Contacts of the helix formed by residues 67 - 75 (chain F) in PDB entry 5OA3
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 PRO 67 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40F ALA* 3.6 4.0 - - + -
41F VAL* 3.5 22.0 - - + +
45F TYR* 4.2 20.2 - - + +
47F LYS* 4.5 20.0 - - + +
50F PRO* 5.0 1.8 - - + +
56F TYR* 4.4 9.4 - - - +
65F GLN 3.8 3.5 - - - +
66F CYS* 1.4 87.9 - - + +
68F ILE* 1.3 66.4 + - - +
69F VAL* 3.2 2.7 - - + +
70F GLU* 3.0 46.9 + - + +
71F ARG* 3.1 9.4 + - - +
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Residues in contact with ILE 68 (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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39F ILE* 3.7 16.6 - - + -
40F ALA* 3.2 33.6 - - - +
41F VAL* 3.4 13.2 - - + +
66F CYS 3.4 4.0 + - - -
67F PRO* 1.3 71.4 - - - +
69F VAL* 1.3 64.8 + - + +
71F ARG* 2.9 24.7 + - + +
72F LEU* 3.0 14.0 + - + +
109F LEU* 5.4 5.6 - - + -
112F LEU* 3.7 33.6 - - + +
113F VAL* 4.8 6.5 - - + +
116F ILE* 3.6 34.1 - - + -
147F VAL* 6.2 0.2 - - + -
151F ILE* 5.0 0.8 - - + +
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Residues in contact with VAL 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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19F LEU* 3.9 29.8 - - + -
20F PHE* 4.6 1.1 - - + -
41F VAL* 4.0 20.2 - - + -
50F PRO* 4.3 22.2 - - + -
67F PRO* 4.9 2.7 - - + -
68F ILE* 1.3 81.4 - - + +
70F GLU* 1.3 57.0 + - - +
71F ARG 3.2 0.2 + - - -
72F LEU* 3.3 5.6 + - + +
73F THR* 2.9 30.3 + - - -
93F VAL* 4.4 6.3 - - + +
97F PHE* 3.7 28.5 - - + -
109F LEU* 4.3 12.6 - - + -
112F LEU* 4.4 8.5 - - + -
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Residues in contact with GLU 70 (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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16752 A 5.1 2.3 + - - -
50F PRO* 3.0 31.7 - - + +
52F SER* 3.5 26.7 + - - -
53F ALA 4.4 4.0 + - - -
54F GLY 4.9 1.4 + - - -
56F TYR* 4.5 13.5 - - - -
66F CYS* 5.3 4.5 - - + -
67F PRO* 3.0 37.3 + - + +
69F VAL* 1.3 79.4 - - - +
71F ARG* 1.3 56.8 + - - +
73F THR* 3.4 7.4 - - - -
74F ASN* 2.9 38.4 + - - +
86F LYS* 4.2 17.1 + - - +
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Residues in contact with ARG 71 (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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16762 U 4.5 14.4 + - - +
16772 U 3.6 17.1 + - - +
63F LYS* 2.9 53.3 + - - +
64F ALA* 4.7 2.8 + - - +
66F CYS* 3.6 20.4 + - - +
67F PRO 3.1 7.4 + - - +
68F ILE* 2.9 18.0 + - + +
70F GLU* 1.3 76.7 - - - +
72F LEU* 1.3 64.4 + - - +
73F THR 3.4 0.2 + - - -
74F ASN* 3.5 6.3 + - - +
75F SER* 3.5 18.4 + - - -
144F LEU* 3.8 11.1 - - - +
147F VAL* 4.8 7.0 - - + +
148F ASN* 2.7 31.9 + - - +
151F ILE* 3.5 25.8 - - + +
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Residues in contact with LEU 72 (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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68F ILE 3.0 10.8 + - - +
69F VAL* 3.8 7.0 - - + +
71F ARG* 1.3 76.3 - - - +
73F THR* 1.3 63.8 + - - +
75F SER 3.2 8.7 + - - -
76F MET* 3.6 27.4 + - + +
93F VAL* 4.9 9.4 - - + -
97F PHE* 5.5 6.3 - - + -
112F LEU* 3.8 29.8 - - + -
151F ILE* 3.6 29.0 - - + +
154F LEU* 4.3 20.2 - - + -
155F CYS* 3.6 21.2 - - - +
173F LEU* 4.3 19.3 - - + -
177F LEU* 4.9 4.7 - - + -
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Residues in contact with THR 73 (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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50F PRO* 3.6 16.1 - - + +
69F VAL 2.9 18.4 + - - -
70F GLU* 3.4 12.3 - - - -
71F ARG 3.2 0.2 - - - -
72F LEU* 1.3 75.0 - - - +
74F ASN* 1.3 68.5 + - - +
75F SER 3.0 1.2 + - - -
76F MET* 3.1 6.1 + - - +
77F MET* 4.4 1.9 + - - +
86F LYS* 3.5 30.1 - - + +
89F THR* 3.0 44.6 + - + +
90F VAL* 4.1 11.5 - - + +
93F VAL* 3.8 16.6 - - - +
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Residues in contact with ASN 74 (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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16752 A 3.2 38.2 + - - +
16762 U 2.6 30.3 + - - +
70F GLU* 2.9 31.3 + - - +
71F ARG* 3.8 9.8 - - - +
73F THR* 1.3 76.7 - - - +
75F SER* 1.3 57.4 + - - +
76F MET 3.3 4.0 + - - -
77F MET* 3.3 27.4 - - - +
78F MET* 4.9 1.0 + - - +
86F LYS* 2.6 32.2 + - - +
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Residues in contact with SER 75 (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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16762 U 5.0 15.7 + - - -
71F ARG 3.5 10.0 + - - -
72F LEU 3.2 4.2 + - - -
73F THR 3.0 2.0 + - - -
74F ASN* 1.3 78.1 - - - +
76F MET* 1.3 51.3 + - - +
77F MET 3.4 0.7 - - - -
78F MET* 3.6 17.5 - - - +
151F ILE* 4.1 14.4 + - - -
152F TRP* 4.5 8.0 - - - -
155F CYS* 3.2 31.1 - - - +
159F ARG* 2.6 24.8 + - - -
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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