Contacts of the helix formed by residues 375 - 389 (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 THR 375 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334B GLU* 4.4 7.4 - - - +
373B ASN* 2.3 37.4 + - - +
374B LYS* 1.3 69.4 - - - +
376B ILE* 1.3 67.7 + - - +
377B HIS 3.2 2.0 - - - -
378B GLY* 2.7 15.1 + - - -
379B LEU* 2.9 37.8 + - + +
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Residues in contact with ILE 376 (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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325B VAL 5.7 2.7 - - - +
327B SER 5.1 4.9 - - - +
330B PHE* 5.4 4.5 - - - +
333B ALA* 4.3 23.3 - - + -
334B GLU* 5.0 5.4 - - - +
337B LEU* 5.2 4.3 - - + -
368B SER* 6.5 0.7 - - - -
371B HIS* 3.2 50.5 - - + +
373B ASN* 3.1 24.8 - - - +
375B THR* 1.3 75.4 - - - +
377B HIS* 1.3 74.2 + - - +
379B LEU* 2.6 32.8 + - + -
380B ILE* 2.7 29.6 + - + +
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Residues in contact with HIS 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B SER* 2.8 53.0 + - - +
369B LYS* 3.7 25.4 - - + -
371B HIS* 6.0 2.7 - - + -
373B ASN 4.5 2.2 + - - +
374B LYS* 5.4 6.5 - - - +
375B THR 3.1 1.9 + - - +
376B ILE* 1.3 84.5 - - + +
378B GLY* 1.3 60.5 + - - +
380B ILE* 3.7 4.9 + - - +
381B TYR* 3.3 20.4 + - + +
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Residues in contact with GLY 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B LYS 5.3 1.2 + - - -
375B THR 2.7 9.3 + - - -
376B ILE 2.7 2.2 + - - -
377B HIS* 1.3 75.6 - - - +
379B LEU* 1.3 63.1 + - - -
380B ILE 3.0 2.9 + - - -
381B TYR* 3.2 9.0 + - - +
382B ASN* 3.2 22.0 + - - +
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Residues in contact with LEU 379 (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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334B GLU* 4.1 31.2 - - + +
337B LEU* 4.0 23.3 - - + +
338B TYR* 6.3 5.2 - - + -
375B THR* 2.9 37.5 + - + +
376B ILE* 2.6 23.9 + - + +
378B GLY* 1.3 73.5 - - - +
380B ILE* 1.3 57.4 + - - +
382B ASN* 3.6 9.3 - - + +
383B ALA* 3.4 14.9 + - - +
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Residues in contact with ILE 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B VAL* 4.3 19.7 - - + +
337B LEU* 3.6 22.2 - - + -
363B SER 4.5 3.6 - - - +
364B LEU* 3.1 34.8 - - + +
368B SER* 3.5 24.0 - - - +
376B ILE* 2.7 33.0 + - + +
377B HIS 3.8 3.6 - - - +
379B LEU* 1.3 69.8 - - - +
381B TYR* 1.3 73.8 + - - +
382B ASN 3.0 1.8 - - - -
383B ALA* 2.6 17.1 + - - +
384B LEU* 2.9 17.6 + - + +
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Residues in contact with TYR 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B HIS* 3.3 13.5 + - + +
378B GLY* 3.2 12.5 + - - +
380B ILE* 1.3 80.8 - - - +
382B ASN* 1.3 67.8 + - + +
384B LEU* 3.0 13.9 + - + +
385B LYS* 2.9 60.0 + - + +
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Residues in contact with ASN 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B TRP* 5.6 1.0 - - - +
341B ASN* 4.5 5.2 - - - +
378B GLY 3.2 8.5 + - - +
379B LEU* 3.6 14.3 - - + +
380B ILE 2.9 0.8 + - - -
381B TYR* 1.3 85.9 - - + +
383B ALA* 1.3 63.5 + - - +
385B LYS* 3.3 9.9 + - - +
386B LEU* 3.0 49.7 + - - +
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Residues in contact with ALA 383 (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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337B LEU* 5.1 4.9 - - + +
340B TRP* 3.7 40.8 - - + +
364B LEU* 4.6 13.7 - - + -
379B LEU 3.4 9.3 + - - +
380B ILE* 2.6 17.6 + - - +
382B ASN* 1.3 75.5 + - - +
384B LEU* 1.3 64.3 + - - +
386B LEU* 2.8 8.8 + - - +
387B PHE* 2.8 23.0 + - - +
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Residues in contact with LEU 384 (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* 4.7 8.7 - - + -
364B LEU* 3.6 38.4 - - + +
365B TYR* 4.1 35.9 - - + +
380B ILE* 2.9 18.2 + - + +
381B TYR* 3.2 15.7 - - + +
383B ALA* 1.3 75.0 - - - +
385B LYS* 1.3 56.5 - - - +
387B PHE* 2.6 27.9 + - + +
388B MSE 3.0 8.5 + - - -
395B PHE* 3.5 29.0 - - + -
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Residues in contact with LYS 385 (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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381B TYR* 2.9 55.6 + - + +
382B ASN* 3.5 12.1 - - - +
384B LEU* 1.3 74.2 - - - +
386B LEU* 1.3 56.2 + - + +
387B PHE 2.7 1.2 + - - -
388B MSE 2.7 38.4 + - - +
389B GLU* 3.3 23.2 + - - +
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Residues in contact with LEU 386 (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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340B TRP* 4.0 32.8 - - + +
341B ASN* 4.2 7.2 - - - +
346B MSE 4.9 13.0 - - + +
382B ASN* 3.0 38.4 + - - +
383B ALA* 2.8 13.9 + - - +
385B LYS* 1.3 76.0 - - + +
387B PHE* 1.3 59.3 + - - +
389B GLU* 3.4 24.3 - - - +
390B MSE 4.2 6.6 - - - +
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Residues in contact with PHE 387 (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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340B TRP* 2.8 48.2 - + - -
346B MSE 4.3 11.2 - - + -
349B ILE* 3.9 21.3 - - + -
356B ILE* 4.5 4.7 - - + -
357B LEU* 3.0 56.0 - - + +
360B MSE 4.3 11.9 - - + -
361B PHE* 5.1 0.4 - + - -
364B LEU* 4.4 9.6 - - + -
383B ALA 2.8 5.4 + - - +
384B LEU* 2.6 21.9 + - + +
386B LEU* 1.3 74.5 - - - +
388B MSE 1.3 63.8 + - - +
390B MSE 3.7 26.4 - - + +
391B ASN 4.2 2.6 + - - +
395B PHE* 3.7 19.2 - + + +
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Residues in contact with MSE 388 (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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384B LEU 3.0 5.8 + - - +
385B LYS* 2.7 24.2 + - - +
387B PHE* 1.3 67.4 - - - +
389B GLU* 1.3 56.8 + - + +
390B MSE 2.4 18.9 + - - -
391B ASN 2.9 20.0 + - - -
392B GLN* 3.0 53.1 + - - +
395B PHE* 3.5 44.0 - - + -
396B ASP* 4.6 8.1 - - - +
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Residues in contact with GLU 389 (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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385B LYS* 3.3 21.2 + - - +
386B LEU* 3.4 13.8 - - - +
388B MSE 1.3 76.7 - - + +
390B MSE 1.3 63.2 - - - +
392B GLN* 5.0 3.6 - - - +
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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
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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