Contacts of the helix formed by residues 57 - 69 (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 57 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLY 3.4 1.4 - - - -
56A ASP* 1.3 75.1 - - - +
58A GLY* 1.3 52.9 + - - +
59A TRP* 3.0 18.1 + - - +
60A LEU* 2.9 46.1 + - + +
61A ASN* 2.8 40.3 + - - +
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Residues in contact with GLY 58 (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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56A ASP 3.4 6.5 + - - -
57A ASN* 1.3 73.7 + - - +
59A TRP* 1.3 58.5 + - - +
61A ASN 3.9 0.2 - - - -
62A LEU* 3.0 19.1 + - - +
92A LYS* 3.3 27.9 - - - +
94A GLY 2.9 40.1 + - - -
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Residues in contact with TRP 59 (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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57A ASN* 3.0 12.2 + - - +
58A GLY* 1.3 75.5 - - - +
60A LEU* 1.3 61.6 + - - +
62A LEU* 3.5 11.5 + - + +
63A TYR* 3.0 27.4 + - - +
94A GLY* 3.7 27.8 + - - -
95A ASN* 3.6 27.1 + - - -
250A LEU* 4.0 22.7 - - + -
251A PRO* 3.9 14.1 - - + -
254A LEU* 3.7 25.4 - - + -
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ASN* 2.9 32.9 + - + +
59A TRP* 1.3 75.8 - - - +
61A ASN* 1.3 62.4 + - - +
63A TYR* 3.1 17.4 + - + +
64A HIS* 2.9 57.9 + - + +
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Residues in contact with ASN 61 (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* 3.8 32.9 - - - +
55A GLY* 3.0 28.5 + - - +
57A ASN* 2.8 21.2 + - - +
58A GLY* 3.8 0.4 - - - +
60A LEU* 1.3 79.7 - - - +
62A LEU* 1.3 58.4 + - - +
64A HIS* 3.5 7.7 + - - +
65A PHE* 2.9 30.3 + - - +
77A HIS* 5.4 0.2 - - - -
91A GLU* 4.3 8.4 - - - +
92A LYS* 3.0 33.9 + - - +
93A LEU* 4.0 8.7 - - + +
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Residues in contact with LEU 62 (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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58A GLY 3.0 17.0 + - - +
59A TRP* 3.6 20.4 - - + +
61A ASN* 1.3 76.5 - - - +
63A TYR* 1.3 57.8 + - - +
65A PHE* 3.4 8.7 + - + +
66A TRP* 2.9 83.5 + - + +
93A LEU* 4.0 10.3 - - + +
94A GLY* 4.0 20.9 - - - +
249A ASN* 3.8 26.7 - - + +
250A LEU* 4.1 14.1 - - + -
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Residues in contact with TYR 63 (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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59A TRP 3.0 15.7 + - - +
60A LEU* 3.1 19.9 + - + +
62A LEU* 1.3 76.3 - - - +
64A HIS* 1.3 77.7 + + - +
66A TRP* 3.2 11.4 + + + +
67A ARG* 3.1 68.1 + - + +
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Residues in contact with HIS 64 (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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60A LEU* 2.9 43.7 + - + +
61A ASN* 4.0 7.7 + - - +
63A TYR* 1.3 89.5 - + - +
65A PHE* 1.3 65.5 + - - +
67A ARG* 3.1 30.8 + - - +
68A GLU* 3.1 43.2 + - - +
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Residues in contact with PHE 65 (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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61A ASN 2.9 18.4 + - - +
62A LEU* 3.5 12.8 - - + +
64A HIS* 1.3 76.2 - - - +
66A TRP* 1.3 79.6 + + - +
69A THR* 3.2 14.0 + - - +
70A GLY 3.0 47.6 + - - -
71A THR* 4.1 9.4 - - + -
74A VAL* 3.8 32.1 - - + -
77A HIS* 3.5 52.2 - + + -
93A LEU* 4.2 15.9 - - + -
249A ASN* 4.4 14.4 - - - -
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Residues in contact with TRP 66 (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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62A LEU* 2.9 62.3 + - + +
63A TYR* 3.8 9.0 - + + +
65A PHE* 1.3 89.2 - + - +
67A ARG* 1.3 61.2 + - - +
70A GLY* 3.6 18.8 - - - +
71A THR* 3.3 35.2 - - + +
246A PRO 5.2 4.9 - - - -
249A ASN* 4.7 5.8 - - + +
250A LEU* 4.6 17.5 - - + -
259A ARG* 3.4 30.5 - - - -
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Residues in contact with ARG 67 (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 TYR* 3.1 56.0 + - + +
64A HIS* 3.1 24.3 + - - +
66A TRP* 1.3 77.8 - - - +
68A GLU* 1.3 90.4 + - - +
69A THR 5.3 0.2 - - - -
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Residues in contact with GLU 68 (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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64A HIS* 3.1 30.7 + - - +
67A ARG* 1.3 111.2 + - - +
69A THR* 1.3 66.8 + - - +
80A GLN* 6.0 0.3 + - - -
84A LYS* 5.1 8.5 + - - -
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Residues in contact with THR 69 (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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65A PHE* 3.2 16.3 + - - -
66A TRP 4.5 0.2 - - - -
68A GLU* 1.3 85.3 + - - +
70A GLY* 1.3 63.0 + - - +
73A LYS* 3.3 48.2 - - + +
76A LEU* 4.1 8.3 - - + -
77A HIS* 3.8 24.4 + - + +
80A GLN* 3.4 20.4 + - - +
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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
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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