Contacts of the helix formed by residues 405 - 415 (chain A) in PDB entry 6QNW
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 405 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A LEU* 5.2 1.5 - - - +
404A SER* 1.3 73.9 - - - +
406A TRP* 1.3 61.4 + - - +
407A ILE 3.4 1.2 + - - -
408A GLN* 3.8 13.5 + - - +
409A ASN* 3.0 20.7 + - - +
533A GLU* 5.4 5.6 - - - -
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Residues in contact with TRP 406 (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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276A CYS* 3.0 19.6 + - - -
277A PHE 3.2 26.2 - - - -
278A GLN* 3.5 30.3 - - + -
285A MET* 4.8 3.1 - - + +
404A SER* 3.3 19.7 - - - -
405A SER* 1.3 78.4 - - - +
407A ILE* 1.3 77.8 + - + +
408A GLN 3.3 0.2 - - - -
409A ASN* 3.3 10.3 + - - +
410A GLU* 2.9 35.2 + - - +
533A GLU* 3.5 28.8 + - + +
535A HIS 6.0 0.2 - - - -
536A LYS* 3.5 41.6 - - + +
650A TYR* 3.7 20.0 - + - -
698A PRO* 3.7 23.8 - - + -
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Residues in contact with ILE 407 (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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276A CYS* 5.5 0.2 - - - -
403A LEU* 4.6 4.7 - - + -
404A SER 3.7 18.6 - - - +
406A TRP* 1.3 108.0 - - + +
408A GLN* 1.3 60.4 + - - +
410A GLU* 3.3 8.3 + - + +
411A PHE* 2.9 24.3 + - - +
646A PHE* 4.8 2.9 - - + -
650A TYR* 4.1 24.0 - - + +
698A PRO* 4.0 33.2 - - + +
699A TRP* 4.4 13.5 - - + +
702A LEU* 3.5 34.6 - - + +
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Residues in contact with GLN 408 (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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404A SER 5.7 0.4 - - - +
405A SER* 3.8 10.0 + - - +
406A TRP 3.3 0.4 - - - -
407A ILE* 1.3 82.8 - - - +
409A ASN* 1.3 53.2 + - - +
411A PHE* 3.3 6.8 + - - +
412A ASN* 2.7 53.6 + - - +
702A LEU* 3.2 22.0 - - + +
706A TRP* 3.0 26.2 + - - -
2B ASP* 3.7 22.9 - - - +
3B VAL 2.7 40.3 + - - +
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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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285A MET* 4.3 12.4 - - + +
405A SER* 3.0 22.8 + - - +
406A TRP* 3.3 10.3 + - - +
407A ILE 3.3 0.4 - - - -
408A GLN* 1.3 74.7 - - - +
410A GLU* 1.3 61.0 + - - +
412A ASN* 3.3 15.5 + - - +
413A LYS* 2.9 31.0 + - - +
533A GLU* 5.5 1.9 - - - +
2B ASP* 5.0 4.2 + - - -
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Residues in contact with GLU 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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278A GLN* 4.0 8.8 + - - -
284A LEU* 3.1 17.7 + - + +
285A MET* 2.9 48.4 + - - +
286A ASP* 5.1 0.7 - - - +
406A TRP* 2.9 15.1 + - + +
407A ILE* 3.4 17.3 - - + +
409A ASN* 1.3 76.9 - - - +
411A PHE* 1.3 57.3 + - - +
413A LYS* 3.4 2.8 + - - +
414A ALA* 2.9 27.0 + - - +
458A TYR* 4.6 2.5 + - - +
536A LYS* 3.2 30.5 + - - -
646A PHE* 3.9 18.1 - - + -
650A TYR* 4.7 5.8 - - - +
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Residues in contact with PHE 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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407A ILE 2.9 14.4 + - - +
408A GLN* 3.7 8.3 - - - +
410A GLU* 1.3 74.4 - - - +
412A ASN* 1.3 64.3 + - - +
414A ALA* 3.0 10.5 + - + -
415A CYS* 3.1 17.1 + - - -
639A THR* 3.8 25.8 - - + -
642A ALA* 3.5 29.2 - - + -
643A LYS* 3.8 14.8 - - + -
646A PHE* 3.7 25.9 - + + -
699A TRP* 4.5 2.0 - + - -
702A LEU* 4.4 7.6 - - + -
706A TRP* 3.3 36.1 - + - -
3B VAL* 3.6 30.3 - - + -
5B PRO* 3.8 9.0 - - + -
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Residues in contact with ASN 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 GLN* 2.7 36.7 + - - +
409A ASN* 3.6 16.4 - - - +
411A PHE* 1.3 74.8 - - - +
413A LYS* 1.3 62.0 + - - +
415A CYS* 3.3 12.6 + - - +
416A GLU* 3.6 10.0 + - - +
1B MET 3.8 10.4 + - - +
2B ASP* 3.4 22.3 + - - -
3B VAL* 2.7 43.6 + - + +
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Residues in contact with LYS 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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285A MET* 3.9 31.4 - - + +
409A ASN 2.9 17.2 + - - +
410A GLU 3.7 4.0 - - - +
412A ASN* 1.3 76.6 - - - +
414A ALA* 1.3 60.9 + - - +
416A GLU* 3.2 46.0 + - + +
454A ARG* 3.8 30.7 - - - +
458A TYR* 4.6 5.8 - - - +
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Residues in contact with ALA 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 GLU 2.9 15.0 + - - +
411A PHE* 3.0 12.3 + - + +
413A LYS* 1.3 76.4 - - - +
415A CYS* 1.3 56.4 + - - +
416A GLU 3.4 0.4 + - - -
453A CYS* 3.4 20.3 - - - -
454A ARG* 3.9 3.4 - - - +
455A ALA 3.5 9.0 + - - -
458A TYR* 3.8 29.8 + - + -
642A ALA* 3.9 19.8 - - + +
646A PHE* 3.9 13.7 - - + -
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Residues in contact with CYS 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 PHE* 3.1 46.6 + - - -
412A ASN 3.3 7.6 + - - +
413A LYS 3.2 0.6 - - - -
414A ALA* 1.3 75.6 - - - +
416A GLU* 1.3 64.6 + - - +
453A CYS* 4.3 4.5 - - - -
635A LYS* 5.5 1.8 - - + +
638A ARG* 3.4 30.3 + - + -
639A THR* 4.0 18.8 - - - +
642A ALA* 4.3 1.8 - - - -
3B VAL* 4.0 24.2 - - + -
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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