Contacts of the helix formed by residues 58 - 67 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56E ARG 3.8 0.4 + - - -
57E ARG* 1.3 93.3 + - - +
59E HIS* 1.3 56.9 + - - +
60E ALA 3.5 1.6 - - - -
61E ARG* 3.4 14.0 + - + +
62E GLU* 2.9 48.4 + - + +
86E GLU* 3.3 28.2 + - - +
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Residues in contact with HIS 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E LEU 3.6 21.8 - - - -
54E THR* 3.5 16.2 + - - +
55E GLU 4.1 4.2 + - - -
56E ARG* 3.3 63.9 + - + +
57E ARG 2.8 7.2 + - - -
58E ASN* 1.3 72.3 - - - +
60E ALA* 1.3 64.1 + - - +
62E GLU* 3.2 7.8 + - + +
63E LEU* 3.1 33.8 + - + +
49F PHE* 3.8 8.7 - + - -
50F THR* 3.1 31.0 - - + +
51F LEU 5.2 0.2 - - - -
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Residues in contact with ALA 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E LEU* 4.9 4.0 - - + -
54E THR* 3.1 19.6 + - + +
56E ARG 4.8 0.2 + - - -
59E HIS* 1.3 78.1 - - - +
61E ARG* 1.3 62.5 + - - +
63E LEU* 3.5 7.1 + - - +
64E VAL* 3.2 30.2 + - - +
83E LEU* 3.3 35.2 - - + -
86E GLU* 4.1 13.2 + - + +
87E VAL* 4.8 5.2 - - + -
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Residues in contact with ARG 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E ASN* 3.4 18.8 + - + +
60E ALA* 1.3 80.7 - - - +
62E GLU* 1.3 59.1 + - + +
64E VAL* 3.6 1.5 + - - -
65E ARG* 3.2 30.0 + - - +
85E HIS* 4.4 11.5 - - - -
86E GLU* 2.8 61.5 + - - +
89E ASN* 3.6 28.9 - - - +
90E GLY* 3.7 13.5 - - - +
93E GLU* 2.9 33.2 + - - +
161E LEU* 6.3 1.0 - - - +
162E ARG 5.7 1.4 + - - -
163E LEU* 4.9 7.7 - - - +
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Residues in contact with GLU 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E ARG* 4.4 15.2 + - - -
58E ASN* 2.9 33.9 + - + +
59E HIS* 3.6 6.3 - - + +
61E ARG* 1.3 74.0 - - + +
63E LEU* 1.3 66.4 + - + +
65E ARG* 3.3 33.3 + - - +
66E SER* 3.1 25.4 + - - -
16F ARG* 5.9 4.6 + - - -
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Residues in contact with LEU 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E LEU* 5.1 3.8 - - + -
52E MET* 3.5 41.1 - - + -
53E LEU 4.8 2.2 - - - +
54E THR* 4.9 2.9 - - - -
59E HIS* 3.1 46.3 + - + +
60E ALA* 3.6 11.4 - - - +
62E GLU* 1.3 77.4 - - - +
64E VAL* 1.3 60.1 + - + +
66E SER* 3.4 2.3 + - - +
67E GLU* 2.9 13.5 + - - +
50F THR* 4.0 4.9 - - + +
71F ARG* 2.6 39.7 + - - +
72F TRP* 4.0 27.6 - - + -
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Residues in contact with VAL 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E LEU* 5.7 3.4 - - + -
20E LEU* 3.7 26.5 - - + -
60E ALA 3.2 17.5 + - - +
61E ARG 4.1 3.6 - - - +
62E GLU 3.2 0.2 - - - -
63E LEU* 1.3 77.4 - - + +
65E ARG* 1.3 61.7 + - - +
66E SER 3.4 0.2 + - - -
67E GLU* 3.5 11.3 + - + +
69E LEU* 4.7 3.2 - - + +
75E LEU* 4.5 9.6 - - + -
87E VAL* 3.5 28.3 - - + +
90E GLY* 4.7 0.2 - - - -
91E LEU* 3.5 42.1 - - + +
94E ARG* 2.9 23.6 + - - -
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Residues in contact with ARG 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E ARG* 3.2 27.4 + - - +
62E GLU* 3.3 35.7 + - - +
64E VAL* 1.3 78.8 - - - +
66E SER* 1.3 56.6 + - - +
90E GLY 3.6 16.8 - - - +
93E GLU* 2.7 54.3 + - + +
94E ARG* 3.1 36.7 + - + +
95E PRO* 5.9 0.7 - - + -
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Residues in contact with SER 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E GLU 3.1 16.7 + - - -
63E LEU* 3.4 4.3 + - - +
65E ARG* 1.3 76.9 - - - +
67E GLU* 1.3 66.7 + - - +
68E GLU 3.7 1.2 + - - -
94E ARG* 3.8 1.1 + - - -
68F GLU* 4.1 15.1 - - - +
71F ARG* 2.9 40.4 + - - +
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Residues in contact with GLU 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E LEU* 4.2 12.9 - - + +
52E MET* 3.9 16.0 - - - +
63E LEU* 2.9 14.7 + - - +
64E VAL* 3.5 15.3 + - + +
66E SER* 1.3 78.6 - - - +
68E GLU* 1.3 64.3 + - - +
69E LEU* 3.2 19.0 + - + +
71E ARG* 2.5 34.8 + - - -
72E TRP* 2.9 25.8 + - + +
94E ARG* 2.8 27.4 + - - -
71F ARG* 2.7 36.3 + - - +
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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