Contacts of the helix formed by residues 391 - 412 (chain B) in PDB entry 2NYM
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 391 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353B ALA* 4.8 10.3 - - + +
357B LEU* 5.8 1.2 - - + +
387B PHE 4.2 2.8 + - - +
388B MSE 2.9 3.6 + - - -
390B MSE 1.3 87.6 + - + +
392B GLN* 1.3 70.3 - - - +
393B LYS* 3.7 8.0 + - - +
394B LEU* 2.7 60.5 + - + +
395B PHE* 3.1 19.6 + - - +
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Residues in contact with GLN 392 (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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388B MSE 3.0 57.4 + - - +
389B GLU* 5.0 2.9 - - - +
391B ASN* 1.3 74.4 - - - +
393B LYS* 1.3 69.3 + - - +
395B PHE* 3.1 4.9 + - - +
396B ASP* 3.0 37.1 + - - +
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Residues in contact with LYS 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ASN* 3.4 5.8 - - - +
392B GLN* 1.3 77.0 - - - +
394B LEU* 1.3 64.9 + - + +
396B ASP* 2.9 8.8 + - - +
397B ASP* 2.7 54.4 + - - +
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Residues in contact with LEU 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ALA* 3.8 10.8 - - + +
354B ALA* 3.7 40.2 - - + +
357B LEU* 5.0 7.0 - - + -
391B ASN* 2.7 43.0 + - + +
393B LYS* 1.3 72.3 - - - +
395B PHE* 1.3 66.1 + - - +
397B ASP* 3.0 10.1 + - + +
398B CYS* 2.8 42.0 + - - -
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Residues in contact with PHE 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B LEU* 4.8 5.5 - - + +
361B PHE* 3.7 32.9 - + - -
365B TYR* 5.5 4.5 - + - -
384B LEU* 3.5 41.1 - - + -
387B PHE* 3.7 28.9 - - + +
388B MSE 3.5 38.6 - - + -
391B ASN 3.1 10.6 + - - +
392B GLN 3.2 10.3 - - - +
394B LEU* 1.3 79.2 - - - +
396B ASP* 1.3 65.7 + - - +
398B CYS* 3.4 8.0 + - - +
399B THR* 2.8 31.4 + - - -
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Residues in contact with ASP 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B MSE 4.6 6.3 - - - +
392B GLN* 3.0 35.9 + - - +
393B LYS* 2.9 11.2 + - - +
395B PHE* 1.3 81.0 - - - +
397B ASP* 1.3 59.0 + - - +
399B THR* 2.7 31.5 + - - -
400B GLN* 2.9 12.1 + - - +
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Residues in contact with ASP 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B LYS* 2.7 57.0 + - - +
394B LEU* 3.6 11.3 + - + +
396B ASP* 1.3 72.5 - - - +
398B CYS* 1.3 58.3 + - - +
400B GLN* 3.1 10.8 - - - +
401B GLN* 2.9 38.2 + - - +
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Residues in contact with CYS 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B LEU* 4.1 24.9 - - - -
358B PRO* 4.7 15.7 - - + -
361B PHE* 4.1 21.4 - - + -
394B LEU* 2.8 47.5 + - - +
395B PHE 3.6 4.9 - - - +
397B ASP* 1.3 69.2 - - - +
399B THR* 1.3 57.0 + - - +
401B GLN* 3.3 12.2 + - - +
402B PHE* 2.7 37.4 + - - +
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Residues in contact with THR 399 (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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361B PHE* 3.9 17.7 - - - -
365B TYR* 4.3 17.1 - - + +
395B PHE* 2.8 24.8 + - - -
396B ASP* 2.7 12.9 + - - -
398B CYS* 1.3 74.4 - - - +
400B GLN* 1.3 72.5 + - - +
402B PHE* 2.8 6.2 + - - +
403B LYS* 2.8 55.2 + - + +
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Residues in contact with GLN 400 (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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396B ASP 2.9 9.9 + - - +
397B ASP* 3.1 15.5 - - - +
399B THR* 1.3 83.0 - - - +
401B GLN* 1.3 67.9 + - + +
403B LYS* 3.6 6.1 - - - +
404B ALA* 2.9 37.7 + - + +
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Residues in contact with GLN 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B PRO* 6.0 2.8 - - - +
397B ASP* 2.9 22.4 + - - +
398B CYS* 3.5 13.0 - - - +
400B GLN* 1.3 79.1 - - + +
402B PHE* 1.3 67.6 + - - +
404B ALA* 3.6 5.6 + - - +
405B GLU* 3.1 37.5 + - - +
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Residues in contact with PHE 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B PHE* 4.7 11.4 - + + -
