Contacts of the helix formed by residues 86 - 101 (chain B) in PDB entry 1EFU
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 ALA 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A GLU* 5.0 1.8 + - - -
84B LYS 3.7 3.0 + - - -
85B ASP* 1.3 71.0 + - - +
87B GLY* 1.3 56.1 - - - +
89B GLN* 3.4 9.3 - - - +
90B ALA* 2.7 36.4 + - - +
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Residues in contact with GLY 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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85B ASP* 3.2 11.2 + - - -
86B ALA* 1.3 79.3 - - - +
88B PHE* 1.3 56.0 + - - +
90B ALA* 3.4 7.9 + - - +
91B PHE* 2.9 28.4 + - - +
121B LEU* 4.2 16.2 - - - +
124B LYS* 4.9 9.0 - - - -
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Residues in contact with PHE 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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60B VAL* 3.8 32.5 - - + -
75B VAL* 3.4 44.0 - - + -
76B ASN 4.1 3.8 - - - -
77B CYS* 3.8 22.4 - - + -
82B VAL* 3.1 35.2 - - + +
83B ALA* 3.6 24.7 - - - -
85B ASP* 3.1 10.1 + - + +
87B GLY* 1.3 71.8 - - - +
89B GLN* 1.3 61.6 + - - +
91B PHE* 3.1 8.2 + + - +
92B ALA* 2.9 27.8 + - + +
121B LEU* 4.4 6.1 - - + -
125B ILE* 4.4 3.6 - - + +
129B ILE* 4.3 19.1 - - + -
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Residues in contact with GLN 89 (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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60B VAL* 3.8 17.6 - - - +
62B LYS* 2.8 28.6 + - - +
83B ALA 2.8 24.2 + - - +
84B LYS* 4.5 6.8 - - - +
85B ASP 2.8 20.6 + - - +
86B ALA* 3.4 11.4 - - - +
88B PHE* 1.3 77.7 - - - +
90B ALA* 1.3 53.6 + - - +
92B ALA* 3.3 4.3 + - - +
93B ASP* 2.8 46.3 + - - +
149B ALA* 5.4 3.4 - - - +
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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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86B ALA 2.7 21.0 + - - +
87B GLY* 3.5 9.2 - - - +
89B GLN* 1.3 74.7 - - - +
91B PHE* 1.3 59.4 + - - +
93B ASP* 3.9 6.1 - - - +
94B LYS* 3.1 26.1 + - - +
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Residues in contact with PHE 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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75B VAL* 3.9 21.3 - - + -
87B GLY 2.9 7.8 + - - +
88B PHE* 3.1 9.4 + + - +
90B ALA* 1.3 74.3 - - - +
92B ALA* 1.3 66.7 + - - +
94B LYS* 3.2 8.1 + - + +
95B VAL* 3.0 39.6 + - + +
114B PHE* 4.2 11.0 - + + -
117B GLU* 4.3 16.6 - - + -
118B ARG* 3.8 39.7 - - + -
121B LEU* 3.4 31.9 - - + -
129B ILE* 3.8 19.5 - - + -
131B ILE* 4.0 21.5 - - + -
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Residues in contact with ALA 92 (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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60B VAL* 4.0 17.5 - - + -
62B LYS* 4.0 21.7 - - + +
73B LEU* 4.0 3.5 - - - +
75B VAL* 4.0 25.6 - - + -
88B PHE* 2.9 20.5 + - + +
89B GLN* 3.9 3.6 - - - +
91B PHE* 1.3 74.3 - - - +
93B ASP* 1.3 57.3 + - - +
95B VAL* 3.3 3.9 + - - +
96B LEU* 2.9 29.2 + - - +
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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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62B LYS* 3.1 30.5 + - - +
89B GLN* 2.8 32.6 + - - +
90B ALA* 3.9 5.6 - - - +
92B ALA* 1.3 72.9 - - - +
94B LYS* 1.3 57.0 + - - +
96B LEU* 3.3 13.2 + - - +
97B ASP* 2.9 39.9 + - - +
