Contacts of the helix formed by residues 57 - 69 (chain F) in PDB entry 3B4V
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 SER 57 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E LEU* 4.3 9.8 - - - +
107E ASN* 4.0 23.8 - - - +
55F SER 3.7 2.2 + - - -
56F LEU* 1.3 72.6 - - - +
58F PHE* 1.3 61.7 + - - +
59F HIS* 3.5 7.4 + - - +
60F SER* 3.3 23.9 + - - -
61F THR* 2.7 29.5 + - - -
84F THR* 6.2 3.4 - - - -
115F CYS 5.0 1.8 + - - -
24G LEU* 6.4 1.1 - - - -
60G PHE* 3.7 4.7 - - - -
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Residues in contact with PHE 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E PHE* 4.0 6.5 - + - -
25E TRP* 3.6 20.3 - + - -
35E TYR* 3.2 30.7 - + - -
91E MET* 3.8 22.4 - - + -
105E ILE* 4.0 14.6 - - + -
106E GLN 3.9 9.2 - - - +
107E ASN* 3.5 11.5 + - - +
108E MET* 3.7 28.5 - - + -
57F SER* 1.3 74.6 - - - +
59F HIS* 1.3 58.0 + - - +
61F THR* 3.3 2.8 + - - -
62F VAL* 3.0 43.7 + - + +
57G LEU* 4.1 10.5 - - + -
60G PHE* 3.6 44.1 - + + -
61G LEU* 5.6 0.2 - - + -
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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
----------------------------------------------------------
37E ALA* 3.1 23.5 - - + +
38E ASN 2.7 24.7 + - - -
39E TYR* 4.6 3.4 - - + -
83E PRO* 4.5 12.4 - - + +
86E LEU* 4.3 10.3 - - + +
107E ASN 3.0 22.4 + - - +
108E MET 3.6 17.7 - - - +
110E VAL* 3.0 27.8 - - + +
57F SER* 3.3 5.5 + - - +
58F PHE* 1.3 75.5 - - - +
60F SER* 1.3 60.9 + - - +
62F VAL* 3.5 6.4 - - - +
63F ILE* 3.0 49.1 + - + +
116F SER* 5.1 2.8 + - - -
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Residues in contact with SER 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F LEU* 3.8 20.2 - - - +
57F SER* 3.3 16.6 + - - -
59F HIS* 1.3 78.1 + - - +
61F THR* 1.3 60.4 + - - +
63F ILE* 3.8 2.6 - - - +
64F ASN* 2.9 29.3 + - - +
67F ARG* 4.8 1.2 + - - -
115F CYS 2.6 29.4 + - - -
116F SER* 3.3 25.5 + - - +
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Residues in contact with THR 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E TRP* 3.6 29.6 - - + -
56F LEU* 3.4 22.1 - - + +
57F SER 2.7 19.7 + - - -
58F PHE 3.4 4.9 - - - -
60F SER* 1.3 75.3 - - - +
62F VAL* 1.3 67.9 + - - +
64F ASN* 3.2 3.9 + - + +
65F HIS* 3.1 20.4 + - - +
53G ASN* 3.8 22.0 + - + +
56G ASN* 4.5 6.0 + - + -
60G PHE* 3.3 20.4 - - + -
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Residues in contact with VAL 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E VAL* 3.4 38.1 - - + -
23E ILE* 4.2 10.5 - - + -
25E TRP* 4.0 13.7 - - + -
35E TYR* 3.9 6.5 - - + +
37E ALA* 4.2 11.2 - - + -
58F PHE* 3.0 40.4 + - + +
59F HIS* 3.5 10.5 - - - +
61F THR* 1.3 78.5 - - - +
63F ILE* 1.3 67.7 + - + +
65F HIS* 3.1 12.5 + - - +
66F TYR* 3.2 19.1 - - + -
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Residues in contact with ILE 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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16E PHE* 5.0 7.0 - - + -
37E ALA* 5.6 0.9 - - + -
