Contacts of the helix formed by residues 407 - 422 (chain A) in PDB entry 6C9G
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 ARG 407 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405A GLN 4.3 12.1 + - - -
406A SER* 1.3 81.7 - - - +
408A PRO* 1.4 65.9 - - + +
409A ASN* 3.4 2.5 - - + +
410A ASP* 3.1 26.2 + - - +
411A ILE* 2.8 34.3 + - - +
461A TYR* 4.7 2.5 - - + -
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Residues in contact with PRO 408 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407A ARG* 1.4 89.0 - - + +
409A ASN* 1.3 64.6 + - - +
411A ILE* 3.5 10.9 - - + +
412A MET* 3.1 34.7 + - - +
432A TYR* 4.2 13.5 - - + +
453A LEU* 4.1 7.4 - - + -
461A TYR* 3.4 40.4 - - + +
203B PRO* 4.1 19.5 - - + -
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Residues in contact with ASN 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A ARG* 3.4 2.1 - - + +
408A PRO* 1.3 78.6 - - - +
410A ASP* 1.3 68.3 + - - +
412A MET* 4.0 4.1 - - - +
413A ALA* 3.2 23.9 + - - +
432A TYR* 4.2 15.8 + - - -
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Residues in contact with ASP 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A SER* 4.8 8.1 - - - -
407A ARG* 3.1 35.6 + - - +
409A ASN* 1.3 81.8 - - - +
411A ILE* 1.3 57.5 + - - +
412A MET 3.3 0.2 + - - -
413A ALA* 3.4 4.6 + - - +
414A GLU* 3.1 28.2 + - - +
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Residues in contact with ILE 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A ILE* 6.5 0.7 - - + -
404A SER* 3.5 31.9 - - - +
406A SER* 4.1 7.9 - - - +
407A ARG 2.8 19.9 + - - +
408A PRO* 3.5 13.9 - - + +
410A ASP* 1.3 74.4 - - - +
412A MET* 1.3 64.6 + - - +
414A GLU* 3.8 12.5 - - + +
415A VAL* 3.3 31.9 + - + +
453A LEU* 3.5 36.3 - - + -
461A TYR* 5.1 4.3 - - + -
463A LEU* 5.6 6.1 - - + -
548A LEU* 5.6 7.6 - - + -
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Residues in contact with MET 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A PRO 3.1 26.6 + - - +
409A ASN* 4.0 5.6 - - - +
410A ASP 3.2 0.4 - - - -
411A ILE* 1.3 79.5 - - - +
413A ALA* 1.3 65.5 + - - +
415A VAL* 3.4 11.0 + - + +
416A CYS* 3.1 33.0 + - - -
431A PRO 3.5 13.0 - - - +
432A TYR* 3.7 33.9 - - + +
434A LEU* 3.4 40.6 - - + -
451A LEU* 6.5 0.4 - - + -
453A LEU* 4.3 17.7 - - + -
463A LEU* 5.7 5.8 - - + -
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Residues in contact with ALA 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A ASN 3.2 15.7 + - - +
410A ASP* 3.7 5.4 - - - +
412A MET* 1.3 77.8 - - - +
414A GLU* 1.3 62.5 + - - +
416A CYS* 3.4 7.2 + - - +
417A ARG* 3.1 51.1 + - - +
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Residues in contact with GLU 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A ASP 3.1 16.7 + - - +
411A ILE* 3.8 15.0 - - + +
412A MET 3.2 0.4 - - - -
413A ALA* 1.3 77.2 - - - +
415A VAL* 1.3 61.5 + - - +
417A ARG* 3.4 26.6 + - - +
418A ALA* 3.1 22.5 + - - +
547A ILE* 5.6 6.4 - - - +
548A LEU* 4.0 18.2 - - + +
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Residues in contact with VAL 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A ILE* 3.3 24.9 + - + +
