Contacts of the helix formed by residues 378 - 401 (chain B) in PDB entry 2NLL
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 ASP 378 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B ASP* 1.3 74.2 - - - +
379B SER* 1.3 58.5 + - - +
381B ARG* 3.0 31.7 + - - +
382B LEU* 2.9 44.6 + - + +
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Residues in contact with SER 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B ASP* 2.7 24.3 + - - -
378B ASP* 1.3 77.7 - - - +
380B LYS* 1.3 60.7 + - - +
382B LEU* 4.1 4.6 - - - +
383B ALA* 3.1 27.9 + - - +
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Residues in contact with LYS 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B ASP 5.3 6.6 + - - -
375B VAL 4.5 2.8 + - - -
376B LEU* 3.6 33.4 - - + +
377B ASP* 2.8 55.7 + - - +
379B SER* 1.3 79.3 - - - +
381B ARG* 1.3 65.4 + - - +
383B ALA* 3.7 5.7 + - - +
384B LYS* 3.3 21.0 + - - +
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Residues in contact with ARG 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B GLN* 3.9 15.9 - - - +
376B LEU* 3.9 19.2 - - + +
377B ASP 2.8 21.0 + - - +
378B ASP* 3.0 28.3 + - - +
380B LYS* 1.3 73.0 - - - +
382B LEU* 1.3 90.9 + - - +
384B LYS* 3.1 15.2 + - - +
385B ARG* 3.1 30.7 + - + +
514C G 3.5 24.0 - - - +
515C G 2.8 40.3 + - - +
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Residues in contact with LEU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B ASP* 2.9 30.8 + - + +
379B SER* 4.2 4.0 - - - +
381B ARG* 1.3 113.6 - - - +
383B ALA* 1.3 58.2 + - - +
385B ARG* 3.4 13.1 + - + +
386B LYS* 3.0 30.0 + - - +
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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
----------------------------------------------------------
379B SER 3.1 20.5 + - - +
380B LYS* 3.8 9.0 - - - +
382B LEU* 1.3 76.7 - - - +
384B LYS* 1.3 57.2 + - - +
386B LYS* 3.5 10.1 + - - +
387B LEU* 2.9 30.0 + - - +
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Residues in contact with LYS 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B LEU* 4.6 10.1 - - + -
380B LYS 3.3 11.0 + - - +
381B ARG* 3.1 10.5 + - - +
383B ALA* 1.3 76.9 - - - +
385B ARG* 1.3 65.3 + - + +
387B LEU* 3.4 7.9 + - + +
388B ILE* 3.1 49.3 + - + +
513C A 3.1 42.2 + - - +
514C G 3.3 30.2 + - - +
528D G 5.5 3.8 - - - +
529D A 5.1 14.6 - - - -
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Residues in contact with ARG 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ARG* 3.1 29.3 + - + +
382B LEU* 3.4 16.1 + - + +
384B LYS* 1.3 75.3 - - + +
386B LYS* 1.3 60.6 + - - +
388B ILE* 3.8 7.6 - - - +
389B GLU* 2.9 53.5 + - - +
514C G 5.2 0.9 - - - +
515C G 2.8 68.1 + - - +
516C T 4.0 11.1 + - - -
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Residues in contact with LYS 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B LEU 3.0 18.0 + - - +
383B ALA* 3.5 10.3 - - - +
385B ARG* 1.3 75.3 - - - +
387B LEU* 1.3 63.2 + - - +
389B GLU* 3.4 6.8 + - - +
390B GLU* 2.9 69.0 + - - +
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Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B ALA 2.9 18.1 + - - +
384B LYS* 3.5 9.4 - - + +
385B ARG 3.3 0.2 - - - -
386B LYS* 1.3 77.3 - - - +
388B ILE* 1.3 56.4 + - + +
390B GLU* 3.8 4.2 - - + -
391B ASN* 2.8 54.6 + - - +
529D A 3.9 37.5 - - - +
530D A 4.1 12.3 - - - +
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Residues in contact with ILE 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 LYS* 3.1 44.4 + - + +
385B ARG* 3.8 6.7 - - - +
386B LYS 3.4 0.2 - - - -
387B LEU* 1.3 75.7 - - - +
389B GLU* 1.3 68.9 + - + +
391B ASN* 3.4 7.0 + - - +
392B ARG* 3.1 55.9 + - - +
394B LYS* 5.2 0.4 + - - +
527D T 6.1 0.9 - - - +
528D G 3.9 23.3 - - - +
529D A 4.0 24.4 + - - +
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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
----------------------------------------------------------
385B ARG* 2.9 42.2 + - - +
386B LYS* 3.8 5.4 - - - +
388B ILE* 1.3 77.6 - - + +
390B GLU* 1.3 64.3 + - + +
