Contacts of the helix formed by residues 335 - 349 (chain B) in PDB entry 3NA1
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 335 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B GLU* 3.2 28.7 - - + +
317B VAL* 3.9 28.0 - - + -
320B ALA* 4.6 3.6 - - + -
331B MET 3.9 12.3 - - - +
332B LEU* 4.4 12.2 + - - +
333B GLN 3.6 1.2 - - - -
334B LEU* 1.3 79.1 - - - +
336B PRO* 1.4 65.7 - - - +
338B LEU* 3.0 32.0 + - + -
339B LYS* 3.2 12.1 + - + +
434B THR* 4.0 20.9 - - + -
438B ILE* 4.8 7.2 - - + -
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Residues in contact with PRO 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B GLU* 3.3 11.2 - - - +
333B GLN 5.0 2.5 - - - +
334B LEU* 3.2 10.1 - - - +
335B VAL* 1.4 89.8 - - - +
337B LEU* 1.3 57.7 + - - +
339B LYS* 3.5 11.2 + - + +
340B ALA* 3.0 27.2 + - - +
402B LEU* 4.2 22.3 - - + +
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Residues in contact with LEU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B VAL* 6.1 0.9 - - + -
312B MET* 3.5 44.2 - - + +
313B LEU* 3.4 24.0 - - + +
316B GLU* 2.8 26.2 + - + +
336B PRO* 1.3 72.5 - - - +
338B LEU* 1.3 59.9 + - - +
340B ALA* 3.5 4.7 + - - +
341B SER* 3.0 21.8 + - - -
398B PRO* 3.9 18.1 - - + +
399B THR* 3.7 30.1 - - + +
402B LEU* 3.9 18.5 - - + +
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Residues in contact with LEU 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B HIS* 4.2 4.5 - - - +
313B LEU* 3.8 9.4 - - + +
316B GLU* 3.0 5.4 + - - +
317B VAL* 4.1 12.3 - - + -
335B VAL* 3.0 28.0 + - + +
337B LEU* 1.3 73.7 - - - +
339B LYS* 1.3 66.0 + - - +
341B SER* 2.4 37.1 + - - +
342B ILE* 3.2 13.7 + - + +
434B THR* 3.8 32.8 - - + +
437B LEU* 3.9 26.9 - - + -
438B ILE* 3.8 23.3 - - + +
441B LEU* 4.2 11.9 - - + -
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Residues in contact with LYS 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B LEU* 3.0 34.4 + - - +
333B GLN* 4.0 13.1 + - - +
335B VAL* 3.2 18.3 + - + +
336B PRO* 3.8 13.0 - - + +
338B LEU* 1.3 77.3 - - - +
340B ALA* 1.3 60.5 + - - +
342B ILE* 3.3 20.0 + - - +
343B LYS* 3.3 23.7 + - - +
434B THR* 4.6 18.8 - - + +
73D GLU* 5.3 15.2 - - - +
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Residues in contact with ALA 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B PRO 3.0 17.6 + - - +
337B LEU* 3.7 8.1 - - - +
338B LEU 3.3 0.2 - - - -
339B LYS* 1.3 76.0 - - - +
341B SER* 1.3 56.9 + - - +
343B LYS* 3.2 15.4 + - + +
344B GLU* 2.8 28.6 + - - +
398B PRO* 3.3 26.0 - - + +
401B TRP* 3.5 15.3 - - + -
402B LEU* 4.5 11.0 - - + -
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Residues in contact with SER 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B HIS* 2.9 28.4 - - - -
313B LEU* 4.0 10.8 - - - -
337B LEU 3.0 14.2 + - - -
338B LEU* 2.4 30.9 + - - +
340B ALA* 1.3 74.3 - - - +
342B ILE* 1.3 59.1 + - - +
344B GLU* 3.7 3.9 - - - +
345B THR* 2.8 32.4 + - - -
396B PHE* 3.7 4.0 - - - -
398B PRO* 3.8 23.5 - - - +
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Residues in contact with ILE 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B THR* 5.5 2.0 - - + -
299B HIS* 4.5 1.6 - - - +
338B LEU* 3.2 14.7 + - + +
339B LYS* 3.5 11.7 - - - +
340B ALA 3.2 0.2 - - - -
341B SER* 1.3 76.0 + - - +
343B LYS* 1.3 65.4 + - + +
345B THR* 3.1 7.1 + - - -
346B LEU* 3.0 34.3 + - + +
416B PHE* 5.1 4.5 - - + -
430B GLU* 4.5 8.5 - - + +
433B MET* 3.9 35.0 - - + -
434B THR* 3.2 42.0 - - + +