412A MET* 3.8 11.7 - - + +
413A ALA 3.3 0.2 - - - -
414A GLU* 1.3 74.9 - - - +
416A CYS* 1.3 54.3 + - - +
418A ALA* 3.0 3.9 + - - +
419A ILE* 2.7 59.5 + - + +
434A LEU* 4.4 6.7 - - + -
451A LEU* 4.1 16.2 - - + -
463A LEU* 3.7 28.7 - - + -
544A LEU* 4.5 8.1 - - + -
548A LEU* 4.1 18.2 - - + -
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Residues in contact with CYS 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A MET* 3.1 22.6 + - - -
413A ALA* 3.8 9.0 - - - +
415A VAL* 1.3 79.4 - - - +
417A ARG* 1.3 61.1 + - + +
419A ILE* 3.4 10.2 + - - +
420A LYS* 3.1 24.4 + - - +
426A TRP* 3.7 17.7 - - + -
428A VAL* 5.6 2.0 - - - -
434A LEU* 3.9 24.0 - - - -
194B CYS 5.6 1.8 - - - +
195B LYS 3.8 24.5 - - - +
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Residues in contact with ARG 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A ALA* 3.1 38.5 + - - +
414A GLU* 3.6 27.0 + - - +
415A VAL 3.2 0.2 - - - -
416A CYS* 1.3 77.1 - - + +
418A ALA* 1.3 57.4 + - - +
420A LYS* 3.2 8.0 + - - +
421A GLN* 3.0 28.1 + - - +
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Residues in contact with ALA 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414A GLU* 3.1 13.9 + - - +
415A VAL 3.0 5.6 + - - +
417A ARG* 1.3 73.2 - - - +
419A ILE* 1.3 64.1 - - - +
421A GLN* 3.5 11.6 + - - +
422A LEU* 3.4 28.9 + - - +
544A LEU* 3.5 25.1 - - + -
547A ILE* 3.8 25.3 - - + +
548A LEU* 4.3 5.6 - - + -
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Residues in contact with ILE 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415A VAL* 2.7 44.6 + - + +
416A CYS* 3.6 7.6 - - - +
418A ALA* 1.3 73.8 - - - +
420A LYS* 1.3 60.9 + - - +
422A LEU* 3.3 6.4 + - - +
424A TYR* 3.1 54.0 + - + +
426A TRP* 3.4 28.5 - - + -
434A LEU* 3.7 21.8 - - + -
436A VAL* 4.0 24.2 - - + -
449A MET* 6.4 0.2 - - + -
451A LEU* 4.1 2.2 - - + -
544A LEU* 4.7 12.1 - - + -
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Residues in contact with LYS 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416A CYS 3.1 14.1 + - - +
417A ARG* 3.2 9.8 + - - +
419A ILE* 1.3 74.1 - - - +
421A GLN* 1.3 66.4 + - - +
423A ASP* 3.0 14.8 + - - +
424A TYR 4.5 2.5 - - - -
426A TRP* 3.9 22.4 - - + -
192B TYR* 3.0 37.1 + - + -
193B VAL 5.6 3.1 + - - +
194B CYS* 5.9 7.2 - - - +
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Residues in contact with GLN 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A ARG 3.0 12.6 + - - +
418A ALA* 3.6 11.9 - - - +
419A ILE 3.3 0.4 - - - -
420A LYS* 1.3 77.8 - - - +
422A LEU* 1.3 63.8 + - + +
423A ASP* 3.5 1.4 + - - +
547A ILE* 4.0 34.3 - - + +
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Residues in contact with LEU 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A ALA 3.4 13.9 + - - +
419A ILE 3.3 4.8 + - - +
420A LYS 3.2 1.0 - - - -
421A GLN* 1.3 81.5 - - + +
423A ASP* 1.3 64.4 + - - +
424A TYR* 3.1 43.8 + - + -
543A ASN* 3.6 44.6 - - + +
544A LEU* 3.7 7.0 - - + +
547A ILE* 3.6 23.3 - - + -
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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