Contacts of the helix formed by residues 64 - 72 (chain C) in PDB entry 1SNF
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 ARG 64 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A ASN* 4.6 0.4 - - - -
1170A UMP 3.9 19.7 + - - +
28C ASP* 3.7 22.8 + - - +
63C PRO* 1.3 72.9 - - - +
65C SER* 1.3 64.1 + - - +
66C GLY 3.5 3.1 + - - +
67C LEU* 3.9 20.9 + - + +
68C ALA* 3.3 21.9 + - - +
73C LEU* 4.8 1.7 - - + +
110C ARG* 3.5 50.7 + - - +
111C ILE 4.1 3.9 + - - +
112C ALA* 3.8 34.7 - - - +
113C GLN* 4.4 4.7 - - - +
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Residues in contact with SER 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ASN* 3.4 27.5 - - - +
1170A UMP 2.7 57.6 + - - -
63C PRO 4.1 0.4 + - - -
64C ARG* 1.3 69.9 - - - +
66C GLY* 1.3 66.7 + - - +
68C ALA* 3.2 4.8 + - - +
69C THR* 3.2 24.9 + - - -
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Residues in contact with GLY 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1170A UMP 4.7 2.0 + - - -
64C ARG* 3.5 2.0 - - - +
65C SER* 1.3 79.4 + - - +
67C LEU* 1.3 56.2 + - - +
69C THR* 3.9 2.5 - - - -
70C ARG* 2.9 41.1 + - - +
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Residues in contact with LEU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C ARG* 3.9 23.7 + - + +
65C SER 3.5 0.2 - - - -
66C GLY* 1.3 71.7 - - - +
68C ALA* 1.3 65.8 + - - +
70C ARG* 4.4 7.6 - - + -
71C VAL* 3.0 40.3 + - + +
73C LEU* 3.3 41.7 + - + -
105C VAL* 6.3 1.1 - - + -
109C ASP* 6.2 2.0 - - + -
110C ARG 4.0 20.6 - - - +
111C ILE* 5.3 1.8 - - + -
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Residues in contact with ALA 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ARG* 3.5 4.7 + - - -
76A VAL* 3.6 19.5 - - + +
77A ASN* 3.7 25.1 - - + +
93A ALA* 5.1 1.1 - - + -
63C PRO* 5.4 0.2 - - + -
64C ARG 3.3 16.2 + - - +
65C SER 3.2 10.0 + - - +
66C GLY 3.2 0.8 - - - -
67C LEU* 1.3 77.5 - - - +
69C THR* 1.3 64.4 + - - +
72C GLY* 3.1 21.1 + - - -
73C LEU 3.3 20.4 + - - +
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Residues in contact with THR 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ARG* 2.6 30.3 + - - +
43A ALA 5.5 0.8 - - - -
44A LEU* 3.5 42.9 - - + +
93A ALA* 3.4 24.5 - - - +
65C SER 3.2 11.6 + - - -
66C GLY* 4.0 2.9 - - - -
68C ALA* 1.3 78.7 - - - +
70C ARG* 1.3 66.6 + - + +
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Residues in contact with ARG 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ARG* 3.2 10.1 + - - -
66C GLY* 2.9 30.6 + - - +
67C LEU* 4.2 7.9 - - + +
69C THR* 1.3 83.2 - - + +
71C VAL* 1.3 70.5 + - + +
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Residues in contact with VAL 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ARG* 3.4 9.0 - - - +
67C LEU* 3.0 33.2 + - + +
70C ARG* 1.3 88.7 - - + +
72C GLY* 1.3 62.4 + - - +
73C LEU* 4.0 9.0 - - + -
98C ASP* 3.6 15.9 - - - +
101C ALA* 5.1 0.3 - - - +
102C PRO 5.8 2.5 - - - +
103C ILE* 3.4 41.8 - - + +
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Residues in contact with GLY 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ARG* 3.4 21.9 - - - +
76A VAL* 4.3 5.2 - - - -
68C ALA 3.1 18.5 + - - -
71C VAL* 1.3 79.7 - - - +
73C LEU* 1.3 61.5 + - - +
74C SER 3.5 0.9 + - - -
95C ILE 3.6 0.3 - - - +
97C LEU* 2.9 33.6 + - - +
98C ASP 4.2 5.2 - - - -
103C ILE* 4.1 1.1 - - - -
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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