Contacts of the helix formed by residues 58 - 67 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56F ARG 4.0 0.2 + - - -
57F ARG* 1.3 86.7 - - - +
59F HIS* 1.3 57.6 + - - +
60F ALA 3.6 1.6 - - - -
61F ARG* 3.6 21.6 + - - +
62F GLU* 3.1 45.0 + - + +
86F GLU* 3.2 36.2 + - - +
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Residues in contact with HIS 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E PHE 3.7 9.0 - - - -
50E THR* 2.9 37.2 - - + +
53F LEU 3.5 22.2 - - - -
54F THR* 3.4 5.9 - - - -
55F GLU* 3.0 26.5 + - + +
56F ARG* 3.3 55.7 + - + +
57F ARG 2.9 2.2 + - - -
58F ASN* 1.3 75.8 - - - +
60F ALA* 1.3 65.3 + - - +
62F GLU* 3.4 6.0 + - + +
63F LEU* 3.2 27.2 + - + +
86F GLU* 5.8 0.4 - - - +
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Residues in contact with ALA 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F LEU* 4.2 14.1 - - + -
54F THR* 3.7 16.6 - - + +
56F ARG 5.0 0.2 + - - -
59F HIS* 1.3 78.4 - - - +
61F ARG* 1.3 58.1 + - - +
63F LEU* 3.2 8.0 + - - +
64F VAL* 2.8 36.2 + - - +
83F LEU* 3.2 35.2 - - + -
86F GLU* 4.4 5.1 - - + +
87F VAL* 4.4 5.6 - - + -
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Residues in contact with ARG 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F ASN* 3.6 25.1 + - - +
59F HIS 3.2 0.2 - - - -
60F ALA* 1.3 77.8 - - - +
62F GLU* 1.3 62.5 + - + +
64F VAL* 4.8 1.1 - - - -
65F ARG* 3.0 34.0 + - - +
85F HIS* 4.5 7.5 - - - -
86F GLU* 3.2 56.7 + - + +
89F ASN* 3.3 37.0 - - - +
90F GLY* 3.7 6.6 - - - -
93F GLU* 2.4 42.6 + - - +
161F LEU* 6.2 1.4 - - - +
162F ARG 5.7 1.2 + - - -
163F LEU* 5.3 5.1 - - - +
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Residues in contact with GLU 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ARG* 3.7 28.8 + - - -
56F ARG* 5.2 6.8 + - - -
58F ASN* 3.1 31.7 + - + +
59F HIS* 4.0 7.1 - - + +
60F ALA 3.3 0.2 - - - -
61F ARG* 1.3 74.3 - - + +
63F LEU* 1.3 65.0 + - + +
65F ARG* 3.2 37.3 + - - +
66F SER* 3.1 25.7 + - - -
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Residues in contact with LEU 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E THR* 4.0 6.7 - - + -
71E ARG* 2.8 39.2 + - - +
72E TRP* 3.8 27.8 - - + -
20F LEU* 4.7 7.2 - - + -
52F MET* 4.0 32.5 - - + -
53F LEU 4.9 0.2 - - - +
54F THR* 4.7 3.6 - - + -
59F HIS* 3.2 47.3 + - + +
60F ALA* 3.4 12.8 - - - +
62F GLU* 1.3 77.7 - - + +
64F VAL* 1.3 60.1 + - + +
66F SER* 3.2 3.0 + - - +
67F GLU* 2.9 17.5 + - - +
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Residues in contact with VAL 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F LEU* 5.7 3.6 - - + -
20F LEU* 3.8 25.8 - - + -
60F ALA 2.8 23.5 + - - +
61F ARG 4.1 2.7 - - - +
63F LEU* 1.3 74.4 - - + +
65F ARG* 1.3 57.6 + - - +
66F SER 3.2 0.7 + - - -
67F GLU* 3.3 10.6 + - - +
69F LEU* 4.5 2.6 - - + +
75F LEU* 4.1 15.5 - - + -
87F VAL* 3.7 27.1 - - + +
90F GLY 4.7 0.2 - - - -
91F LEU* 3.7 37.9 - - + +
94F ARG* 2.8 24.4 + - - -
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Residues in contact with ARG 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F ARG* 3.0 23.1 + - - +
62F GLU* 3.2 42.4 + - - +
63F LEU 3.3 0.2 - - - -
64F VAL* 1.3 76.1 - - - +
66F SER* 1.3 56.3 + - - +
67F GLU 3.5 0.2 - - - -
90F GLY 3.6 19.0 + - - +
93F GLU* 3.0 45.0 + - + +
94F ARG* 3.4 29.2 + - + +
95F PRO* 5.6 2.6 - - + +
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Residues in contact with SER 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E GLU* 3.7 22.6 - - - +
71E ARG* 3.0 40.9 + - - +
62F GLU 3.1 15.7 + - - -
63F LEU* 4.0 1.9 - - - +
64F VAL 3.2 0.4 - - - -
65F ARG* 1.3 76.4 - - - +
67F GLU* 1.3 66.0 + - - +
94F ARG* 4.1 0.4 - - - -
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Residues in contact with GLU 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E ARG* 2.8 30.4 + - - +
18F LEU* 4.3 15.7 - - + +
52F MET* 4.4 10.9 - - - +
63F LEU* 2.9 13.2 + - - +
64F VAL* 3.3 15.8 + - + +
66F SER* 1.3 78.3 - - - +
68F GLU* 1.3 69.4 + - - +
69F LEU* 3.2 18.4 + - + -
71F ARG* 2.7 34.5 + - - -
72F TRP* 3.1 21.4 + - + +
75F LEU* 5.5 0.4 - - + -
94F ARG* 2.8 27.7 + - - -
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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