Contacts of the helix formed by residues 345 - 363 (chain A) 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 ASN 345 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341A GLU* 3.0 32.4 + - - +
342A MET 3.2 7.7 - - - +
344A ARG* 1.3 95.8 + - - +
346A LEU* 1.3 60.9 + - - +
347A LYS* 3.3 2.9 - - + -
348A VAL* 3.3 21.3 + - + +
349A GLN 3.0 21.5 + - - -
434A ASN* 4.3 13.0 - - - +
435A PHE* 3.4 31.3 + - + +
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Residues in contact with LEU 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A MET 3.8 6.3 - - - +
343A ALA 3.9 13.5 - - - +
344A ARG 3.9 1.2 + - - -
345A ASN* 1.3 72.3 - - - +
347A LYS* 1.3 59.2 + - + +
349A GLN* 3.3 25.8 + - - +
350A ASP* 2.9 37.0 + - - +
485A VAL 3.7 13.2 - - - +
486A GLU* 4.6 21.8 - - + +
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Residues in contact with LYS 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ASN* 3.3 0.8 - - + -
346A LEU* 1.3 76.5 - - + +
348A VAL* 1.3 64.6 + - + +
350A ASP* 3.2 14.4 + - - +
351A MET* 3.0 35.0 + - - +
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Residues in contact with VAL 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A GLU 5.8 0.2 - - - +
342A MET* 5.8 1.3 - - + -
345A ASN* 3.6 21.3 - - + +
347A LYS* 1.3 77.4 - - + +
349A GLN* 1.3 65.0 + - - +
351A MET* 3.3 16.5 + - + +
352A LEU* 3.1 31.5 + - + +
376A LEU* 6.0 1.3 - - + -
435A PHE* 3.9 37.2 - - + +
436A ASP* 5.5 0.7 - - - -
437A PRO* 3.9 29.6 - - + -
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Residues in contact with GLN 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A MET* 3.0 58.6 - - + +
345A ASN 3.0 6.9 + - - -
346A LEU* 3.5 16.9 - - - +
348A VAL* 1.3 76.3 - - - +
350A ASP* 1.3 62.9 + - - +
352A LEU* 3.2 3.2 + - - +
353A ARG* 2.9 59.7 + - - +
480A LEU* 4.2 1.4 - - + +
484A ARG* 3.6 3.2 - - - +
485A VAL* 3.0 45.2 - - - +
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Residues in contact with ASP 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU* 2.9 26.3 + - - +
347A LYS* 3.4 15.4 - - - +
349A GLN* 1.3 74.0 - - - +
351A MET* 1.3 62.1 + - + +
353A ARG* 3.4 18.3 + - - +
354A ALA* 3.1 23.7 + - - +
484A ARG* 5.3 8.1 + - - -
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Residues in contact with MET 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LYS* 3.0 19.0 + - - +
348A VAL* 3.3 19.5 + - + +
350A ASP* 1.3 75.3 - - + +
352A LEU* 1.3 58.5 + - - +
354A ALA* 3.4 7.5 + - - +
355A GLU* 3.0 27.7 + - - +
376A LEU* 3.4 30.1 - - + +
437A PRO* 6.2 1.6 - - + -
438A THR* 4.1 22.7 - - + -
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Residues in contact with LEU 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A HIS* 4.2 4.7 - - - +
342A MET* 4.0 23.1 - - + -
348A VAL* 3.1 33.4 + - + +
349A GLN* 3.7 4.3 - - - +
351A MET* 1.3 74.9 - - - +
353A ARG* 1.3 65.0 + - - +
355A GLU* 3.3 7.0 + - - +
356A VAL* 3.1 25.8 + - - +
376A LEU* 3.4 50.9 - - + +
377A LEU* 3.7 12.8 - - + +
380A SER* 3.9 20.0 - - - +
435A PHE* 5.0 1.1 - - + -
437A PRO* 5.1 0.7 - - + -
480A LEU* 3.9 15.5 - - + -
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Residues in contact with ARG 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A GLN* 2.9 42.7 + - - +
350A ASP* 3.7 23.6 + - - +
352A LEU* 1.3 75.5 - - - +
354A ALA* 1.3 57.6 + - - +
356A VAL* 3.0 4.4 + - + +
357A LEU* 2.9 43.7 + - + +
480A LEU* 2.8 49.7 + - + +
483A PHE 2.5 29.1 + - - -
484A ARG* 3.7 18.6 - - - +
485A VAL* 5.2 0.2 - - - +
514A PHE* 3.5 33.1 - - - -
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Residues in contact with ALA 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A ASP 3.1 17.2 + - - +