392B ARG* 3.1 38.2 + - - +
393B GLU 4.2 0.2 + - - -
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Residues in contact with GLU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B LYS* 2.9 59.3 + - - +
387B LEU* 4.2 4.7 - - + +
389B GLU* 1.3 75.4 - - + +
391B ASN* 1.3 67.7 + - - +
393B GLU* 2.9 36.8 + - - +
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Residues in contact with ASN 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B LEU* 2.8 39.5 + - - +
388B ILE 3.6 3.4 - - - +
389B GLU 3.3 0.2 - - - -
390B GLU* 1.3 71.9 - - - +
392B ARG* 1.3 54.4 + - - +
393B GLU* 2.4 30.5 + - - +
394B LYS* 3.1 28.2 + - - +
529D A 2.8 44.1 + - - +
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Residues in contact with ARG 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ILE* 3.1 43.0 + - + +
389B GLU* 3.1 28.1 + - - +
391B ASN* 1.3 72.7 - - - +
393B GLU* 1.4 49.6 + - - +
394B LYS* 2.9 31.7 + - - +
395B ARG* 3.1 24.2 + - + +
527D T 3.7 13.3 + - - -
528D G 3.0 29.3 + - - +
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Residues in contact with GLU 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B GLU 4.2 0.6 + - - -
390B GLU* 2.9 26.9 + - - +
391B ASN* 2.4 25.5 + - - +
392B ARG* 1.4 63.1 - - - +
394B LYS* 1.3 58.8 + - + +
395B ARG* 2.8 8.5 - - - +
396B ARG* 3.3 51.0 + - - +
397B ARG* 3.3 41.3 + - - +
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Residues in contact with LYS 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ILE* 5.2 0.4 + - - +
391B ASN* 3.1 22.4 + - - +
392B ARG* 4.2 25.0 - - - +
393B GLU* 1.3 79.6 - - + +
395B ARG* 1.3 63.0 + - - +
397B ARG* 3.1 14.8 + - - +
398B GLU* 2.8 30.8 + - + +
528D G 4.7 15.0 + - - -
529D A 3.9 22.0 + - - -
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Residues in contact with ARG 395 (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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392B ARG* 3.1 17.5 + - + +
393B GLU* 2.8 2.4 - - - -
394B LYS* 1.3 81.1 - - - +
396B ARG* 1.3 65.3 + - + +
398B GLU* 2.8 41.6 + - - +
399B GLU* 3.2 60.0 + - - +
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Residues in contact with ARG 396 (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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393B GLU* 3.3 47.2 + - - +
395B ARG* 1.3 78.2 - - + +
397B ARG* 1.3 58.2 + - + +
399B GLU* 3.6 10.3 + - - +
400B LEU* 3.1 25.0 + - - +
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Residues in contact with ARG 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B GLU* 3.3 40.1 + - - +
394B LYS* 3.1 14.8 + - - +
396B ARG* 1.3 76.8 - - + +
398B GLU* 1.3 58.7 + - - +
400B LEU* 2.6 31.0 + - + +
401B GLU* 2.9 15.2 + - - +
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Residues in contact with GLU 398 (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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394B LYS* 2.8 19.8 + - + +
395B ARG* 2.8 48.8 + - - +
397B ARG* 1.3 74.2 - - - +
399B GLU* 1.3 62.7 + - + +
401B GLU* 2.8 46.3 + - - +
402B LYS 3.9 4.2 - - - +
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Residues in contact with GLU 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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395B ARG* 3.2 48.4 + - - +
396B ARG* 3.7 8.2 - - - +
397B ARG 3.1 0.4 - - - -
398B GLU* 1.3 76.8 - - + +
400B LEU* 1.3 62.6 + - - +
401B GLU 3.4 0.4 - - - -
402B LYS* 4.1 20.2 + - - +
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Residues in contact with LEU 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B ARG 3.1 13.6 + - - +
397B ARG* 2.6 24.5 + - + +
399B GLU* 1.3 73.3 - - - +
401B GLU* 1.3 68.9 + - - +
402B LYS* 3.2 7.2 + - - +
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Residues in contact with GLU 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B ARG 2.9 13.3 + - - +
398B GLU* 2.8 36.7 - - - +
400B LEU* 1.3 81.8 - - - +
402B LYS* 1.3 79.9 + - + +
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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