Contacts of the helix formed by residues 86 - 100 (chain B) in PDB entry 1E96
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 LYS 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B GLU* 4.7 12.3 + - - -
81B TYR* 2.8 38.2 + - + +
84B THR* 3.8 27.6 + - - +
85B GLU* 1.3 72.7 - - - +
87B TYR* 1.3 62.4 + - - +
88B ASP 3.3 2.7 - - - -
89B LEU* 3.1 23.9 + - + -
90B ALA* 2.9 21.0 + - - +
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Residues in contact with TYR 87 (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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82B TYR* 3.8 13.9 - + - -
85B GLU* 2.0 48.8 + - + -
86B LYS* 1.3 71.1 - - - +
88B ASP* 1.3 57.8 + - - +
90B ALA* 3.1 2.1 + - - +
91B ILE* 2.8 35.2 + - - +
130B MET* 3.0 34.5 - - + +
133B LYS* 3.5 46.5 + - + +
134B LYS* 3.8 28.9 - - + -
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Residues in contact with ASP 88 (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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86B LYS 3.2 1.0 + - - -
87B TYR* 1.3 77.0 - - - +
89B LEU* 1.3 67.3 + - + +
91B ILE* 3.4 8.4 + - - +
92B LYS* 3.0 25.6 + - - +
134B LYS* 2.9 39.5 + - - +
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Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B TYR* 3.4 49.8 - - + +
86B LYS* 3.1 25.8 + - + +
88B ASP* 1.3 81.1 - - + +
90B ALA* 1.3 56.0 + - - +
92B LYS* 3.9 22.5 - - + +
93B ASP* 3.1 23.6 + - - +
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Residues in contact with ALA 90 (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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78B GLY* 3.5 21.5 - - - +
81B TYR* 3.8 9.6 - - + +
82B TYR 3.9 2.7 - - - +
86B LYS 2.9 12.9 + - - +
87B TYR 3.2 8.7 - - - +
88B ASP 3.0 0.2 - - - -
89B LEU* 1.3 75.9 - - - +
91B ILE* 1.3 54.6 + - - +
93B ASP* 3.1 4.3 + - - +
94B LEU* 2.8 41.0 + - + +
130B MET* 3.6 26.2 - - + -
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Residues in contact with ILE 91 (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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87B TYR 2.8 22.4 + - - +
88B ASP* 3.8 7.4 - - - +
90B ALA* 1.3 71.3 - - - +
92B LYS* 1.3 53.5 + - - +
94B LEU* 3.1 9.8 + - - +
95B LYS* 2.7 69.4 + - + +
127B ILE* 4.2 13.2 - - + +
130B MET* 3.4 28.9 - - + +
131B TYR* 3.7 33.7 - - + +
134B LYS* 4.3 16.2 - - + -
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Residues in contact with LYS 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ARG* 6.1 2.2 - - - +
88B ASP 3.0 17.8 + - - +
89B LEU* 3.9 21.7 - - + +
91B ILE* 1.3 75.5 - - - +
93B ASP* 1.3 69.8 + - - +
95B LYS* 4.1 7.6 - - - +
96B GLU* 3.3 22.7 + - - +
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Residues in contact with ASP 93 (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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74B TYR* 3.5 27.2 - - - +
77B ARG* 2.8 52.6 + - - +
78B GLY* 3.4 22.2 + - - -
81B TYR* 3.0 18.2 - - - -
89B LEU 3.1 15.4 + - - +
90B ALA 3.1 1.8 + - - -
92B LYS* 1.3 81.8 - - - +
94B LEU* 1.3 59.0 + - - +
96B GLU* 3.4 3.6 + - - +
97B ALA* 3.0 23.2 + - - +
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Residues in contact with LEU 94 (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 PHE* 3.5 45.5 - - + +
78B GLY* 4.8 3.1 - - - -
79B MET* 4.2 16.4 - - - -
90B ALA* 2.8 18.5 + - + +
91B ILE* 3.1 2.7 + - - +
93B ASP* 1.3 78.4 - - - +
95B LYS* 1.3 55.8 + - - +
97B ALA* 3.2 3.1 + - - +
98B LEU* 3.0 23.4 + - - +
123B VAL* 3.3 18.8 - - + +
126B ASN* 3.7 37.9 - - + +
127B ILE* 3.4 17.7 - - + +
130B MET* 3.9 17.5 - - + -
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Residues in contact with LYS 95 (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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91B ILE* 2.7 37.4 + - + +
92B LYS* 4.1 7.4 - - - +
94B LEU* 1.3 73.1 - - - +
96B GLU* 1.3 58.0 + - - +
98B LEU* 3.3 9.2 + - + +
99B ILE* 3.0 35.8 + - + +
127B ILE* 4.0 24.2 - - + -
131B TYR* 2.9 25.6 + - - -
143B GLN* 4.9 9.4 - - - +
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Residues in contact with GLU 96 (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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74B TYR* 3.4 39.3 + - + -
92B LYS 3.3 15.8 + - - +
93B ASP* 3.7 4.7 - - - +
95B LYS* 1.3 74.9 - - - +
97B ALA* 1.3 66.6 + - - +
99B ILE* 3.3 21.7 + - - +
100B GLN* 2.8 55.0 + - - +
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Residues in contact with ALA 97 (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 ALA* 3.6 32.6 - - + +
74B TYR* 3.9 6.9 - - - +
75B PHE* 3.8 19.5 - - + +
93B ASP 3.0 15.0 + - - +
94B LEU* 3.2 12.3 + - - +
96B GLU* 1.3 77.4 - - - +
98B LEU* 1.3 63.0 + - - +
100B GLN* 3.1 11.4 + - - -
101B LEU* 3.4 12.2 + - - +
118B LEU* 5.0 1.5 - - + +
123B VAL* 4.3 9.0 - - + -
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Residues in contact with LEU 98 (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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94B LEU 3.0 12.5 + - - +
95B LYS* 3.4 11.7 - - + +
96B GLU 3.2 0.2 - - - -
97B ALA* 1.3 77.1 - - - +
99B ILE* 1.3 58.5 + - + +
101B LEU* 2.9 34.1 + - + +
102B ARG 3.9 1.4 + - - -
103B GLY 4.9 2.4 + - - -
120B ALA* 3.9 37.7 - - + +
123B VAL* 4.2 9.8 - - + +
124B LEU* 3.7 32.5 - - + -
127B ILE* 4.7 6.7 - - + -
143B GLN* 5.5 0.4 - - - +
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Residues in contact with ILE 99 (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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95B LYS* 3.0 22.4 + - + +
96B GLU* 3.4 27.4 - - - +
98B LEU* 1.3 78.2 - - + +
100B GLN* 1.3 75.7 + - - +
101B LEU 3.0 0.2 - - - -
102B ARG* 3.0 25.7 + - - +
103B GLY 6.0 0.2 - - - +
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Residues in contact with GLN 100 (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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28A PHE 5.5 0.5 + - - -
68B LYS 4.0 6.4 + - - -
69B HIS* 2.8 58.1 + - - +
71B ALA* 3.7 11.2 - - + -
74B TYR* 4.1 17.7 - - + -
96B GLU* 2.8 43.4 + - - +
97B ALA 3.1 7.7 + - - +
99B ILE* 1.3 88.3 - - - +
101B LEU* 1.3 55.2 + - - +
102B ARG* 3.2 31.0 + - - +
107B ILE* 3.9 8.0 - - - +
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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