Contacts of the helix formed by residues 413 - 424 (chain A) in PDB entry 3NYN
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 413 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285A GLU* 2.9 37.2 + - - -
411A ARG 3.6 1.0 + - - -
412A PHE* 1.3 76.7 - - - +
414A PRO* 1.3 78.9 - - - +
415A GLN* 3.6 3.8 + - - +
416A ALA* 3.2 17.2 + - - +
417A ARG* 3.3 17.5 + - - +
447A LEU* 4.8 0.9 - - - +
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Residues in contact with PRO 414 (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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413A SER* 1.3 95.0 - - - +
415A GLN* 1.3 67.6 + - + +
417A ARG* 3.3 16.7 + - + +
418A SER* 3.6 5.4 + - - -
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Residues in contact with GLN 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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413A SER* 3.5 3.5 + - - +
414A PRO* 1.3 80.5 - - + +
416A ALA* 1.3 66.0 + - - +
417A ARG 3.1 2.5 - - - -
418A SER* 2.6 35.2 + - - -
419A LEU* 3.3 5.7 + - - +
445A HIS* 3.4 18.8 + - + -
446A PRO* 3.9 31.0 - - + +
447A LEU* 4.5 15.7 - - + +
449A LYS* 5.9 7.7 - - - +
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Residues in contact with ALA 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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285A GLU* 3.4 20.6 - - - +
379A ILE* 4.2 15.9 - - + -
412A PHE* 4.4 4.8 - - + -
413A SER* 3.2 29.7 + - - +
414A PRO 3.3 0.2 - - - -
415A GLN* 1.3 77.6 - - - +
417A ARG* 1.3 59.8 + - - +
419A LEU* 3.9 1.9 + - - +
420A CYS* 3.3 28.2 + - - -
447A LEU* 3.9 18.3 - - + +
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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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408A TYR* 3.4 60.7 + - + +
412A PHE* 4.6 5.4 - - + +
413A SER 3.3 8.7 + - - +
414A PRO* 3.4 11.7 - - + +
415A GLN 3.1 0.8 - - - -
416A ALA* 1.3 78.0 - - - +
418A SER* 1.3 61.4 + - - +
419A LEU 3.3 0.2 + - - -
420A CYS* 3.4 1.9 + - - +
421A SER* 2.9 33.0 + - - -
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Residues in contact with SER 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 PRO 3.6 5.0 + - - -
415A GLN* 2.6 33.0 + - - -
417A ARG* 1.3 80.4 - - - +
419A LEU* 1.3 54.8 + - - +
421A SER* 3.4 6.2 - - - -
422A GLN* 2.8 48.9 + - - +
445A HIS* 2.9 16.5 + - - -
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Residues in contact with LEU 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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375A LEU* 3.5 19.5 - - + -
415A GLN 3.3 5.3 + - - +
416A ALA 4.2 1.3 - - - +
417A ARG 3.3 0.4 - - - -
418A SER* 1.3 77.2 + - - +
420A CYS* 1.3 67.7 + - - +
422A GLN* 3.0 4.2 + - - +
423A LEU* 2.8 37.3 + - + +
432A LEU* 3.5 22.2 - - + -
442A VAL* 4.7 8.1 - - + +
445A HIS* 3.4 40.8 - - + +
447A LEU* 3.4 30.7 - - + -
448A PHE* 3.8 22.2 - - + -
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Residues in contact with CYS 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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372A GLY* 4.8 4.7 - - - +
375A LEU* 3.7 29.8 - - - -
376A TYR* 4.1 18.6 - - + -
379A ILE* 5.4 2.0 - - - -
408A TYR* 3.9 13.7 - - + +
412A PHE* 4.4 11.0 - - - -
416A ALA 3.3 17.4 + - - -
417A ARG 3.4 5.9 + - - +
419A LEU* 1.3 78.5 - - - +
421A SER* 1.3 53.9 + - - +
423A LEU* 3.4 9.3 + - - +
424A LEU* 2.8 50.1 + - + +
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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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406A GLU* 3.4 18.0 + - - +
408A TYR* 3.3 8.9 + - - -
417A ARG* 2.9 21.4 + - - -
418A SER* 3.4 8.9 + - - -
420A CYS* 1.3 77.7 - - - +
422A GLN* 1.3 61.4 + - - +
424A LEU 3.0 4.2 + - - -
425A CYS* 2.8 27.9 + - - +
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Residues in contact with GLN 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 SER* 2.8 34.3 + - - +
419A LEU 3.6 3.6 - - - +
421A SER* 1.3 77.1 - - - +
423A LEU* 1.3 59.9 + - - +
425A CYS* 3.5 17.0 - - - +
431A ARG* 3.7 0.7 - - - +
432A LEU* 3.1 43.2 + - + +
435A ARG* 3.6 28.2 + - - +
445A HIS* 3.4 29.8 + - - -
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Residues in contact with LEU 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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368A TRP* 3.7 18.6 - - + +
369A TRP* 3.7 10.9 - - - -
371A LEU* 3.9 17.5 - - + +
372A GLY* 3.5 36.3 - - - +
375A LEU* 4.8 5.2 - - + -
419A LEU* 2.8 37.7 + - + +
420A CYS* 3.7 2.2 - - - +
422A GLN* 1.3 76.6 - - - +
424A LEU* 1.3 59.2 + - - +
425A CYS 3.2 0.4 - - - -
431A ARG* 3.3 27.2 - - - -
432A LEU* 3.9 34.5 - - + +
442A VAL* 4.5 12.3 - - + -
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Residues in contact with LEU 424 (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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369A TRP* 3.2 51.1 - - + +
372A GLY 4.3 13.0 - - - +
373A CYS* 3.7 28.3 - - - +
376A TYR* 4.6 18.4 - - + -
384A PRO* 5.2 4.9 - - + -
385A PHE* 4.8 6.3 - - + -
406A GLU* 3.9 36.2 - - + +
420A CYS* 2.8 24.9 + - + +
421A SER 3.0 5.6 + - - +
423A LEU* 1.3 75.6 - - - +
425A CYS* 1.3 63.1 + - - +
426A LYS* 3.3 7.4 + - - +
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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