Contacts of the helix formed by residues 404 - 418 (chain B) in PDB entry 3N6J
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 ASN 404 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378B TYR 4.8 0.4 - - - +
379B LEU 2.7 23.8 + - - +
380B THR 4.7 0.6 - - - -
381B LYS* 3.8 33.4 - - + +
402B GLU 3.6 0.2 + - - -
403B LEU* 1.3 74.4 - - - +
405B MSE 1.3 54.1 + - - +
406B ASP* 2.7 28.9 + - - +
407B ASN* 2.8 49.7 + - + +
408B VAL* 3.2 9.6 + - - +
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Residues in contact with MSE 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LYS* 4.0 24.5 - - + -
17B ILE* 3.9 19.7 - - + -
43B ILE* 4.9 5.8 - - - -
381B LYS* 5.7 0.2 - - - +
403B LEU* 3.5 24.7 + - + +
404B ASN* 1.3 72.0 - - - +
406B ASP* 1.3 59.5 + - - +
408B VAL* 3.4 15.1 + - - -
409B LEU* 3.0 60.0 + - + +
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Residues in contact with ASP 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B ASN* 2.7 16.1 + - - +
405B MSE 1.3 75.5 + - - +
407B ASN* 1.3 62.8 + - - +
409B LEU* 3.0 15.4 + - - +
410B LYS* 2.9 41.9 + - - +
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Residues in contact with ASN 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B PHE* 3.2 41.1 - - + -
378B TYR* 2.8 32.6 + - - +
379B LEU* 3.9 2.9 - - + -
404B ASN* 2.8 37.3 + - + +
406B ASP* 1.3 77.3 - - - +
408B VAL* 1.3 56.7 + - - +
410B LYS* 3.3 14.2 + - - -
411B ALA* 2.9 24.3 + - - +
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Residues in contact with VAL 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ILE* 4.1 24.0 - - + -
19B VAL* 3.8 18.8 - - + +
41B ILE* 4.4 15.5 - - + -
43B ILE* 4.8 2.9 - - + -
379B LEU* 3.6 24.7 - - + -
403B LEU* 3.8 26.7 - - + -
404B ASN 3.2 14.3 + - - +
405B MSE 3.6 10.5 - - - +
406B ASP 3.1 0.6 - - - -
407B ASN* 1.3 74.1 - - - +
409B LEU* 1.3 61.0 + - - +
411B ALA* 4.5 1.3 - - - -
412B HIS* 2.9 27.7 + - - +
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Residues in contact with LEU 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ILE* 4.7 13.5 - - + -
405B MSE 3.0 54.3 + - + +
406B ASP* 3.0 16.1 + - - +
408B VAL* 1.3 75.9 - - - +
410B LYS* 1.3 61.0 + - - +
412B HIS* 3.5 13.3 - - + +
413B GLU* 3.3 27.6 + - - +
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Residues in contact with LYS 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B PHE* 4.3 16.5 - - + -
406B ASP* 2.9 23.6 + - - +
407B ASN* 3.5 21.6 + - - +
409B LEU* 1.3 75.1 - - - +
411B ALA* 1.3 60.0 + - - +
412B HIS 3.0 1.6 - - - -
413B GLU* 2.8 25.2 + - - +
414B LEU* 3.0 12.5 + - - +
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Residues in contact with ALA 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B VAL* 3.7 19.1 - - + -
20B ALA 3.0 41.9 + - - +
345B PHE* 4.6 1.6 - - + -
377B PHE* 3.8 17.2 - - + -
379B LEU* 4.5 4.5 - - + -
407B ASN 2.9 20.1 + - - +
408B VAL* 4.0 2.0 - - - +
410B LYS* 1.3 73.0 - - - +
412B HIS* 1.3 56.1 + - - +
414B LEU* 3.5 8.5 + - - +
415B HIS 3.0 13.9 + - - -
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Residues in contact with HIS 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ILE* 3.6 17.5 - - + +
18B PRO* 2.9 47.2 + - + +
19B VAL* 4.0 0.2 - - - +
408B VAL 2.9 18.9 + - - +
409B LEU* 3.5 16.6 - - + +
410B LYS 3.0 0.2 - - - -
411B ALA* 1.3 75.4 - - - +
413B GLU* 1.3 61.0 + - - +
415B HIS* 3.0 4.7 + + - +
416B LYS* 2.7 69.2 + - + +
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Residues in contact with GLU 413 (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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409B LEU 3.3 15.3 + - - +
410B LYS* 2.8 11.7 + - - +
412B HIS* 1.3 78.7 - - - +
414B LEU* 1.3 64.7 + - - +
416B LYS* 2.6 45.3 + - - +
417B LYS* 3.1 28.7 + - + +
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Residues in contact with LEU 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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20B ALA* 3.8 26.9 - - + +
21B GLY* 4.7 0.7 - - - +
22B HIS* 3.7 27.4 - - + +
36B TYR* 3.6 32.1 - - + +
410B LYS 3.0 10.8 + - - +
411B ALA* 3.6 10.3 - - - +
412B HIS 3.2 0.2 - - - -
413B GLU* 1.3 77.0 - - - +
415B HIS* 1.3 61.4 + - - +
417B LYS* 3.2 26.6 + - + +
418B LEU* 3.5 12.4 - - + +
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Residues in contact with HIS 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B PRO* 3.4 35.9 - - + +
19B VAL 3.4 19.1 + - - -
20B ALA* 3.6 15.0 - - - +
38B THR* 4.0 14.8 - - - +
39B ARG 5.0 1.6 - - - -
40B ASN* 5.4 0.2 - - - -
59B GLY* 5.3 6.1 - - - -
63B GLU* 4.9 4.2 + - - -
411B ALA 3.0 14.7 + - - +
412B HIS* 3.0 13.0 + + - +
414B LEU* 1.3 76.3 - - - +
416B LYS* 1.3 66.0 + - + +
418B LEU* 3.2 23.0 + - + +
421B GLY* 3.7 31.6 + - - -
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Residues in contact with LYS 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B HIS* 2.7 48.9 + - + +
413B GLU* 2.6 50.2 + - - +
415B HIS* 1.3 76.4 - - + +
417B LYS* 1.3 62.3 + - + +
418B LEU 3.5 6.6 - - - +
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Residues in contact with LYS 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B GLU* 3.1 20.8 + - - +
414B LEU* 3.3 17.3 - - + +
415B HIS 3.1 1.0 - - - -
416B LYS* 1.3 76.0 - - + +
418B LEU* 1.3 68.5 + - + +
419B PRO* 3.7 2.6 - - - +
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Residues in contact with LEU 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ALA* 4.0 14.1 - - + -
36B TYR* 3.7 42.4 - - + +
38B THR* 3.6 30.5 - - + -
414B LEU* 3.5 17.5 - - + +
415B HIS* 3.2 15.9 + - - +
416B LYS 3.5 9.4 - - - +
417B LYS* 1.3 80.5 - - + +
419B PRO* 1.3 71.7 - - + +
420B ASN* 3.0 18.8 + - - +
421B GLY* 4.7 1.8 - - - -
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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