351A MET* 3.6 7.6 - - - +
353A ARG* 1.3 74.6 - - - +
355A GLU* 1.3 62.9 + - - +
357A LEU* 4.0 8.7 - - - +
358A ALA* 3.0 26.2 + - - +
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Residues in contact with GLU 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A MET 3.0 13.8 + - - +
352A LEU* 3.6 10.2 - - - +
353A ARG 3.2 0.2 - - - -
354A ALA* 1.3 78.3 - - - +
356A VAL* 1.3 55.5 + - - +
358A ALA* 3.6 5.3 - - + +
359A ALA* 2.9 28.8 + - - +
373A LEU 3.9 10.7 - - - +
374A VAL* 3.2 19.7 - - - +
375A PRO* 3.1 14.8 - - + +
376A LEU* 2.8 32.5 + - + +
377A LEU* 2.9 28.4 + - - +
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Residues in contact with VAL 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A LEU 3.1 14.3 + - - +
353A ARG* 3.0 11.0 + - - +
355A GLU* 1.3 74.4 - - + +
357A LEU* 1.3 61.4 + - + +
359A ALA* 3.2 5.1 + - - -
360A ARG* 2.8 28.8 + - - +
370A MET* 3.6 3.8 - - + +
374A VAL* 3.9 18.2 - - + -
377A LEU* 3.9 22.0 - - + -
477A ILE* 3.8 26.2 - - + +
480A LEU* 4.3 13.5 - - + -
481A GLU* 3.7 27.4 - - + -
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Residues in contact with LEU 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A ARG* 2.9 28.0 + - + +
354A ALA* 4.0 7.4 - - - +
356A VAL* 1.3 72.1 - - + +
358A ALA* 1.3 66.4 + - - +
360A ARG* 3.4 6.7 + - + +
361A HIS* 3.1 22.9 + - - +
481A GLU* 4.4 24.2 - - + +
514A PHE* 3.8 37.7 - - + -
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Residues in contact with ALA 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A ALA 3.0 19.4 + - - +
355A GLU* 3.6 5.8 - - - +
357A LEU* 1.3 75.1 - - - +
359A ALA* 1.3 58.5 + - - +
361A HIS* 3.3 7.3 + - - +
362A GLN* 2.8 32.7 + - - +
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Residues in contact with ALA 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A GLU 2.9 18.6 + - - +
356A VAL 3.2 4.7 + - - +
358A ALA* 1.3 75.5 - - - +
360A ARG* 1.3 63.1 + - - +
362A GLN* 4.5 3.1 - - - -
363A ALA* 3.0 28.1 + - - +
370A MET* 3.6 11.6 - - + +
373A LEU* 3.7 34.8 - - + +
374A VAL* 3.8 15.0 - - + -
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Residues in contact with ARG 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ASP* 5.1 3.6 + - - -
176A ARG* 5.2 10.3 - - - +
356A VAL 2.8 14.6 + - - +
357A LEU* 3.9 6.3 - - + +
359A ALA* 1.3 76.9 - - - +
361A HIS* 1.3 62.0 + - - +
363A ALA 3.9 0.2 - - - -
364A GLN* 3.3 2.3 + - - -
365A GLY* 3.0 61.6 + - - -
367A MET* 3.8 21.2 - - - +
370A MET* 3.3 23.6 - - - +
477A ILE* 3.8 11.5 - - - +
478A ASN* 4.1 9.1 + - - -
481A GLU* 2.7 44.0 + - - +
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Residues in contact with HIS 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A LEU 3.1 16.8 + - - +
358A ALA* 3.7 6.3 - - - +
360A ARG* 1.3 74.3 - - - +
362A GLN* 1.3 71.2 + - - +
364A GLN* 2.8 28.8 + - + +
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Residues in contact with GLN 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A ALA 2.8 22.0 + - - +
359A ALA* 4.2 0.9 - - - +
361A HIS* 1.3 83.2 - - - +
363A ALA* 1.3 56.7 + - - +
364A GLN* 3.4 7.8 + - - +
369A THR* 5.2 1.2 - - - +
373A LEU* 4.1 26.2 - - + +
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Residues in contact with ALA 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A ALA 3.0 20.2 + - - +
360A ARG 4.2 1.6 - - - +
362A GLN* 1.3 75.6 - - - +
364A GLN* 1.3 72.1 + - - +
365A GLY 3.1 0.4 - - - -
366A ASP* 3.1 33.1 + - - +
369A THR* 3.6 29.9 - - + -
370A MET* 3.6 11.4 - - + +
373A LEU* 4.1 2.0 - - + -
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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