362B PRO* 4.7 27.1 - - + -
365B TYR* 3.2 51.6 - + + -
366B ARG* 5.4 1.6 - - - -
367B ASN* 4.9 15.0 - - - -
398B CYS 2.7 18.2 + - - +
399B THR* 2.8 10.7 + - - +
401B GLN* 1.3 71.3 - - - +
403B LYS* 1.3 72.5 + - + +
405B GLU* 2.9 13.7 + - + +
406B LYS* 2.8 48.6 + - + -
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Residues in contact with LYS 403 (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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365B TYR* 3.5 20.8 + - + +
399B THR* 2.8 45.7 + - + +
400B GLN* 3.7 4.7 - - - +
402B PHE* 1.3 80.2 - - + +
404B ALA* 1.3 65.9 + - - +
406B LYS* 3.0 8.8 + - - +
407B LEU* 2.7 23.9 + - - +
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Residues in contact with ALA 404 (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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400B GLN* 2.9 36.1 + - - +
401B GLN* 3.6 7.2 - - - +
403B LYS* 1.3 70.8 - - - +
405B GLU* 1.3 67.6 + - + +
407B LEU* 2.9 24.8 - - - +
408B LYS* 3.5 8.6 + - - +
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Residues in contact with GLU 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B GLN* 3.1 29.7 + - - +
402B PHE* 2.9 14.1 + - + +
404B ALA* 1.3 77.7 - - + +
406B LYS* 1.3 66.4 + - - +
407B LEU 2.7 2.1 + - - -
408B LYS* 2.8 20.8 + - - +
409B GLU* 3.4 14.8 + - + +
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Residues in contact with LYS 406 (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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367B ASN* 4.4 22.0 - - - +
402B PHE* 2.8 43.9 + - + +
403B LYS* 3.3 12.8 - - - +
405B GLU* 1.3 71.4 - - - +
407B LEU* 1.3 65.7 + - - +
409B GLU* 3.4 14.6 + - + +
410B LYS* 3.3 48.0 + - + +
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Residues in contact with LEU 407 (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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403B LYS 2.7 14.6 + - - +
404B ALA* 2.9 17.7 - - - +
405B GLU 2.7 4.0 + - - -
406B LYS* 1.3 70.3 - - - +
408B LYS* 1.3 60.8 + - + +
410B LYS* 2.7 34.9 + - + +
411B LEU* 3.1 22.7 + - + -
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Residues in contact with LYS 408 (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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404B ALA 4.2 8.5 - - - +
405B GLU* 2.8 12.9 + - - +
407B LEU* 1.3 82.5 - - + +
409B GLU* 1.3 54.9 + - + +
410B LYS 2.6 12.5 + - - -
411B LEU* 2.8 15.4 + - - +
412B LYS* 3.2 49.3 + - + +
413B MSE 4.0 0.7 + - - -
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Residues in contact with GLU 409 (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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405B GLU* 3.4 10.5 + - + +
406B LYS* 3.4 17.4 + - + +
407B LEU 3.3 1.2 - - - -
408B LYS* 1.3 78.9 - - + +
410B LYS* 1.3 56.9 + - - +
413B MSE 3.0 35.2 - - + +
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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
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406B LYS* 3.3 34.1 + - + +
407B LEU* 2.7 15.8 + - + +
408B LYS 2.6 5.7 + - - -
409B GLU* 1.3 76.9 - - - +
411B LEU* 1.3 61.6 + - - +
413B MSE 4.1 2.9 - - - +
414B LYS* 3.7 25.6 - - + +
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Residues in contact with LEU 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B LEU* 3.1 24.7 + - + +
408B LYS* 2.8 8.2 + - - +
410B LYS* 1.3 77.2 - - - +
412B LYS* 1.3 78.8 + - + +
413B MSE 3.2 1.0 + - - -
414B LYS* 3.3 20.4 + - - +
415B GLU* 4.9 1.1 - - - +
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Residues in contact with LYS 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B LYS* 3.2 43.7 + - + +
409B GLU* 5.9 0.2 - - - -
411B LEU* 1.3 90.9 - - + +
413B MSE 1.3 60.3 + - + +
414B LYS 2.7 14.0 + - - -
415B GLU* 3.5 22.6 + - - +
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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
------------------------------------------------------------
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