Contacts of the helix formed by residues 80 - 90 (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 ASN 80 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53E ALA* 3.9 11.3 + - + +
58E GLN* 5.9 1.7 - - - +
79E VAL* 1.3 82.0 - - + +
81E ALA* 1.3 64.0 + - - +
82E PRO* 3.4 6.2 - - - +
83E GLY* 3.5 5.4 + - - +
84E VAL* 3.3 23.9 + - + +
101E LEU* 3.8 4.8 - - - +
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Residues in contact with ALA 81 (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* 6.1 1.3 - - + -
53E ALA* 4.7 5.2 - - - +
75E LEU* 4.3 12.3 - - - +
76E TYR 4.9 0.2 - - - -
77E ASP* 4.5 9.6 - - + +
79E VAL 2.9 6.3 + - - +
80E ASN* 1.3 76.2 - - - +
82E PRO* 1.3 66.4 - - + +
83E GLY 3.3 0.3 + - - -
84E VAL* 3.3 4.8 + - - +
85E THR* 2.6 32.7 + - - -
99E GLY* 5.1 0.4 - - - -
100E PHE 3.4 33.0 - - - +
101E LEU* 3.9 8.5 - - + -
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Residues in contact with PRO 82 (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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80E ASN* 3.5 4.9 - - - -
81E ALA* 1.3 94.0 - - + +
83E GLY* 1.3 52.3 + - - +
85E THR* 3.2 8.4 + - - +
86E ALA* 2.8 36.0 + - - +
99E GLY* 5.3 5.8 - - - +
101E LEU* 4.1 26.7 - - + -
260F ALA* 3.7 17.3 - - + +
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Residues in contact with GLY 83 (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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80E ASN* 3.5 8.9 + - - -
81E ALA 3.2 0.8 - - - -
82E PRO* 1.3 82.3 - - - +
84E VAL* 1.3 61.0 + - - +
86E ALA* 3.3 2.1 + - - +
87E ASP* 3.0 23.2 + - - +
257F VAL* 4.2 0.7 - - - +
260F ALA* 3.1 22.8 + - - -
261F LYS* 3.6 26.9 - - - -
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Residues in contact with VAL 84 (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* 4.2 8.1 - - + +
53E ALA* 3.7 13.2 - - + -
58E GLN* 3.6 37.9 - - + +
61E ALA* 4.6 1.1 - - + -
75E LEU* 4.0 17.9 - - + -
80E ASN* 3.3 15.4 + - + +
81E ALA* 3.3 7.4 + - - +
83E GLY* 1.3 74.5 - - - +
85E THR* 1.3 58.5 + - - +
87E ASP* 3.3 7.6 + - - +
88E ILE* 2.9 31.0 + - + +
261F LYS* 4.9 5.8 - - - +
269F LEU* 3.8 23.3 - - + -
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Residues in contact with THR 85 (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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75E LEU* 4.2 15.4 - - - +
81E ALA 2.6 20.2 + - - -
82E PRO* 3.3 10.3 - - - -
84E VAL* 1.3 75.2 - - - +
86E ALA* 1.3 61.2 + - - +
88E ILE* 3.3 2.4 + - - +
89E SER* 2.8 33.5 + - - -
97E VAL* 4.0 15.6 - - + +
98E ARG* 3.7 11.4 - - - -
99E GLY* 3.2 38.7 - - - +
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Residues in contact with ALA 86 (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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82E PRO 2.8 11.1 + - - +
83E GLY 3.7 2.5 - - - +
85E THR* 1.3 73.2 - - - +
87E ASP* 1.3 65.2 + - - +
89E SER* 2.7 24.2 + - - -
90E HIS* 3.6 13.2 - - - +
256F GLU* 4.2 4.3 - - + +
257F VAL* 4.0 16.1 - - + +
260F ALA* 3.3 32.8 - - + -
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Residues in contact with ASP 87 (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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83E GLY 3.0 13.2 + - - +
84E VAL* 3.4 12.6 - - - +
86E ALA* 1.3 79.5 - - - +
88E ILE* 1.3 61.7 + - - +
90E HIS* 3.4 6.6 + - - +
257F VAL* 3.9 15.8 - - + +
261F LYS* 4.0 6.5 + - - -
267F ALA* 3.6 6.0 - - - -
268F THR* 2.7 32.3 + - - -
269F LEU* 2.9 19.4 + - + +
270F SER* 2.7 56.8 + - - -
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Residues in contact with ILE 88 (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* 3.3 46.7 - - + +
62E MET* 3.5 4.7 - - - +
65E LYS* 3.3 37.0 - - + -
73E LEU* 5.1 0.7 - - + -
75E LEU* 3.9 12.6 - - + -
84E VAL* 2.9 17.6 + - + +
85E THR* 3.9 2.9 - - - +
87E ASP* 1.3 71.6 - - - +
89E SER* 1.3 59.9 + - - +
90E HIS 3.1 2.7 - - - -
91E MET* 3.0 40.2 + - - +
97E VAL* 4.2 12.6 - - + -
269F LEU* 3.9 19.7 - - + -
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Residues in contact with SER 89 (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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65E LYS* 4.6 3.3 - - - +
85E THR* 2.8 19.7 + - - -
86E ALA* 2.7 24.3 + - - -
88E ILE* 1.3 71.9 - - - +
90E HIS* 1.3 70.4 + - - +
91E MET 3.2 3.7 + - - +
97E VAL* 3.6 21.5 - - - -
199F THR* 3.4 19.1 - - - +
200F PHE* 5.1 0.5 - - - -
203F GLU* 4.8 4.3 - - - +
249F ARG* 5.3 3.2 + - - -
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Residues in contact with HIS 90 (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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86E ALA* 3.6 8.1 + - - +
87E ASP 3.4 8.9 + - - +
88E ILE 3.1 1.2 - - - -
89E SER* 1.3 90.5 + - - +
91E MET* 1.3 60.3 + - - +
192F LEU* 5.2 1.1 - - + -
195F VAL* 3.2 17.1 - - - +
196F ARG* 2.9 35.9 + - + +
199F THR* 2.8 23.2 + - - -
200F PHE* 3.6 25.2 - + - -
249F ARG* 4.6 1.6 - - - -
253F GLY 3.3 26.2 - - - -
256F GLU* 3.0 24.7 + - + +
257F VAL* 3.7 17.3 - - + +
270F SER* 4.3 8.9 + - - -
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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