Contacts of the helix formed by residues 56 - 66 (chain E) in PDB entry 1SMK
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 ILE 56 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55E GLY* 1.3 77.9 - - - +
57E GLY* 1.3 67.7 + - - +
58E GLN 3.5 0.2 - - - -
59E PRO* 3.3 2.8 - - - +
60E LEU* 3.1 24.2 + - + +
119E PRO* 4.1 28.0 - - + +
160E ILE* 5.2 7.0 - - + -
266E SER* 5.9 0.9 - - - +
267E ALA 3.9 10.1 - - - +
268E THR* 3.7 26.2 - - + -
271E MET* 3.5 33.9 - - + -
272E ALA* 3.8 15.6 - - - +
275E ALA* 5.5 0.9 - - + -
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Residues in contact with GLY 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E ILE* 4.7 1.8 - - - +
51E GLY 3.2 25.4 + - - -
52E ALA* 2.9 12.1 - - - -
54E GLY* 3.4 5.6 + - - -
56E ILE* 1.3 78.7 - - - +
58E GLN* 1.3 50.4 + - - +
60E LEU* 3.2 8.3 - - - +
61E ALA* 2.6 36.0 + - - +
119E PRO* 4.4 8.6 - - - +
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Residues in contact with GLN 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E ALA 2.7 18.2 + - - +
53E ALA* 3.0 20.1 + - - +
54E GLY 3.2 9.1 + - - +
57E GLY* 1.3 70.5 - - - +
59E PRO* 1.3 77.1 - - + +
61E ALA* 2.8 8.1 + - - +
62E MET* 2.8 23.4 + - - +
80E ASN* 5.9 1.6 - - - +
84E VAL* 3.6 26.6 - - + +
261F LYS* 4.6 8.8 + - - +
268F THR* 4.3 7.8 + - - -
269F LEU* 3.7 32.2 - - + +
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Residues in contact with PRO 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E GLY 3.2 25.6 - - - +
56E ILE* 3.3 4.5 - - - +
58E GLN* 1.3 94.5 - - + +
60E LEU* 1.3 59.9 - - - +
62E MET* 3.3 10.4 + - + +
63E LEU* 3.0 26.7 + - - +
268E THR 5.1 1.3 - - - +
269E LEU* 3.9 22.7 - - + -
272E ALA* 3.7 19.1 - - + -
59F PRO* 5.2 5.8 - - + -
62F MET* 4.0 17.7 - - + +
269F LEU* 4.3 8.0 - - + -
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Residues in contact with LEU 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E ILE* 4.0 14.4 - - + -
56E ILE* 3.1 12.7 + - + +
57E GLY 3.2 7.4 - - - +
58E GLN 3.0 0.4 - - - -
59E PRO* 1.3 77.8 - - - +
61E ALA* 1.3 67.1 + - - +
63E LEU* 2.9 14.2 + - - +
64E MET* 2.9 17.4 + - + +
117E ILE* 3.7 28.7 - - + -
119E PRO* 4.0 27.4 - - + -
272E ALA* 3.5 12.3 - - + +
275E ALA* 3.4 27.4 - - + -
276E VAL* 3.1 30.9 - - + +
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Residues in contact with ALA 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E ILE* 3.5 14.7 - - + +
52E ALA* 4.6 1.8 - - + +
57E GLY 2.6 18.1 + - - +
58E GLN* 2.8 12.4 + - - +
60E LEU* 1.3 69.6 - - - +
62E MET* 1.3 61.3 - - - +
64E MET 3.4 0.3 + - - -
65E LYS* 3.1 24.1 + - - +
73E LEU* 3.7 4.5 - - - +
75E LEU* 3.5 24.9 - - + -
84E VAL* 4.6 2.0 - - + -
88E ILE* 3.3 23.6 - - + +
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Residues in contact with MET 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E GLN 2.8 14.1 + - - +
59E PRO* 3.5 8.7 - - + +
61E ALA* 1.3 75.0 - - - +
63E LEU* 1.3 57.9 + - - +
65E LYS* 3.6 5.2 + - - +
66E MET* 3.1 31.7 + - - +
88E ILE* 3.5 9.3 - - - +
91E MET* 3.8 20.4 - - + -
59F PRO* 4.0 13.7 - - + -
62F MET* 3.6 31.6 - - + -
63F LEU* 3.7 31.9 - - + -
269F LEU* 3.5 42.2 - - + +
272F ALA* 4.1 5.2 - - - -
273F TYR 4.3 0.9 - - - -
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Residues in contact with LEU 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E PRO 3.0 12.3 + - - +
60E LEU 2.9 3.0 + - - +
62E MET* 1.3 76.2 - - + +
64E MET* 1.3 62.8 + - - +
66E MET* 3.4 15.1 + - + +
67E ASN* 3.4 16.6 + - - +
272E ALA* 4.0 12.8 - - + +
273E TYR* 4.1 7.6 - - - -
276E VAL* 3.3 40.9 - - + +
62F MET* 3.5 30.3 - - + -
63F LEU* 3.7 28.0 - - + -
66F MET* 4.1 21.1 - - + -
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Residues in contact with MET 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E VAL* 3.6 28.7 - - + -
49E ILE* 3.9 9.9 - - + -
60E LEU* 2.9 16.4 + - + +
61E ALA 3.9 0.4 - - - +
62E MET 3.4 0.2 - - - -
63E LEU* 1.3 72.3 - - - +
65E LYS* 1.3 57.3 + - - +
66E MET 2.9 5.2 - - - -
67E ASN* 2.6 33.9 + - - +
70E VAL* 3.6 23.2 - - + +
73E LEU* 3.7 22.4 - - + -
115E LEU* 4.4 0.9 - - + -
117E ILE* 3.4 34.3 - - + -
276E VAL* 3.9 23.3 - - + -
279E ALA* 3.8 17.3 - - + -
280E ASP 5.6 0.2 - - - -
283E LEU* 4.2 7.9 - - + -
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Residues in contact with LYS 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E ALA 3.1 17.8 + - - +
62E MET 3.6 6.1 - - - +
64E MET* 1.3 76.5 - - - +
66E MET* 1.3 56.6 + - - +
67E ASN 3.6 1.9 + - - +
73E LEU* 3.5 9.3 - - + +
88E ILE* 3.3 41.3 - - + -
89E SER* 4.6 3.4 - - - +
91E MET* 3.2 31.0 + - + -
93E THR* 2.5 63.6 + - - +
95E ALA* 3.0 41.1 + - + +
97E VAL* 4.3 18.8 - - + +
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Residues in contact with MET 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E MET* 3.1 26.0 + - - +
63E LEU* 3.5 15.9 - - + +
64E MET 2.9 1.0 - - - -
65E LYS* 1.3 78.4 - - - +
67E ASN* 1.3 59.9 + - - +
68E PRO* 3.4 8.3 - - - +
91E MET* 3.4 17.9 - - + -
93E THR* 4.2 10.8 - - + +
63F LEU* 4.0 32.1 - - + -
273F TYR* 3.9 28.9 - - + -
276F VAL* 6.1 3.1 - - + -
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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