Contacts of the helix formed by residues 391 - 412 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353E ALA* 4.6 13.1 - - + +
357E LEU* 5.8 1.7 - - + +
387E PHE 4.2 2.4 + - - +
388E MSE 3.0 5.1 + - - -
390E MSE 1.3 85.3 + - + +
392E GLN* 1.3 70.8 + - - +
393E LYS* 3.4 5.5 + - - +
394E LEU* 2.6 63.2 + - + +
395E PHE* 3.0 15.6 + - - +
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Residues in contact with GLN 392 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388E MSE 3.2 56.8 + - - +
389E GLU* 4.8 3.5 - - - +
390E MSE 4.7 0.4 - - - +
391E ASN* 1.3 74.0 - - - +
393E LYS* 1.3 67.9 + - - +
395E PHE* 2.9 12.9 + - - +
396E ASP* 3.0 25.9 + - - +
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Residues in contact with LYS 393 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391E ASN* 3.4 4.9 - - - +
392E GLN* 1.3 77.6 - - - +
394E LEU* 1.3 63.9 + - - +
396E ASP* 3.0 9.2 + - - +
397E ASP* 2.7 51.1 + - - +
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Residues in contact with LEU 394 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353E ALA* 3.7 24.9 - - + +
354E ALA* 3.7 27.4 - - + +
357E LEU* 5.0 6.1 - - + -
391E ASN* 2.6 46.9 + - + +
393E LYS* 1.3 71.3 - - + +
395E PHE* 1.3 65.3 + - - +
397E ASP* 3.1 12.8 + - + +
398E CYS* 2.9 41.9 + - - -
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Residues in contact with PHE 395 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357E LEU* 4.7 6.8 - - + +
361E PHE* 3.4 38.4 - + - -
365E TYR* 5.4 4.5 - + - -
384E LEU* 3.6 38.1 - - + -
387E PHE* 3.8 14.8 - - + +
388E MSE 3.5 51.1 - - + -
391E ASN 3.0 11.5 + - - +
392E GLN* 2.9 15.1 + - - +
394E LEU* 1.3 72.9 - - - +
396E ASP* 1.3 67.2 + - - +
398E CYS* 3.5 7.8 + - - +
399E THR* 2.9 29.9 + - - -
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Residues in contact with ASP 396 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388E MSE 4.8 6.1 - - - +
392E GLN* 3.0 33.1 + - - +
393E LYS* 3.0 11.1 + - - +
395E PHE* 1.3 80.2 - - - +
397E ASP* 1.3 58.8 + - - +
399E THR* 2.6 34.5 + - - -
400E GLN* 3.0 11.1 + - - +
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Residues in contact with ASP 397 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393E LYS* 2.7 53.1 + - - +
394E LEU* 3.5 14.7 + - + +
396E ASP* 1.3 73.3 - - - +
398E CYS* 1.3 57.9 + - - +
400E GLN* 3.2 10.9 - - - +
401E GLN* 2.9 39.1 + - - +
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Residues in contact with CYS 398 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357E LEU* 4.2 25.6 - - - -
358E PRO* 4.4 18.8 - - + -
361E PHE* 4.2 22.2 - - + -
394E LEU* 2.9 38.3 + - - +
395E PHE 3.6 5.4 - - - +
397E ASP* 1.3 73.6 - - - +
399E THR* 1.3 56.7 + - - +
401E GLN* 3.3 15.8 + - - +
402E PHE* 2.7 37.0 + - - +
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Residues in contact with THR 399 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361E PHE* 4.1 9.9 - - - -
365E TYR* 4.1 17.7 - - + +
395E PHE* 2.9 28.1 + - - -
396E ASP* 2.6 19.6 + - - -
398E CYS* 1.3 71.2 - - - +
400E GLN* 1.3 65.7 + - - +
402E PHE* 2.9 8.1 + - - +
403E LYS* 2.7 62.0 + - + +
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Residues in contact with GLN 400 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396E ASP 3.0 4.2 + - - +
397E ASP* 3.2 16.6 - - - +
399E THR* 1.3 81.1 - - - +
401E GLN* 1.3 70.5 + - + +
403E LYS* 3.6 7.1 - - - +
404E ALA* 2.8 43.3 + - + +
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Residues in contact with GLN 401 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358E PRO* 5.5 8.5 - - - +
397E ASP* 2.9 23.9 + - - +
398E CYS* 3.4 16.4 - - - +
400E GLN* 1.3 81.5 - - + +
402E PHE* 1.3 64.4 + - - +
404E ALA* 3.5 4.7 - - - +
405E GLU* 3.0 40.7 + - - +
