Contacts of the helix formed by residues 73 - 86 (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 LYS 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A THR* 3.3 35.4 - - + +
70A GLY 3.1 6.1 + - - -
72A HIS* 1.3 87.9 - - + +
74A VAL* 1.3 64.2 + - - +
75A HIS* 3.2 17.5 + - + -
76A LEU* 2.9 32.6 + - + +
77A HIS 3.2 8.3 + - - -
495A THR 3.0 21.6 + - - +
496A THR* 4.6 4.4 - - - +
504A GLU* 3.0 39.4 + - - -
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Residues in contact with VAL 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 3.8 31.9 - - + -
70A GLY 3.8 1.0 + - - -
71A THR 3.7 6.3 + - - +
72A HIS 3.7 0.4 - - - -
73A LYS* 1.3 77.1 - - - +
75A HIS* 1.3 65.2 + - - +
77A HIS* 3.1 16.1 + - + +
78A HIS* 3.1 34.2 + - + +
93A LEU* 5.8 4.0 - - + -
248A LEU* 5.8 4.7 - - + -
392A VAL* 4.0 11.2 - - + -
497A PHE* 3.3 46.7 - - + -
602A 2DC 6.2 0.2 - - - +
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Residues in contact with HIS 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A HIS 3.5 6.9 + - - -
73A LYS* 3.5 29.5 + - + +
74A VAL* 1.3 76.8 + - - +
76A LEU* 1.3 71.8 + - + +
78A HIS* 3.5 9.8 + - - +
79A VAL* 3.3 24.9 + - - +
392A VAL* 3.8 19.1 - - + -
420A TYR* 3.6 51.3 - + + -
495A THR* 2.8 44.8 + - + -
497A PHE* 4.2 5.4 - - - +
501A LEU* 4.1 9.9 - - + +
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Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A THR* 4.1 8.7 - - + -
73A LYS* 2.9 34.7 + - + +
75A HIS* 1.3 95.1 - - + +
77A HIS* 1.3 60.0 + - - +
79A VAL* 3.2 10.2 + - + +
80A GLN* 2.9 47.2 + - + +
420A TYR* 4.6 12.6 - - + +
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Residues in contact with HIS 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 3.5 56.8 - + + -
69A THR* 3.8 11.6 + - + +
73A LYS 3.2 3.3 + - - +
74A VAL* 3.1 12.5 + - + +
76A LEU* 1.3 78.1 - - - +
78A HIS* 1.3 66.7 + + - +
80A GLN* 3.5 10.6 + - - +
81A ASN* 2.8 59.8 + - - -
91A GLU* 2.8 37.7 + - - -
93A LEU* 4.8 4.6 - - + +
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Residues in contact with HIS 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A VAL* 3.1 32.9 + - + +
75A HIS* 3.7 12.2 - - - +
76A LEU 3.2 0.2 - - - -
77A HIS* 1.3 84.1 - + - +
79A VAL* 1.3 65.4 + - - +
81A ASN* 3.2 2.3 + - - +
82A PHE* 3.0 31.5 + - + -
89A TYR* 3.6 22.2 - - - +
93A LEU* 6.3 0.8 - - - +
100A TYR* 3.7 21.4 + + - -
392A VAL* 4.4 13.4 + - + +
393A THR* 3.6 31.0 - - + +
416A GLN* 5.3 0.2 - - - -
418A ALA* 4.4 21.2 - - + +
420A TYR* 5.8 1.6 - - - +
421A ALA* 4.4 4.5 - - + +
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Residues in contact with VAL 79 (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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75A HIS 3.3 14.1 + - - +
76A LEU* 3.2 14.9 + - + +
78A HIS* 1.3 76.4 - - - +
80A GLN* 1.3 66.1 + - + +
82A PHE* 3.2 3.9 + - - +
83A GLN* 3.1 46.6 + - + +
420A TYR* 4.1 14.8 - - + -
421A ALA* 3.9 28.2 - - + +
424A ARG* 5.3 6.5 - - + -
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Residues in contact with GLN 80 (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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68A GLU 6.0 0.2 + - - -
69A THR* 3.4 24.0 + - - +
76A LEU* 2.9 36.3 + - + +
77A HIS* 3.8 6.8 + - - +
79A VAL* 1.3 73.8 - - + +
81A ASN* 1.3 63.3 + - - +
83A GLN* 3.2 18.5 + - - +
84A LYS* 3.0 41.3 + - - +
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Residues in contact with ASN 81 (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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54A PRO* 5.6 0.7 - - - +
77A HIS* 2.8 56.8 + - - +
78A HIS 3.2 1.3 + - - +
80A GLN* 1.3 77.5 - - - +
82A PHE* 1.3 56.8 + - - +
84A LYS* 3.0 12.2 + - - -
85A TYR* 2.8 53.6 + - + +
89A TYR* 3.1 43.4 + - + +
91A GLU* 3.6 8.2 + - - +
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Residues in contact with PHE 82 (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* 3.0 29.1 + - + -
79A VAL* 3.2 6.0 + - - +
81A ASN* 1.3 74.6 - - - +
83A GLN* 1.3 58.5 + - + +
86A GLY* 3.0 47.1 + - - +
87A PRO* 3.6 20.9 - - + -
89A TYR* 3.6 27.4 - + - -
100A TYR* 3.8 12.8 - - + -
101A VAL 3.6 22.7 - - - -
102A ILE* 3.7 32.8 - - + -
418A ALA* 3.3 26.9 - - + -
421A ALA* 4.0 4.0 - - + -
425A GLU* 5.7 2.0 - - - +
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Residues in contact with GLN 83 (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* 3.1 35.6 + - + +
80A GLN* 3.2 20.6 + - - +
82A PHE* 1.3 76.3 - - + +
84A LYS* 1.3 58.7 + - - +
86A GLY 4.7 0.7 + - - -
425A GLU* 6.0 2.2 - - - +
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Residues in contact with LYS 84 (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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68A GLU* 5.1 8.1 + - - -
80A GLN* 3.0 32.5 + - - +
81A ASN* 3.0 13.1 + - - +
83A GLN* 1.3 79.0 - - - +
85A TYR* 1.3 89.7 + - + +
86A GLY 3.7 0.7 - - - -
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Residues in contact with TYR 85 (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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52A PRO* 3.7 40.6 - - + +
53A SER 3.9 15.7 - - - -
54A PRO* 3.2 39.2 - - + +
81A ASN* 2.8 51.9 + - - +
84A LYS* 1.3 97.9 - - + +
86A GLY* 1.3 60.9 + - - +
87A PRO* 4.5 1.0 - - - +
88A ILE 3.9 2.4 - - - +
89A TYR* 3.8 25.4 - + + -
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Residues in contact with GLY 86 (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* 3.0 34.6 + - - +
83A GLN 4.7 0.8 + - - -
84A LYS 3.7 1.4 - - - -
85A TYR* 1.3 82.4 - - - +
87A PRO* 1.3 67.7 - - - +
88A ILE 3.3 10.3 + - - +
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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