Contacts of the helix formed by residues 379 - 385 (chain A) 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 ALA 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A HIS* 4.3 15.3 - - + +
43A PHE* 3.3 36.6 - - + -
61A TYR* 5.2 3.8 - - + -
62A VAL 2.9 10.0 + - - +
63A ILE* 4.3 1.8 - - + +
353A VAL 4.1 5.6 - - - -
354A THR* 4.2 6.3 - - + -
377A GLN 3.7 2.0 + - - -
378A VAL* 1.3 68.0 - - - +
380A ILE* 1.3 58.8 + - - +
381A TYR 3.3 2.7 - - - -
382A ALA* 3.3 8.9 + - + -
383A LEU* 2.9 30.1 + - - +
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Residues in contact with ILE 380 (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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347A ARG 4.5 4.0 - - - +
350A PRO* 3.5 18.6 - - + +
352A SER* 3.1 28.9 - - - +
353A VAL 3.2 4.7 + - - +
354A THR* 4.6 3.1 - - - +
355A LEU* 3.6 19.7 - - + +
378A VAL* 2.9 36.7 + - + +
379A ALA* 1.3 69.6 - - - +
381A TYR* 1.3 67.2 + - - +
383A LEU* 3.5 8.1 + - + +
384A GLY* 3.1 19.2 + - - -
414A LEU* 3.5 48.2 - - + +
415A GLY* 5.7 1.1 - - - -
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Residues in contact with TYR 381 (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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36A HIS* 3.6 54.1 - + + +
37A LEU* 4.4 9.6 - - + +
39A HIS* 5.9 2.2 - - - +
40A VAL* 4.1 13.0 - - + -
347A ARG 4.8 1.1 - - - +
348A LEU 4.0 2.9 - - - -
349A HIS* 5.7 0.4 - - - -
350A PRO* 3.8 24.0 - - + -
353A VAL* 3.3 11.6 + - + +
380A ILE* 1.3 81.6 - - - +
382A ALA* 1.3 66.5 + - - +
384A GLY* 3.2 11.4 + - - -
385A ARG* 3.3 66.0 + - + +
456A THR* 4.3 13.7 + - + -
462A LEU* 4.0 19.3 - - + -
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Residues in contact with ALA 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A HIS* 4.5 3.9 + - + +
40A VAL* 4.0 32.3 - - + +
43A PHE* 4.1 11.2 - - + -
63A ILE* 3.7 16.2 - - + +
379A ALA* 3.3 20.9 + - + +
381A TYR* 1.3 80.2 - - - +
383A LEU* 1.3 62.1 + - - +
385A ARG* 3.3 11.8 + - - +
386A GLU* 3.3 15.8 + - - +
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Residues in contact with LEU 383 (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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63A ILE* 3.6 34.7 - - + +
65A PRO* 3.9 10.8 - - + -
68A VAL* 5.1 1.3 - - + -
378A VAL* 4.8 4.9 - - + -
379A ALA 2.9 17.5 + - - +
380A ILE* 3.6 13.5 - - + +
382A ALA* 1.3 77.6 - - - +
384A GLY* 1.3 61.6 + - - +
386A GLU* 3.2 14.3 + - - +
389A PHE* 3.7 27.1 - - + -
390A PHE* 3.5 20.7 - - + -
411A PHE 4.5 6.1 - - - +
412A ARG* 5.2 4.5 - - - +
414A LEU* 3.8 28.9 - - + -
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Residues in contact with GLY 384 (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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347A ARG* 3.6 47.6 + - - +
348A LEU* 4.7 0.9 - - - +
380A ILE 3.1 10.9 + - - -
381A TYR 3.2 2.4 + - - -
383A LEU* 1.3 76.4 - - - +
385A ARG* 1.3 66.6 + - - +
386A GLU 3.4 0.2 - - - -
390A PHE* 4.0 6.9 - - - -
393A PRO* 3.7 15.1 - - - +
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Residues in contact with ARG 385 (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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40A VAL* 5.4 6.1 - - + -
348A LEU* 2.8 50.3 + - - +
349A HIS* 3.8 19.8 + - - -
381A TYR* 3.3 53.7 + - + +
382A ALA* 3.3 7.8 + - - +
383A LEU 3.2 0.6 - - - -
384A GLY* 1.3 81.3 - - - +
386A GLU* 1.3 57.8 - - - +
387A PRO* 3.3 12.5 - - - +
393A PRO* 3.4 16.5 - - - +
394A GLU* 3.5 34.7 + - - +
456A THR* 4.3 4.8 + - - -
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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