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Residues in contact with PHE 402 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361E PHE* 5.0 9.6 - + + -
362E PRO* 4.8 27.4 - - + -
365E TYR* 3.2 49.6 - + + -
366E ARG* 5.7 1.6 - - - -
367E ASN* 4.6 17.5 - - - -
398E CYS 2.7 18.8 + - - +
399E THR* 2.9 10.5 + - - +
401E GLN* 1.3 67.8 - - - +
403E LYS* 1.3 70.0 + - + +
405E GLU* 3.0 9.1 + - + +
406E LYS* 2.7 55.6 + - + +
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Residues in contact with LYS 403 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365E TYR* 3.6 18.6 - - + +
399E THR* 2.7 46.7 + - + +
400E GLN* 3.6 5.8 - - - +
402E PHE* 1.3 79.5 - - + +
404E ALA* 1.3 66.3 + - - +
406E LYS* 2.9 8.2 + - - +
407E LEU* 2.8 24.0 + - - +
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Residues in contact with ALA 404 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400E GLN* 2.8 38.6 + - + +
401E GLN* 3.5 7.4 - - - +
403E LYS* 1.3 73.6 - - - +
405E GLU* 1.3 65.2 + - + +
407E LEU* 3.0 23.2 - - - +
408E LYS* 3.5 7.8 + - - +
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Residues in contact with GLU 405 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401E GLN* 3.0 30.0 + - - +
402E PHE* 3.5 10.3 - - + +
404E ALA* 1.3 78.9 - - + +
406E LYS* 1.3 66.0 + - - +
407E LEU 2.8 1.7 + - - -
408E LYS* 2.9 19.1 + - - +
409E GLU* 3.4 16.6 + - + +
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Residues in contact with LYS 406 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367E ASN* 4.7 19.7 - - - +
402E PHE* 2.7 46.3 + - + +
403E LYS* 3.3 12.1 - - - +
405E GLU* 1.3 72.0 - - - +
407E LEU* 1.3 65.8 + - - +
409E GLU* 3.6 15.0 + - + +
410E LYS* 3.4 50.1 + - + +
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Residues in contact with LEU 407 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403E LYS 2.8 11.5 + - - +
404E ALA* 3.0 16.4 - - - +
405E GLU 2.8 1.2 + - - -
406E LYS* 1.3 78.1 - - - +
408E LYS* 1.3 69.2 + - + +
410E LYS* 2.8 25.0 + - + +
411E LEU* 3.2 22.2 + - + +
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Residues in contact with LYS 408 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404E ALA 4.4 7.0 - - - +
405E GLU* 2.9 13.0 + - - +
407E LEU* 1.3 75.3 - - + +
409E GLU* 1.3 56.3 + - + +
410E LYS 2.5 16.5 + - - -
411E LEU* 2.8 16.8 + - - +
412E LYS* 3.2 49.9 + - + +
413E MSE 4.0 0.7 + - - -
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Residues in contact with GLU 409 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405E GLU* 3.4 10.2 + - + +
406E LYS* 4.0 17.4 + - + +
407E LEU 3.4 0.8 - - - -
408E LYS* 1.3 76.5 - - + +
410E LYS* 1.3 56.8 + - - +
412E LYS* 5.8 0.2 - - - -
413E MSE 2.9 38.7 - - + +
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Residues in contact with LYS 410 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406E LYS* 3.4 36.5 + - + +
407E LEU* 2.8 16.1 + - + +
408E LYS 2.5 6.7 + - - -
409E GLU* 1.3 76.7 - - - +
411E LEU* 1.3 61.0 + - - +
413E MSE 4.3 1.6 - - - -
414E LYS* 3.7 28.8 - - + +
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Residues in contact with LEU 411 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407E LEU* 3.2 24.3 + - + +
408E LYS* 2.8 7.9 + - - +
410E LYS* 1.3 77.0 - - - +
412E LYS* 1.3 76.7 + - + +
413E MSE 3.4 0.2 + - - -
414E LYS* 3.4 18.5 + - - +
415E GLU* 4.8 3.0 - - - +
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Residues in contact with LYS 412 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408E LYS* 3.2 44.1 + - + +
409E GLU* 5.8 0.2 - - - -
411E LEU* 1.3 90.6 - - + +
413E MSE 1.3 58.4 + - + +
414E LYS 2.6 15.1 + - - -
415E GLU* 3.7 21.3 + - - +
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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
------------------------------------------------------------
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