Contacts of the helix formed by residues 374 - 388 (chain B) in PDB entry 3NA0
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 VAL 374 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355B GLU* 3.1 15.5 - - + +
356B VAL* 4.0 26.0 - - + -
359B ALA* 3.9 16.4 - - + -
370B MET* 3.7 17.9 - - + +
371B LEU* 4.1 15.6 + - - +
372B GLN 3.7 1.2 - - - -
373B LEU* 1.3 85.0 - - - +
375B PRO* 1.4 65.8 - - - +
377B LEU* 3.1 11.4 + - + -
378B LYS* 3.1 24.2 + - + +
473B THR* 4.1 24.7 - - + -
477B ILE* 4.6 3.8 - - + -
72D ASP* 5.8 0.2 - - - -
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Residues in contact with PRO 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B GLU* 3.2 15.5 - - - +
372B GLN 5.0 2.9 - - - +
373B LEU* 3.3 9.6 - - - +
374B VAL* 1.4 88.3 - - - +
376B LEU* 1.3 55.1 + - - +
378B LYS* 3.4 7.9 + - + +
379B ALA* 3.1 27.4 + - - +
441B LEU* 4.0 23.9 - - + +
72D ASP* 4.8 14.8 - - - +
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Residues in contact with LEU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B VAL* 5.3 1.8 - - + +
351B MET* 3.7 43.7 - - + +
352B LEU* 3.4 23.4 - - + +
355B GLU* 3.1 22.2 + - + +
375B PRO* 1.3 75.6 - - - +
377B LEU* 1.3 60.8 + - - +
379B ALA* 3.4 3.9 + - - +
380B SER* 3.0 22.9 + - - -
437B PRO* 3.9 20.0 - - + +
438B THR* 3.8 22.4 - - + +
441B LEU* 3.6 25.9 - - + +
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Residues in contact with LEU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B HIS* 4.2 4.0 - - + +
352B LEU* 3.6 9.5 - - + +
355B GLU* 3.2 6.1 + - - +
356B VAL* 4.0 18.8 - - + -
374B VAL* 3.1 19.4 + - + +
376B LEU* 1.3 75.7 - - - +
378B LYS* 1.3 60.2 + - - +
380B SER* 2.3 40.2 + - - +
381B ILE* 3.1 11.5 + - + +
473B THR* 3.8 35.9 - - + +
476B LEU* 4.0 27.4 - - + -
477B ILE* 3.9 19.7 - - + +
480B LEU* 4.3 12.6 - - + -
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Residues in contact with LYS 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B LEU* 2.9 35.4 + - - +
372B GLN* 3.9 5.1 + - - -
374B VAL* 3.1 18.0 + - + +
375B PRO* 3.8 9.2 - - + +
376B LEU 3.3 0.2 - - - -
377B LEU* 1.3 75.3 - - - +
379B ALA* 1.3 60.4 + - - +
381B ILE* 3.5 11.8 + - - +
382B LYS* 3.3 31.7 + - - +
470B LEU* 6.4 0.8 - - - +
473B THR* 4.6 22.0 - - + +
72D ASP* 3.0 33.6 + - + +
73D GLU* 3.2 24.0 + - - +
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Residues in contact with ALA 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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375B PRO 3.1 17.3 + - - +
376B LEU* 3.7 7.9 - - - +
377B LEU 3.2 0.2 - - - -
378B LYS* 1.3 74.3 - - - +
380B SER* 1.3 55.4 + - - +
381B ILE 3.1 0.2 - - - -
382B LYS* 3.3 12.0 + - - +
383B GLU* 2.7 34.0 + - - +
437B PRO* 3.2 28.3 - - + +
440B TRP* 3.5 16.7 - - + -
441B LEU* 4.6 9.0 - - + -
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Residues in contact with SER 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B HIS* 3.0 25.8 - - - -
352B LEU* 4.0 10.8 - - - -
376B LEU 3.0 12.6 + - - -
377B LEU* 2.3 34.1 + - - +
379B ALA* 1.3 77.8 - - - +
381B ILE* 1.3 56.1 + - - +
383B GLU* 3.3 3.8 + - - +
384B THR* 2.8 32.6 + - - -
435B PHE* 3.9 4.5 - - - -
437B PRO* 3.8 23.6 - - - -
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Residues in contact with ILE 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B THR* 5.5 1.8 - - + -
338B HIS* 4.3 5.6 - - - +
377B LEU* 3.1 16.0 + - + +
378B LYS* 3.7 10.1 - - - +
379B ALA 3.1 0.2 - - - -
380B SER* 1.3 76.5 - - - +
382B LYS* 1.3 64.8 + - + +
384B THR* 3.2 5.5 + - - -
385B LEU* 3.1 33.0 + - + +
455B PHE* 5.3 3.8 - - + -
469B GLU* 4.6 7.6 - - + +
472B MET* 3.8 31.4 - - + -
