Contacts of the helix formed by residues 413 - 424 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285B GLU* 3.2 34.0 + - - -
411B ARG 3.7 0.8 + - - -
412B PHE* 1.3 76.3 - - - +
414B PRO* 1.3 79.4 - - - +
415B GLN* 3.6 5.0 + - - +
416B ALA* 3.1 20.7 + - - +
417B ARG* 3.3 17.7 + - - +
447B LEU* 5.1 1.2 - - - +
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Residues in contact with PRO 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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413B SER* 1.3 92.2 - - - +
415B GLN* 1.3 67.4 + - + +
417B ARG* 3.3 16.4 + - + +
418B SER* 3.7 5.4 + - - -
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Residues in contact with GLN 415 (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 SER* 3.6 4.7 + - - +
414B PRO* 1.3 81.6 - - + +
416B ALA* 1.3 66.7 + - - +
418B SER* 2.6 36.0 + - - -
419B LEU 3.4 3.3 + - - -
445B HIS* 3.6 12.6 - - + -
446B PRO* 4.0 36.7 - - + +
447B LEU* 4.7 13.7 - - + -
449B LYS* 5.5 10.2 - - - +
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Residues in contact with ALA 416 (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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285B GLU* 3.7 13.0 - - - +
379B ILE* 4.5 9.9 - - + -
412B PHE* 4.5 11.7 - - + -
413B SER* 3.1 33.7 + - - +
415B GLN* 1.3 77.6 - - - +
417B ARG* 1.3 61.7 + - - +
419B LEU* 3.6 2.6 + - - +
420B CYS* 3.1 29.0 + - - -
447B LEU* 4.2 19.5 - - + +
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Residues in contact with ARG 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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408B TYR* 3.3 63.2 + - + +
412B PHE* 4.6 5.3 - - + +
413B SER 3.3 8.9 + - - +
414B PRO* 3.5 11.4 - - - +
415B GLN 3.1 0.6 - - - -
416B ALA* 1.3 80.9 - - - +
418B SER* 1.3 54.1 + - - +
420B CYS 3.5 0.3 + - - -
421B SER* 2.7 34.4 + - - +
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Residues in contact with SER 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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414B PRO 3.7 4.9 + - - -
415B GLN* 2.6 30.6 + - - -
417B ARG* 1.3 78.6 - - - +
419B LEU* 1.3 56.2 + - - +
421B SER* 2.8 17.5 + - - -
422B GLN* 2.9 34.7 + - - +
445B HIS* 2.8 21.0 + - - -
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Residues in contact with LEU 419 (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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375B LEU* 3.8 15.9 - - + -
415B GLN 3.4 0.8 + - - -
416B ALA 4.0 6.7 - - - +
417B ARG 3.3 0.4 - - - -
418B SER* 1.3 78.4 + - - +
420B CYS* 1.3 57.5 + - - +
422B GLN* 3.1 2.9 + - - +
423B LEU* 2.7 53.6 + - + +
432B LEU* 3.4 32.1 - - + -
442B VAL* 4.7 6.3 - - + +
445B HIS* 3.6 31.0 - - + -
447B LEU* 3.3 31.0 - - + -
448B PHE* 4.2 20.6 - - + -
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Residues in contact with CYS 420 (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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372B GLY* 5.0 4.7 - - - +
375B LEU* 4.0 27.6 - - - -
376B TYR* 4.6 9.2 - - + +
379B ILE* 5.0 2.7 - - - -
408B TYR* 3.5 17.5 - - + +
412B PHE* 4.2 20.9 - - + -
416B ALA* 3.1 20.6 + - - +
417B ARG 3.9 0.7 - - - +
419B LEU* 1.3 77.9 - - - +
421B SER* 1.3 52.9 + - - +
423B LEU* 3.4 9.2 + - - +
424B LEU* 2.7 50.1 + - + +
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Residues in contact with SER 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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406B GLU* 3.4 19.9 - - - +
408B TYR* 3.1 16.0 + - - -
417B ARG* 2.7 21.2 + - - +
418B SER* 2.8 17.2 + - - -
420B CYS* 1.3 75.7 - - - +
422B GLN* 1.3 54.1 + - - +
424B LEU 2.9 2.3 + - - -
425B CYS* 2.8 34.3 + - - +
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Residues in contact with GLN 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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418B SER* 2.9 35.1 + - - +
419B LEU 3.6 3.1 - - - +
421B SER* 1.3 77.8 + - - +
423B LEU* 1.3 59.9 + - - +
425B CYS* 3.6 14.2 - - - +
430B GLU 4.9 0.3 - - - +
431B ARG* 3.7 0.2 - - - +
432B LEU* 3.2 49.7 + - + +
435B ARG* 4.3 17.7 + - - +
445B HIS* 3.3 31.5 + - - -
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Residues in contact with LEU 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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368B TRP* 3.6 36.6 - - + +
369B TRP* 3.9 8.0 - - - -
371B LEU* 4.4 14.8 - - + +
372B GLY* 4.0 23.1 - - - +
375B LEU* 4.9 4.9 - - + -
419B LEU* 2.7 49.5 + - + +
420B CYS* 3.6 5.6 - - - +
422B GLN* 1.3 73.9 - - - +
424B LEU* 1.3 57.0 + - - +
425B CYS 3.2 2.0 + - - -
431B ARG* 3.2 29.3 + - - +
432B LEU* 4.1 29.8 - - + +
442B VAL* 4.5 4.9 - - + -
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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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369B TRP* 3.4 47.3 - - + +
372B GLY* 4.1 18.2 - - - +
373B CYS* 3.8 23.8 - - - +
376B TYR* 4.7 13.0 - - + -
384B PRO* 5.4 3.4 - - + -
385B PHE* 4.7 6.3 - - + -
406B GLU* 3.5 44.1 - - + +
420B CYS* 2.7 31.5 + - + +
421B SER 2.9 4.9 + - - -
423B LEU* 1.3 71.3 - - - +
425B CYS* 1.3 62.6 + - - +
426B LYS* 3.5 6.2 + - - +
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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