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Residues in contact with LYS 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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90B ALA 3.1 18.2 + - - +
91B PHE* 3.2 8.3 + - + +
93B ASP* 1.3 73.6 - - - +
95B VAL* 1.3 64.8 + - - +
97B ASP* 3.6 9.1 + - + +
98B ALA* 3.1 25.1 + - - +
114B PHE* 3.6 13.6 - - + -
117B GLU* 3.2 39.4 + - - +
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Residues in contact with VAL 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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73B LEU* 3.7 20.4 - - + -
75B VAL* 4.9 1.1 - - + -
91B PHE* 3.0 37.8 + - + +
92B ALA* 3.6 7.9 - - - +
94B LYS* 1.3 74.6 - - - +
96B LEU* 1.3 63.9 + - - +
98B ALA* 3.6 2.4 + - - +
99B ALA* 3.1 22.9 + - - +
110B LEU* 3.8 27.2 - - + +
114B PHE* 3.7 29.6 - - + -
131B ILE* 4.1 14.8 - - + -
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Residues in contact with LEU 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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62B LYS* 3.6 28.5 - - + +
63B THR* 4.0 11.0 - - - +
64B LYS* 3.5 43.7 - - + +
71B ILE* 3.7 24.0 - - + +
73B LEU* 3.8 9.4 - - + +
92B ALA 2.9 13.3 + - - +
93B ASP* 3.4 20.4 - - - +
94B LYS 3.3 0.2 - - - -
95B VAL* 1.3 74.4 - - - +
97B ASP* 1.3 68.3 + - - +
99B ALA* 3.1 5.0 + - - +
100B VAL* 3.1 19.7 + - + +
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Residues in contact with ASP 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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64B LYS* 3.0 38.0 + - - +
93B ASP* 2.9 27.9 + - - +
94B LYS* 3.9 8.6 - - - +
95B VAL 3.5 0.2 - - - -
96B LEU* 1.3 77.4 - - - +
98B ALA* 1.3 58.1 + - - +
100B VAL* 3.2 3.5 + - - +
101B ALA* 2.8 31.7 + - - +
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Residues in contact with ALA 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 LYS 3.1 6.1 + - - +
95B VAL 3.8 0.4 - - - +
97B ASP* 1.3 80.0 - - - +
99B ALA* 1.3 57.3 + - - +
101B ALA* 3.8 6.1 - - - +
102B GLY* 2.9 27.4 + - - -
104B ILE* 3.8 7.7 - - - +
110B LEU* 4.9 0.9 - - + -
113B GLN* 3.9 12.1 - - - +
114B PHE* 3.4 38.4 - - + -
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Residues in contact with ALA 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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71B ILE* 3.9 25.1 - - + +
73B LEU* 5.7 0.7 - - + -
95B VAL 3.1 17.8 + - - +
96B LEU* 3.1 6.9 + - - +
98B ALA* 1.3 73.6 - - - +
100B VAL* 1.3 60.7 + - - +
103B LYS* 3.0 8.8 + - - -
104B ILE* 2.9 45.6 + - - +
110B LEU* 4.0 17.0 - - + +
134B VAL* 4.4 1.3 - - + -
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Residues in contact with VAL 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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64B LYS* 3.7 40.6 - - + +
66B ASP* 3.5 40.6 - - + +
69B TYR* 4.4 9.4 - - + +
71B ILE* 3.6 28.5 - - + +
96B LEU 3.1 13.9 + - - +
97B ASP 3.6 5.4 - - - +
99B ALA* 1.3 73.8 - - - +
101B ALA* 1.3 66.6 + - - +
103B LYS* 3.2 18.9 + - - +
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Residues in contact with ALA 101 (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 ASP* 5.8 1.1 - - - -
97B ASP 2.8 18.2 + - - +
98B ALA* 3.8 7.6 - - - +
100B VAL* 1.3 81.0 - - - +
102B GLY* 1.3 58.0 + - - +
103B LYS* 3.7 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