38E ASN 4.0 7.6 - - - +
39E TYR* 4.1 4.0 - - + -
59F HIS* 3.0 49.6 + - + +
60F SER* 3.8 7.2 - - - +
62F VAL* 1.3 81.3 - - + +
64F ASN* 1.3 58.3 + - - +
66F TYR* 3.0 9.4 + - + +
67F ARG* 2.9 47.4 + - - +
74F PHE* 3.8 40.6 - - + +
116F SER* 4.4 8.5 - - - +
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Residues in contact with ASN 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F PRO* 4.8 15.7 - - - +
46F SER 5.2 5.3 + - - +
56F LEU* 3.9 22.3 - - + +
60F SER 2.9 18.4 + - - +
61F THR* 3.2 4.9 + - - +
63F ILE* 1.3 73.1 - - - +
65F HIS* 1.3 65.1 + - - +
67F ARG* 2.8 38.7 + - - +
68F MET* 3.0 45.8 + - - +
79F SER* 6.4 0.2 - - - -
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Residues in contact with HIS 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E ASP* 3.2 34.6 + - + -
23E ILE* 3.9 29.8 - - + +
61F THR 3.1 11.7 + - - +
62F VAL 3.1 11.6 + - - +
64F ASN* 1.3 79.4 - - - +
66F TYR* 1.3 89.5 + + + +
68F MET* 3.5 6.0 + - - -
69F ARG* 3.3 73.1 + - - +
53G ASN* 4.6 11.7 - - - +
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Residues in contact with TYR 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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16E PHE* 4.0 22.0 - + - -
17E PHE 4.9 0.5 + - - -
18E VAL* 3.4 27.3 - - + +
19E SER 3.5 31.5 + - - -
22E ASP* 4.1 12.2 + - + +
23E ILE* 4.0 8.5 - - + +
62F VAL* 3.2 25.1 - - + -
63F ILE* 3.0 8.9 + - - +
65F HIS* 1.3 96.3 - + - +
67F ARG* 1.3 66.2 + - - +
69F ARG* 3.2 11.5 + - + +
71F HIS* 3.3 51.0 + + + +
74F PHE* 3.7 21.8 - - + -
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Residues in contact with ARG 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F PRO 5.5 4.5 - - - -
46F SER* 5.9 5.8 - - - +
56F LEU* 6.0 0.2 - - - +
60F SER 4.8 1.0 + - - -
63F ILE* 2.9 27.9 + - - +
64F ASN* 2.8 59.9 + - - +
66F TYR* 1.3 77.0 - - - +
68F MET* 1.3 63.8 + - + +
69F ARG 3.2 0.9 + - - -
70F GLY 3.6 4.7 + - - -
74F PHE* 3.4 26.1 + - - +
75F ALA* 3.6 21.0 - - - +
77F LEU* 2.8 32.5 + - - +
78F LYS* 4.0 3.5 + - - +
79F SER* 3.6 30.3 - - - +
116F SER* 4.0 9.5 + - - -
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Residues in contact with MET 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F SER 5.1 10.8 - - - +
47F HIS* 5.7 8.1 - - + +
64F ASN* 3.0 43.9 + - - +
65F HIS* 4.1 4.9 - - - +
66F TYR 3.3 0.2 - - - -
67F ARG* 1.3 79.6 - - + +
69F ARG* 1.3 73.1 + - - +
70F GLY 3.5 1.4 + - - -
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Residues in contact with ARG 69 (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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22E ASP 5.2 0.4 + - - -
65F HIS* 3.3 63.0 + - - +
66F TYR* 3.2 6.6 + - + +
67F ARG 3.2 1.0 - - - -
68F MET* 1.3 95.8 - - - +
70F GLY* 1.3 61.6 + - - +
71F HIS* 3.1 7.3 + - + +
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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
------------------------------------------------------------
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