473B THR* 3.2 45.1 - - + +
476B LEU* 4.1 22.2 - - + -
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Residues in contact with LYS 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B LYS* 3.3 20.6 + - - +
379B ALA* 3.3 8.6 + - - +
381B ILE* 1.3 78.0 - - + +
383B GLU* 1.3 62.5 + - - +
385B LEU* 3.4 9.2 + - - +
386B ARG* 3.1 21.5 + - - +
440B TRP* 3.9 43.0 + - + +
452B ASN* 3.4 34.3 - - - +
469B GLU* 6.1 0.2 - - - -
76D ASP* 2.6 41.8 + - - +
79D ASP* 5.3 4.2 + - - -
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Residues in contact with GLU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B ALA 2.7 20.5 + - - +
380B SER* 3.6 8.5 - - - +
381B ILE 3.3 0.2 - - - -
382B LYS* 1.3 73.3 - - - +
384B THR* 1.3 60.5 + - - +
386B ARG* 2.9 52.6 + - - +
387B LEU* 3.4 14.4 + - - +
434B ASN 3.0 1.9 - - - +
435B PHE* 3.5 24.0 - - + -
436B ASP 2.7 36.0 + - - +
437B PRO* 4.1 4.3 - - + -
439B ARG* 3.2 12.1 + - - -
440B TRP* 3.0 22.6 + - + +
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Residues in contact with THR 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B THR* 3.5 35.4 - - + +
337B TRP* 3.7 13.0 - - + +
338B HIS* 3.2 31.9 + - + +
341B GLU* 5.3 0.4 - - + -
380B SER 2.8 22.6 + - - -
381B ILE* 3.7 6.5 - - - -
382B LYS 3.2 0.4 - - - -
383B GLU* 1.3 71.4 - - - +
385B LEU* 1.3 52.2 + - - +
386B ARG 3.3 0.3 + - - -
387B LEU* 3.3 2.0 + - - -
388B HIS* 2.8 42.3 + - + +
435B PHE* 3.6 15.4 - - - -
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Residues in contact with LEU 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B THR* 4.0 24.7 - - + +
381B ILE* 3.1 26.1 + - + +
382B LYS* 3.4 8.3 + - - +
384B THR* 1.3 73.5 - - - +
386B ARG* 1.3 62.7 + - - +
388B HIS 3.9 13.2 - - - +
389B PRO* 3.3 23.8 - - + +
390B ILE 4.4 6.5 - - - +
419B ILE* 5.2 1.7 - - - +
452B ASN* 5.7 4.0 - - - +
454B GLY* 4.6 18.3 + - - +
455B PHE* 3.3 41.3 - - + -
601B HEM 3.5 25.1 - - + -
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Residues in contact with ARG 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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382B LYS 3.1 13.1 + - - +
383B GLU* 2.9 47.5 + - - +
384B THR 3.2 0.2 - - - -
385B LEU* 1.3 79.3 - - - +
387B LEU* 1.3 78.4 + - - +
389B PRO* 3.7 7.6 - - - +
419B ILE* 4.7 3.6 - - - +
420B TYR 4.8 2.1 - - - +
423B GLY* 2.6 55.9 + - - -
424B ARG* 4.9 0.3 + - - -
429B PHE* 3.6 38.4 - - + +
432B PRO* 2.7 35.5 + - - +
434B ASN 3.1 11.7 + - - -
439B ARG* 3.8 8.8 - - - +
440B TRP* 4.2 8.7 - - + -
451B ARG 5.6 3.1 - - - +
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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
----------------------------------------------------------
341B GLU* 4.1 19.1 - - + +
344B ARG* 5.3 1.6 - - - +
383B GLU 3.4 3.5 + - - +
384B THR 3.3 3.8 + - - +
386B ARG* 1.3 101.1 - - - +
388B HIS* 1.3 74.7 + - + +
389B PRO* 3.6 5.2 - - - +
420B TYR* 4.1 1.7 - - - -
424B ARG* 2.6 61.3 + - - +
432B PRO 3.3 21.3 - - - +
433B GLU* 4.5 9.9 - - + +
434B ASN 4.5 1.6 - - - +
435B PHE* 4.3 28.9 - - + +
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Residues in contact with HIS 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B THR* 5.1 3.5 + - - +
337B TRP* 3.3 80.7 - + + +
340B TYR* 4.8 1.6 - + - -
341B GLU* 2.8 34.7 + - + -
384B THR* 2.8 27.3 + - + +
385B LEU* 3.8 10.5 - - - +
387B LEU* 1.3 92.8 + - + +
389B PRO* 1.3 69.6 - - - +
390B ILE* 3.7 1.9 + - - +
420B TYR* 5.6 1.1 - - - -
424B ARG* 3.9 11.9 + - - -
493B VAL 5.3 2.7 - - - -
495B THR* 4.6 3.7 + - - -
501B LEU* 6.1 0.2 - - - -
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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