437B LEU* 4.2 17.0 - - + -
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Residues in contact with LYS 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B LYS* 3.3 20.2 + - - +
340B ALA* 3.2 8.7 + - - +
342B ILE* 1.3 76.8 - - + +
344B GLU* 1.3 58.4 + - - +
346B LEU* 3.3 7.9 + - - +
347B ARG* 2.9 28.4 + - - +
401B TRP* 3.8 45.1 + - + +
413B ASN* 3.6 31.7 - - - +
75D ASN* 5.3 2.8 - - - +
76D ASP* 2.7 41.7 + - - +
79D ASP* 4.9 7.9 + - - -
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Residues in contact with GLU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ALA 2.8 16.8 + - - +
341B SER* 3.7 9.2 - - - +
343B LYS* 1.3 75.1 - - - +
345B THR* 1.3 63.6 + - - +
347B ARG* 2.8 43.8 + - - +
348B LEU* 3.4 20.6 + - - +
395B ASN 3.4 0.2 - - - +
396B PHE* 3.6 23.9 - - + -
397B ASP 2.8 36.9 + - - +
398B PRO* 3.9 3.8 - - + -
400B ARG* 3.0 12.1 + - - -
401B TRP* 2.8 29.6 + - + +
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Residues in contact with THR 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B THR* 3.6 35.0 - - + +
298B TRP* 3.8 13.0 - - + +
299B HIS* 3.1 32.7 + - + +
341B SER 2.8 24.0 + - - -
342B ILE* 3.1 6.7 + - - -
344B GLU* 1.3 75.8 - - - +
346B LEU* 1.3 58.1 + - - +
348B LEU 3.4 1.7 + - - -
349B HIS* 2.8 36.2 + - + +
396B PHE* 3.4 15.7 - - + -
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Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B THR* 3.9 24.9 - - + +
342B ILE* 3.0 26.5 + - + +
343B LYS* 3.8 5.6 - - - +
345B THR* 1.3 75.4 - - - +
347B ARG* 1.3 63.8 + - - +
349B HIS 3.7 15.7 - - - +
350B PRO* 3.2 31.4 - - + +
351B ILE 4.3 1.1 - - - +
380B ILE* 5.6 0.3 - - - +
413B ASN* 5.9 2.0 - - - +
415B GLY* 4.2 21.1 + - - +
416B PHE* 3.5 41.1 - - + -
433B MET* 4.8 0.2 - - + -
601B HEM 3.7 24.2 - - + -
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Residues in contact with ARG 347 (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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343B LYS 2.9 16.6 + - - +
344B GLU* 2.8 44.1 + - - +
345B THR 3.3 0.2 - - - -
346B LEU* 1.3 79.3 - - - +
348B LEU* 1.3 77.3 + - - +
350B PRO* 3.9 6.2 - - - +
380B ILE 4.5 4.0 - - - +
381B TYR 4.9 1.0 - - - +
384B GLY* 2.7 54.9 + - - -
385B ARG* 5.0 0.3 + - - -
390B PHE* 3.6 38.5 - - + +
393B PRO* 2.8 33.9 + - - +
395B ASN 2.9 12.9 + - - -
400B ARG* 3.6 10.5 - - - +
401B TRP* 4.0 11.7 - - + -
412B ARG 5.3 3.4 - - - +
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Residues in contact with LEU 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B GLU* 3.7 29.2 - - + +
305B ARG* 5.1 0.4 - - - +
344B GLU 3.4 3.1 + - - +
345B THR 3.4 4.1 + - - +
347B ARG* 1.3 102.3 - - - +
349B HIS* 1.3 71.5 + - + +
350B PRO* 3.5 6.5 - - - +
381B TYR* 4.1 2.6 - - - -
385B ARG* 2.8 58.5 + - - +
393B PRO 3.3 23.8 - - - +
394B GLU* 4.6 12.3 - - - +
395B ASN 4.7 0.7 - - - +
396B PHE* 4.2 20.6 - - + -
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Residues in contact with HIS 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B THR* 5.0 3.6 + - - +
298B TRP* 3.3 82.4 - + + +
301B TYR* 5.1 1.1 - + - -
302B GLU* 2.7 34.1 + - + -
345B THR* 2.8 17.6 + - + +
346B LEU* 3.6 16.0 - - - +
348B LEU* 1.3 92.3 + - + +
350B PRO* 1.3 69.6 - - - +
351B ILE* 3.6 2.4 + - - +
381B TYR* 5.6 0.7 - - - -
385B ARG* 3.8 18.4 + - - -
454B VAL 5.4 2.0 - - - -
456B THR* 4.4 3.4 + - - -
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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