Contacts of the helix formed by residues 412 - 423 (chain A) in PDB entry 3QFS
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 412 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407A LYS* 4.6 4.5 - - - +
410A SER* 3.2 16.5 + - - -
411A SER* 1.3 83.3 + - - +
413A GLY* 1.3 65.1 + - - +
414A GLU* 4.0 3.1 + - - +
415A GLY* 2.9 19.9 + - - -
416A LYS* 3.0 22.2 + - - +
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Residues in contact with GLY 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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411A SER 3.8 1.0 + - - -
412A SER* 1.3 75.7 - - - +
414A GLU* 1.3 60.9 + - - +
416A LYS* 3.4 8.8 + - - +
417A GLU* 3.3 23.9 + - - +
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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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407A LYS* 3.9 27.1 + - - +
412A SER* 3.4 3.0 + - - +
413A GLY* 1.3 73.1 - - - +
415A GLY* 1.3 60.6 + - - +
417A GLU* 3.4 7.6 + - - +
418A LEU* 3.0 29.6 + - - +
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Residues in contact with GLY 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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407A LYS* 3.2 35.1 - - - +
408A MET* 3.7 4.4 - - - -
410A SER* 4.3 3.4 - - - -
412A SER* 2.9 18.1 + - - -
414A GLU* 1.3 79.7 - - - +
416A LYS* 1.3 56.6 + - - +
418A LEU* 3.3 3.1 + - - +
419A TYR* 3.0 30.0 + - - +
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Residues in contact with LYS 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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408A MET 5.4 0.2 - - - -
410A SER 4.2 9.6 + - - +
411A SER* 3.2 34.8 + - - +
412A SER 3.0 17.9 + - - +
413A GLY* 3.8 7.4 - - - +
415A GLY* 1.3 76.1 - - - +
417A GLU* 1.3 61.6 + - + +
419A TYR* 3.5 8.1 + - - +
420A LEU* 3.0 28.8 + - - +
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Residues in contact with GLU 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 GLY 3.3 13.9 + - - +
414A GLU* 3.8 9.4 - - - +
415A GLY 3.3 0.6 - - - -
416A LYS* 1.3 80.2 - - + +
418A LEU* 1.3 57.6 + - - +
420A LEU* 3.5 22.0 + - - +
421A SER* 3.0 30.5 + - - -
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Residues in contact with LEU 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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404A LEU* 3.5 26.9 - - + -
407A LYS* 4.0 25.8 - - + +
408A MET* 3.4 25.8 - - + -
414A GLU 3.0 17.1 + - - +
415A GLY* 3.7 4.7 - - - +
417A GLU* 1.3 74.3 - - - +
419A TYR* 1.3 56.4 + - - +
421A SER* 4.7 4.0 - - - -
422A TRP* 2.7 58.3 + - + +
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Residues in contact with TYR 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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383A PRO* 4.6 2.4 + - - +
384A PRO 2.7 29.9 + - - -
385A ARG* 3.5 9.7 - - - -
386A THR* 3.7 22.4 + - + -
389A LEU* 3.5 29.4 - - + -
408A MET* 3.4 32.0 - - + +
415A GLY 3.0 12.4 + - - +
416A LYS* 3.7 7.4 - - - +
418A LEU* 1.3 75.4 - - - +
420A LEU* 1.3 61.2 + - - +
423A VAL* 2.9 38.6 + - + +
424A VAL* 3.1 36.5 + - + +
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Residues in contact with LEU 420 (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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416A LYS 3.0 18.3 + - - +
417A GLU* 3.7 25.4 - - - +
419A TYR* 1.3 81.3 - - + +
421A SER* 1.3 54.4 + - - +
424A VAL* 4.2 19.5 - - + -
425A GLU* 2.8 65.2 + - + +
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Residues in contact with SER 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 GLU 3.0 16.8 + - - -
418A LEU* 4.1 5.2 - - - -
420A LEU* 1.3 78.3 - - - +
422A TRP* 1.3 59.2 + - - +
425A GLU* 3.9 15.7 + - - +
426A ALA* 3.3 27.2 + - - +
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Residues in contact with TRP 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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404A LEU* 4.4 15.9 - - + +
408A MET* 3.4 38.4 - - + -
418A LEU* 2.7 37.0 + - + +
421A SER* 1.3 76.2 - - - +
423A VAL* 1.3 62.3 + - + +
426A ALA* 3.3 6.5 - - - +
428A ARG* 2.8 78.9 + - - +
433A ILE* 4.0 23.6 - - + -
436A ASP* 3.7 24.7 - - + -
437A CYS* 4.1 17.9 - - - -
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Residues in contact with VAL 423 (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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383A PRO* 3.7 21.2 - - + +
384A PRO* 3.8 12.1 - - + +
389A LEU* 4.0 9.2 - - + -
408A MET* 4.0 10.1 - - + -
419A TYR* 2.9 50.6 + - + +
422A TRP* 1.3 96.1 - - + +
424A VAL* 1.3 64.9 + - - +
427A ARG* 3.1 3.0 + - - -
428A ARG* 3.0 37.8 + - - +
433A ILE* 4.5 7.0 - - + -
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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