Contacts of the helix formed by residues 418 - 425 (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 ALA 418 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A HIS* 4.4 16.4 - - + +
82A PHE* 3.3 34.8 - - + -
100A TYR* 5.1 4.0 - - + -
101A VAL 2.8 12.2 + - - +
102A ILE* 4.6 1.3 - - - +
392A VAL 4.0 5.2 - - - -
393A THR* 4.3 5.2 - - + -
416A GLN 3.6 2.2 + - - +
417A VAL* 1.3 69.3 - - - +
419A ILE* 1.3 52.7 + - - +
420A TYR 3.3 2.9 - - - -
421A ALA* 3.1 9.7 + - + -
422A LEU* 2.8 34.8 + - - +
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Residues in contact with ILE 419 (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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385A LEU 5.2 2.9 - - - +
386A ARG 4.6 3.2 - - - +
389A PRO* 3.4 18.6 - - + -
391A SER* 3.2 23.8 - - - +
392A VAL 3.1 7.5 + - - +
393A THR* 4.5 2.0 - - - -
394A LEU* 3.7 21.3 - - + -
417A VAL* 2.8 38.1 + - + +
418A ALA* 1.3 70.6 - - - +
420A TYR* 1.3 63.2 + - - +
422A LEU* 3.5 8.6 + - + +
423A GLY* 3.1 18.7 + - - -
453A LEU* 3.6 43.5 - - + +
454A GLY* 5.4 4.5 - - - +
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Residues in contact with TYR 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A HIS* 3.6 53.7 - + + +
76A LEU* 4.6 9.4 - - + +
78A HIS* 5.8 2.5 - - - +
79A VAL* 4.1 12.3 - - + -
386A ARG 4.8 1.0 - - - +
387A LEU 4.1 2.2 - - - -
388A HIS* 5.6 0.4 - - - -
389A PRO* 3.8 31.0 - - + -
392A VAL* 3.3 11.3 + - + +
418A ALA 3.3 0.8 - - - -
419A ILE* 1.3 78.3 - - - +
421A ALA* 1.3 68.5 + - - +
423A GLY* 3.2 11.3 + - - -
424A ARG* 3.3 66.3 + - + +
495A THR* 4.3 13.2 + - + -
501A LEU* 4.0 13.0 - - + -
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Residues in contact with ALA 421 (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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78A HIS* 4.4 3.7 + - + +
79A VAL* 3.9 32.4 - - + +
82A PHE* 4.0 11.2 - - + -
102A ILE* 3.8 17.7 - - + +
418A ALA* 3.1 20.6 + - + +
420A TYR* 1.3 78.7 - - - +
422A LEU* 1.3 63.7 + - - +
424A ARG* 3.3 4.7 + - - +
425A GLU* 3.1 22.2 + - - +
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Residues in contact with LEU 422 (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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102A ILE* 3.6 34.4 - - + +
104A PRO* 4.2 9.6 - - + -
107A VAL* 5.1 1.1 - - + -
417A VAL* 4.9 8.3 - - + -
418A ALA 2.8 16.4 + - - +
419A ILE* 3.5 9.6 - - + +
421A ALA* 1.3 76.9 - - - +
423A GLY* 1.3 57.1 + - - +
425A GLU* 2.9 20.7 + - - +
428A PHE* 3.6 29.6 - - + -
429A PHE* 3.5 20.2 - - + -
450A PHE 4.4 8.3 - - - +
451A ARG* 5.2 4.5 - - - +
453A LEU* 4.1 26.2 - - + -
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Residues in contact with GLY 423 (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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386A ARG* 3.4 61.0 + - - +
387A LEU* 4.6 0.5 - - - +
419A ILE 3.1 9.4 + - - -
420A TYR 3.2 2.1 + - - -
422A LEU* 1.3 77.7 - - - +
424A ARG* 1.3 65.6 + - - +
425A GLU 3.4 0.2 - - - -
429A PHE* 3.9 8.0 - - - -
432A PRO* 3.8 3.8 - - - +
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Residues in contact with ARG 424 (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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79A VAL* 5.3 6.7 - - + -
386A ARG 4.9 0.4 + - - -
387A LEU* 2.7 52.2 + - - +
388A HIS* 3.7 19.4 + - - -
420A TYR* 3.3 56.1 + - + +
421A ALA* 3.3 7.7 + - - +
422A LEU 3.1 0.6 - - - -
423A GLY* 1.3 78.1 - - - +
425A GLU* 1.3 58.9 + - - +
426A PRO* 3.2 13.2 - - - +
432A PRO* 3.5 16.1 - - - +
433A GLU* 3.7 30.1 + - - +
495A THR* 4.3 4.2 + - - -
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Residues in contact with GLU 425 (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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82A PHE* 5.7 1.9 - - - +
83A GLN* 6.0 2.4 - - - +
102A ILE* 4.1 15.5 - - + +
421A ALA 3.1 11.3 + - - +
422A LEU 2.9 16.8 + - - +
423A GLY 3.4 0.4 - - - -
424A ARG* 1.3 75.9 - - - +
426A PRO* 1.4 81.5 - - - +
427A THR* 2.9 36.3 + - - +
428A PHE* 3.0 43.8 + - + +
429A PHE* 3.1 12.3 + - - +
432A PRO* 4.1 1.1 - - - -
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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