Contacts of the helix formed by residues 58 - 67 (chain D) in PDB entry 3VZC
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 58 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56D ARG 3.5 0.8 + - - -
57D ARG* 1.3 90.2 + - - +
59D HIS* 1.3 56.2 + - - +
60D ALA 3.5 1.8 - - - -
61D ARG* 3.1 22.9 + - - +
62D GLU* 2.9 47.1 + - - +
86D GLU* 3.7 26.3 + - - +
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Residues in contact with HIS 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D MET* 6.5 0.4 - - + -
53D LEU 3.6 20.4 - - - -
54D THR* 3.6 18.6 + - - +
55D GLU 4.3 2.4 + - - -
56D ARG* 3.4 59.7 + - + +
57D ARG 3.0 2.7 + - - -
58D ASN* 1.3 77.0 - - - +
60D ALA* 1.3 59.1 + - - +
62D GLU* 3.0 13.4 + - + -
63D LEU* 2.9 47.9 + - + +
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Residues in contact with ALA 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D LEU* 4.4 9.0 - - + -
54D THR* 3.1 26.6 + - + +
56D ARG 4.9 0.4 + - - -
58D ASN 3.5 0.2 - - - -
59D HIS* 1.3 78.4 - - - +
61D ARG* 1.3 62.1 + - - +
63D LEU* 3.5 7.2 + - - +
64D VAL* 3.1 31.3 + - - +
83D LEU* 3.7 32.8 - - + -
86D GLU* 4.6 6.1 - - + -
87D VAL* 4.7 3.4 - - + -
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Residues in contact with ARG 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D ASN* 3.1 28.1 + - - +
60D ALA* 1.3 79.5 - - - +
62D GLU* 1.3 57.4 + - - +
64D VAL* 4.8 0.2 - - - -
65D ARG* 3.1 41.7 + - - +
85D HIS* 4.7 7.1 - - - -
86D GLU* 2.9 64.2 + - - +
89D ASN* 3.6 28.1 - - - +
90D GLY* 3.8 14.7 - - - -
93D GLU* 3.0 26.6 + - - -
163D LEU* 5.2 6.9 - - - +
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Residues in contact with GLU 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ARG* 5.1 6.4 + - - -
57D ARG 5.3 0.9 - - - +
58D ASN* 2.9 34.5 + - + +
59D HIS* 3.0 14.4 + - + +
61D ARG* 1.3 74.3 - - - +
63D LEU* 1.3 67.3 + - - +
65D ARG* 3.3 35.4 + - - +
66D SER* 3.2 21.9 + - - -
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Residues in contact with LEU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 5.4 0.4 - - + -
20D LEU* 3.9 20.0 - - + -
52D MET* 3.3 41.5 - - + -
53D LEU 5.9 0.2 - - - +
54D THR* 5.7 4.0 - - - -
59D HIS* 2.9 34.2 + - + +
60D ALA* 3.6 12.6 - - - +
62D GLU* 1.3 75.4 - - - +
64D VAL* 1.3 55.2 - - + +
66D SER* 3.1 11.1 + - - +
67D GLU* 2.9 45.6 + - - +
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Residues in contact with VAL 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 6.0 2.7 - - + -
20D LEU* 3.7 24.7 - - + -
60D ALA 3.1 17.6 + - - +
61D ARG 4.0 2.2 - - - +
63D LEU* 1.3 79.3 - - + +
65D ARG* 1.3 56.4 + - - +
67D GLU* 3.7 10.5 + - + +
69D LEU* 4.6 1.4 - - - +
75D LEU* 4.4 10.3 - - + -
87D VAL* 3.3 41.5 - - + +
90D GLY 3.9 1.1 - - - -
91D LEU* 3.4 33.7 - - + +
94D ARG* 3.0 24.1 + - - -
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Residues in contact with ARG 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D ARG* 3.1 36.2 + - - +
62D GLU* 3.4 36.0 + - - +
63D LEU 3.2 0.2 - - - -
64D VAL* 1.3 79.3 - - - +
66D SER* 1.3 58.2 + - - +
90D GLY* 4.0 5.2 - - - +
93D GLU* 2.7 53.2 + - - +
94D ARG* 3.3 38.3 + - + +
95D PRO* 5.8 1.9 - - + +
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Residues in contact with SER 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D GLU 3.2 12.1 + - - -
63D LEU* 3.1 16.1 + - - +
65D ARG* 1.3 76.5 - - - +
67D GLU* 1.3 68.1 + - - +
68D GLU* 3.5 1.4 + - - -
94D ARG* 4.1 0.7 - - - -
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Residues in contact with GLU 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 3.9 17.9 - - + +
52D MET* 4.6 11.8 - - - +
63D LEU* 2.9 24.1 + - - +
64D VAL* 3.9 13.2 - - + +
65D ARG 3.6 1.2 - - - -
66D SER* 1.3 77.9 - - - +
68D GLU* 1.3 66.3 + - - +
69D LEU* 3.2 17.8 + - + -
71D ARG* 2.9 24.5 + - - -
72D TRP* 2.8 36.9 + - + +
75D LEU* 5.5 0.4 - - + -
94D ARG* 2.9 28.1 + - - -
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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