Contacts of the helix formed by residues 69 - 80 (chain B) in PDB entry 1S89
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 GLY 69 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B LEU* 4.4 1.1 - - - -
66B GLY 2.9 7.0 + - - -
67B PRO 3.3 2.0 + - - -
68B MET* 1.3 79.7 - - - +
70B GLY* 1.3 64.2 + - - +
71B ASP 3.3 2.9 - - - -
72B GLN* 3.2 7.7 + - - +
73B GLN* 3.1 28.6 + - - +
101B ASP* 5.5 1.3 - - - -
79E SER* 4.1 7.4 + - - -
107E ARG* 5.2 0.9 - - - -
108E LEU* 3.8 23.3 - - - +
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Residues in contact with GLY 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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45B THR* 3.7 8.5 - - - +
63B MET* 4.7 1.2 - - - +
64B LEU* 3.0 27.3 + - - +
65B SER 2.8 12.0 + - - -
66B GLY 3.3 0.2 + - - -
68B MET 3.8 0.2 - - - -
69B GLY* 1.3 77.8 - - - +
71B ASP* 1.3 60.7 + - - +
73B GLN* 3.2 12.9 + - - +
74B VAL* 3.0 27.5 + - - +
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Residues in contact with ASP 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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17B VAL* 3.9 6.2 - - - +
45B THR* 3.9 8.5 - - - +
66B GLY* 3.6 9.7 + - - +
69B GLY 3.3 0.8 - - - -
70B GLY* 1.3 75.0 - - - +
72B GLN* 1.3 58.8 + - - +
74B VAL* 3.3 2.3 + - - +
75B GLY* 2.9 22.3 + - - -
88B PHE* 4.5 4.1 - - - -
98B ASN* 3.0 32.6 + - - +
101B ASP* 3.7 31.8 - - + +
102B VAL* 4.7 2.0 - - - +
105B LEU* 3.4 27.0 - - + +
202B PGA 2.9 22.5 - - - +
72E GLN* 4.0 1.6 - - - +
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Residues in contact with GLN 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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69B GLY 3.2 8.5 + - - +
71B ASP* 1.3 75.5 - - - +
73B GLN* 1.3 61.2 + - - +
75B GLY* 3.7 0.2 - - - -
76B ALA* 2.9 29.6 + - - +
101B ASP* 3.1 28.3 + - + +
104B ALA* 6.1 0.7 - - + -
71E ASP 4.0 2.3 - - - +
72E GLN* 3.5 44.0 - - + +
75E GLY* 3.2 22.0 + - - -
76E ALA* 4.3 6.1 - - - +
101E ASP 5.3 0.3 - - - +
104E ALA* 3.2 32.5 + - + +
105E LEU* 4.2 6.6 + - - -
108E LEU* 3.1 23.7 - - + +
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Residues in contact with GLN 73 (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 MET* 3.3 23.2 - - + +
64B LEU* 2.7 55.0 + - - +
69B GLY 3.1 14.2 + - - +
70B GLY* 3.2 9.0 + - - +
72B GLN* 1.3 75.4 - - - +
74B VAL* 1.3 63.7 + - - +
76B ALA* 3.3 3.6 + - - +
77B LEU* 3.0 28.2 + - - +
76E ALA* 3.9 22.0 - - + -
79E SER* 4.1 3.8 - - - +
80E GLU* 3.7 26.1 + - - +
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Residues in contact with VAL 74 (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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15B ALA* 4.0 25.6 - - + -
17B VAL* 4.7 8.1 - - + -
43B TYR* 6.2 1.1 - - + -
44B ALA* 5.3 2.2 - - - +
45B THR* 4.3 17.0 - - + +
63B MET* 4.5 14.4 - - + -
70B GLY 3.0 19.3 + - - +
71B ASP* 3.6 7.6 - - - +
73B GLN* 1.3 73.7 - - - +
75B GLY* 1.3 65.8 + - - +
77B LEU* 3.0 11.8 + - + +
78B ILE* 2.9 33.5 + - + +
83B ILE* 4.8 4.0 - - + -
86B LEU* 4.4 7.6 - - + -
105B LEU* 3.9 16.6 - - + -
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Residues in contact with GLY 75 (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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71B ASP 2.9 12.1 + - - -
72B GLN 3.3 0.2 + - - -
73B GLN 3.3 0.2 - - - -
74B VAL* 1.3 76.2 - - - +
76B ALA* 1.3 60.6 + - - +
78B ILE* 3.2 7.6 + - - +
79B SER* 3.0 23.9 + - - -
105B LEU* 3.4 13.6 - - - +
108B LEU* 3.7 12.9 - - - +
72E GLN* 3.3 22.0 - - - -
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Residues in contact with ALA 76 (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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72B GLN 2.9 17.2 + - - +
73B GLN* 3.5 6.1 - - - +
74B VAL 3.2 0.2 - - - -
75B GLY* 1.3 75.1 - - - +
77B LEU* 1.3 64.0 + - + +
79B SER* 2.9 23.0 + - - -
80B GLU* 3.0 22.1 + - - +
72E GLN* 4.1 4.8 - - - +
73E GLN* 4.0 32.1 - - + -
76E ALA* 4.4 7.9 - - + -
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Residues in contact with LEU 77 (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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43B TYR* 4.6 12.8 - - + -
63B MET* 4.0 26.9 - - + -
73B GLN* 3.0 18.3 + - + +
74B VAL* 3.4 12.6 - - + +
76B ALA* 1.3 76.9 - - + +
78B ILE* 1.3 63.2 + - - +
80B GLU* 3.1 14.9 + - - +
82B LYS* 3.0 54.9 + - + +
83B ILE* 3.5 27.1 - - + -
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Residues in contact with ILE 78 (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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6B ARG* 5.5 0.3 + - - -
74B VAL* 2.9 26.1 + - + +
75B GLY* 3.4 7.2 - - - +
77B LEU* 1.3 76.0 - - - +
79B SER* 1.3 58.5 + - - +
81B GLY* 2.9 20.1 + - - -
83B ILE* 3.7 30.3 - - + +
86B LEU* 4.3 12.8 - - + -
105B LEU* 4.0 24.7 - - + +
108B LEU* 4.4 2.9 - - + +
109B ALA* 4.3 14.8 - - + +
112B TRP* 4.2 29.3 - - + +
114B ILE* 4.1 29.6 - - + +
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Residues in contact with SER 79 (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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75B GLY 3.0 11.8 + - - -
76B ALA* 2.9 20.6 + - - -
78B ILE* 1.3 77.6 - - - +
80B GLU* 1.3 60.0 + - - +
81B GLY 3.3 1.0 + - - -
108B LEU* 4.4 1.3 - - - -
112B TRP* 3.5 44.0 - - - +
64E LEU* 3.3 23.6 - - - +
68E MET 3.6 13.5 - - - -
69E GLY* 4.2 8.0 - - - -
73E GLN* 4.3 5.5 - - - +
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Residues in contact with GLU 80 (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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76B ALA* 3.0 23.0 + - - +
77B LEU* 3.1 11.8 + - - +
78B ILE 3.0 0.4 - - - -
79B SER* 1.3 78.5 - - - +
81B GLY* 1.3 62.2 + - - +
82B LYS* 3.2 38.9 + - + +
64E LEU* 5.0 2.0 - - + -
73E GLN* 2.9 34.4 + - - +
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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