Contacts of the helix formed by residues 64 - 72 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ASP* 2.9 30.2 + - - +
63B PRO* 1.3 71.4 - - - +
65B SER* 1.3 64.7 + - - +
66B GLY* 3.4 2.9 - - - +
67B LEU* 4.3 19.3 - - + +
68B ALA* 3.3 22.1 + - - +
73B LEU* 4.9 1.3 - - + +
110B ARG* 3.4 54.4 + - - +
111B ILE 3.9 4.5 + - - +
112B ALA* 3.8 27.6 - - - +
113B GLN* 4.4 3.8 - - + +
3172B NO3 3.7 20.7 + - - -
3170C UMP 4.4 22.4 + - - +
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Residues in contact with SER 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B PRO 3.8 1.9 + - - -
64B ARG* 1.3 73.7 - - - +
66B GLY* 1.3 61.6 + - - +
68B ALA* 3.2 5.9 - - - +
69B THR* 3.2 23.2 + - - -
113B GLN* 5.7 1.1 - - - -
77C ASN* 3.3 29.4 + - - +
81C THR 5.8 1.3 - - - -
3170C UMP 2.9 60.9 + - - -
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Residues in contact with GLY 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ARG* 3.4 1.0 - - - +
65B SER* 1.3 74.8 + - - +
67B LEU* 1.3 49.8 + - - +
68B ALA 3.0 4.5 - - - -
69B THR* 3.1 6.2 + - - -
70B ARG* 2.8 38.2 + - - +
3172B NO3 3.0 23.2 + - - -
3170C UMP 3.4 8.7 + - - -
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ARG* 4.0 24.4 + - + +
65B SER 3.8 0.4 - - - -
66B GLY* 1.3 68.2 - - - +
68B ALA* 1.3 65.8 + - - +
70B ARG* 3.7 15.7 - - - +
71B VAL* 3.1 36.9 + - + +
72B GLY 3.2 3.1 + - - -
73B LEU* 3.3 37.3 + - + -
103B ILE* 6.2 1.8 - - + -
109B ASP* 6.3 0.7 - - + -
110B ARG 3.5 24.2 - - - +
111B ILE* 4.8 2.2 - - + +
3172B NO3 3.2 27.1 + - - +
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Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B PRO* 5.3 0.2 - - + -
64B ARG 3.3 14.2 + - - +
65B SER 3.2 12.1 + - - +
66B GLY 3.0 1.0 - - - -
67B LEU* 1.3 80.3 - - - +
69B THR* 1.3 59.1 + - - +
72B GLY* 2.9 26.2 + - - -
73B LEU 3.5 20.2 + - - +
42C ARG* 3.5 4.5 + - - -
76C VAL* 3.7 21.5 - - + +
77C ASN* 3.7 20.4 - - + +
93C ALA* 5.3 1.6 - - + -
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Residues in contact with THR 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B SER 3.2 7.0 + - - -
66B GLY* 3.1 8.1 + - - +
68B ALA* 1.3 75.6 - - - +
70B ARG* 1.3 73.1 + - + +
42C ARG* 3.1 24.0 + - - +
44C LEU* 3.4 47.9 - - + +
93C ALA* 3.9 12.5 - - - +
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Residues in contact with ARG 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B GLY* 2.8 18.0 + - - +
67B LEU* 3.7 17.3 - - - +
69B THR* 1.3 86.5 - - + +
71B VAL* 1.3 77.9 + - - +
3172B NO3 2.8 39.2 + - - +
42C ARG* 3.5 6.8 + - - -
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Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LEU* 3.1 36.6 + - + +
70B ARG* 1.3 98.9 - - - +
72B GLY* 1.3 61.9 + - - +
73B LEU* 4.2 3.1 - - + +
98B ASP* 3.7 15.8 - - - +
101B ALA 5.1 0.3 - - - +
102B PRO 6.0 1.1 - - - +
103B ILE* 3.5 39.3 - - + +
42C ARG* 3.4 9.6 - - - +
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Residues in contact with GLY 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LEU 3.2 0.2 + - - -
68B ALA 2.9 19.8 + - - -
71B VAL* 1.3 79.7 - - - +
73B LEU* 1.3 61.9 + - - +
74B SER* 3.6 0.7 + - - -
97B LEU* 3.0 33.9 + - - +
98B ASP 4.4 4.7 - - - -
103B ILE* 4.2 0.9 - - - -
42C ARG* 3.4 21.3 - - - +
76C VAL* 4.3 4.9 - - - -
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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