Contacts of the helix formed by residues 66 - 79 (chain A) in PDB entry 3NBV
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 GLY 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ALA 3.4 3.8 + - - -
65A PRO* 1.3 74.9 - - - +
67A HIS* 1.3 62.3 + - - -
68A VAL 3.5 2.7 - - - -
69A ALA* 4.1 3.2 - - - +
70A ASP* 2.9 36.4 + - - -
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Residues in contact with HIS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLY* 1.3 69.6 - - - -
68A VAL* 1.3 68.7 + - + +
70A ASP* 3.2 14.9 + - + +
71A PHE* 3.0 20.8 + - - +
67B HIS* 4.2 18.6 - + + -
70B ASP* 6.0 7.0 - - + -
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Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 3.9 41.3 - - + -
37A TRP* 5.5 4.3 - - + -
66A GLY* 3.5 0.4 - - - -
67A HIS* 1.3 73.2 - - + +
69A ALA* 1.3 57.7 + - - +
71A PHE* 2.7 30.8 + - + +
72A LEU* 2.9 18.7 + - + +
94A THR* 3.1 27.6 - - + +
96A SER* 5.9 0.7 - - - -
37B TRP* 4.6 15.7 - - + -
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Residues in contact with ALA 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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63A MET* 4.6 4.7 - - + -
64A ALA 3.1 27.4 - - - +
65A PRO* 4.5 0.2 - - + -
66A GLY* 3.9 8.8 + - - +
67A HIS 3.5 0.2 - - - -
68A VAL* 1.3 77.8 - - - +
70A ASP* 1.3 59.2 + - - +
72A LEU* 3.2 13.8 + - - +
73A VAL* 2.8 36.6 + - - +
88A TRP* 3.9 22.2 - - + -
94A THR* 4.1 9.2 + - + +
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Residues in contact with ASP 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PRO* 5.9 0.3 - - - +
66A GLY 2.9 30.1 + - - +
67A HIS* 3.3 20.8 - - + +
68A VAL 3.0 0.8 + - - -
69A ALA* 1.3 78.1 - - - +
71A PHE* 1.3 62.9 + - - +
73A VAL* 3.4 6.5 + - - +
74A ALA* 3.0 24.5 + - - +
88A TRP* 5.7 3.6 - - - -
67B HIS* 5.2 3.4 - - - +
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Residues in contact with PHE 71 (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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14A LEU* 3.7 24.2 - - + -
37A TRP* 4.0 41.1 - + + -
38A GLN* 4.8 0.2 - - - -
39A ARG* 4.1 13.2 - - + -
67A HIS 3.0 10.5 + - - +
68A VAL* 2.7 16.6 + - - +
70A ASP* 1.3 70.7 - - - +
72A LEU* 1.3 83.8 + - + +
74A ALA* 3.2 8.7 + - + +
75A ASP* 3.0 32.6 + - + +
78A ARG* 6.0 4.9 - - - -
67B HIS* 4.0 35.8 + + + +
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Residues in contact with LEU 72 (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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12A VAL* 4.3 19.3 - - + +
13A VAL 4.2 8.1 - - - +
14A LEU* 4.3 15.3 - - - +
39A ARG* 3.7 36.1 - - + +
63A MET* 4.4 14.4 - - - -
68A VAL* 2.9 33.0 + - + +
69A ALA* 3.5 12.8 - - - +
71A PHE* 1.3 91.8 - - + +
73A VAL* 1.3 57.8 + - - +
75A ASP* 3.0 7.2 + - - +
76A PHE* 2.8 33.3 + - + -
94A THR* 4.5 10.1 - - - +
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Residues in contact with VAL 73 (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 MET* 4.0 13.7 - - + -
69A ALA 2.8 24.0 + - - +
70A ASP* 3.9 6.1 - - - +
72A LEU* 1.3 71.1 - - - +
74A ALA* 1.3 58.3 + - - +
76A PHE* 3.2 10.7 + - + +
77A ARG* 2.8 66.8 + - + +
83A VAL* 4.6 12.3 - - + -
88A TRP* 3.8 32.5 - - + -
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Residues in contact with ALA 74 (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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70A ASP 3.0 14.3 + - - +
71A PHE* 3.4 11.9 - - + +
73A VAL* 1.3 77.0 - - - +
75A ASP* 1.3 57.8 + - - +
77A ARG* 3.2 9.0 + - - +
78A ARG* 2.9 43.6 + - - +
67B HIS* 6.4 1.1 - - + -
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Residues in contact with ASP 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ARG* 2.5 53.9 + - + +
71A PHE* 3.0 24.7 + - + +
72A LEU* 3.0 10.2 + - - +
74A ALA* 1.3 73.4 - - - +
76A PHE* 1.3 67.1 + - - +
78A ARG* 3.1 28.9 + - - +
79A ARG* 3.1 35.6 + - - +
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Residues in contact with PHE 76 (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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12A VAL* 3.7 21.1 - - + -
39A ARG* 3.1 41.8 - - - +
44A SER* 3.8 7.9 - - - -
47A CYS* 4.7 1.6 - - + -
59A PHE* 3.5 44.4 - + + -
63A MET* 4.4 11.4 - - + -
72A LEU 2.8 25.3 + - - -
73A VAL* 3.3 11.0 - - - +
75A ASP* 1.3 72.2 - - - +
77A ARG* 1.3 60.4 + - - +
79A ARG* 3.1 9.4 + - - +
81A VAL* 3.0 45.4 + - + +
83A VAL* 3.4 26.2 - - + -
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Residues in contact with ARG 77 (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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73A VAL* 2.8 45.8 + - + +
74A ALA* 3.7 7.2 - - - +
76A PHE* 1.3 72.9 - - + +
78A ARG* 1.3 62.4 + - - +
80A GLY* 2.9 20.4 + - - +
81A VAL 4.5 9.6 - - - +
83A VAL* 4.5 15.2 - - + +
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Residues in contact with ARG 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PHE* 6.0 4.8 - - - -
74A ALA* 2.9 31.4 + - - +
75A ASP* 3.1 32.9 + - - +
77A ARG* 1.3 76.5 - - - +
79A ARG* 1.3 71.1 + - + +
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Residues in contact with ARG 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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39A ARG* 3.6 15.7 - - - +
48A THR* 3.8 26.8 - - + +
51A SER* 2.7 35.1 + - - +
52A LEU* 3.6 21.8 - - - +
75A ASP* 3.1 22.2 + - - +
76A PHE 3.1 8.6 + - - +
77A ARG 3.0 0.6 - - - -
78A ARG* 1.3 87.5 - - + +
80A GLY* 1.3 61.5 + - - +
81A VAL* 3.9 13.7 - - + -
294A PHE* 4.9 3.8 - - - +
295A ASP* 2.7 37.4 + - - +
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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