 1.3 77.2 - - - +
424B LEU* 1.3 61.9 + - - +
426B THR* 2.8 33.0 + - - +
427B TYR* 3.6 9.7 - - + +
465B LEU* 3.7 22.2 - - + -
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Residues in contact with LEU 424 (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 VAL* 2.9 28.4 + - + +
421B LEU* 3.8 8.3 - - + +
423B THR* 1.3 73.0 - - - +
425B GLN* 1.3 61.0 + - + +
426B THR 3.4 0.7 + - - -
427B TYR* 3.5 22.2 + - + +
429B THR 4.6 5.0 - - - +
430B ASP* 5.6 3.0 - - - -
431B LEU 5.7 1.3 - - - +
462B LYS* 4.1 20.2 - - + -
465B LEU* 3.9 26.2 - - + -
466B HIS* 3.4 40.4 - - + +
469B LEU* 3.5 27.4 - - + -
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Residues in contact with GLN 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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169B GLN* 5.5 0.2 + - - -
421B LEU* 3.1 31.4 + - - +
422B LEU* 3.5 27.8 - - - +
423B THR 3.0 1.0 - - - -
424B LEU* 1.3 78.9 - - + +
426B THR* 1.3 59.5 + - + +
427B TYR 3.3 8.5 - - - +
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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