Contacts of the helix formed by residues 92 - 109 (chain B) in PDB entry 1WOI
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 GLU 92 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B PRO* 3.9 5.9 - - + +
90B SER 3.3 12.6 - - - +
91B LEU* 1.3 80.6 - - - +
93B PRO* 1.3 71.7 - - - +
94B GLN* 3.3 2.7 - - - -
95B LEU* 3.2 19.9 + - + +
96B ALA* 3.0 17.3 + - - +
93E PRO* 5.5 2.0 - - - +
154E ASP 3.2 25.8 - - - +
155E THR* 2.9 20.8 + - - -
156E LYS 4.5 0.7 + - - -
157E TRP* 4.1 15.6 + - - -
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Residues in contact with PRO 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PHE* 4.5 11.2 - - + -
91B LEU* 3.3 6.5 - - + +
92B GLU* 1.3 89.7 - - - +
94B GLN* 1.3 64.4 + - + +
96B ALA* 3.1 7.3 + - + +
97B HIS* 2.9 43.2 + - - +
157B TRP* 4.1 19.7 - - + +
91E LEU* 4.3 31.6 - - + -
92E GLU* 5.6 2.2 - - - +
93E PRO* 5.2 11.9 - - + -
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Residues in contact with GLN 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B GLU 3.3 0.8 - - - -
93B PRO* 1.3 82.7 - - + +
95B LEU* 1.3 62.6 + - - +
97B HIS* 3.3 12.9 + - - +
98B ASP* 3.2 38.2 + - - +
157B TRP* 5.2 17.2 + - + +
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PRO* 3.7 22.0 - - + -
92B GLU* 3.2 23.5 + - + +
94B GLN* 1.3 76.5 - - - +
96B ALA* 1.3 65.7 + - - +
98B ASP* 3.2 13.8 + - + +
99B ARG* 3.1 48.2 + - + +
154E ASP* 3.7 27.6 - - + +
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Residues in contact with ALA 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PHE* 3.9 26.9 - - + -
88B LEU* 3.9 17.2 - - + +
89B PRO* 4.0 17.7 - - + +
91B LEU 4.8 0.7 - - - +
92B GLU 3.0 12.3 + - - +
93B PRO 3.4 8.3 - - - +
95B LEU* 1.3 76.7 - - - +
97B HIS* 1.3 55.8 + - + +
99B ARG* 3.3 4.5 + - - +
100B ILE* 2.9 37.6 + - + +
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Residues in contact with HIS 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PHE* 4.9 9.8 - + - -
93B PRO* 2.9 35.5 + - + +
94B GLN* 3.5 11.0 - - + +
95B LEU 3.2 0.2 - - - -
96B ALA* 1.3 81.0 - - + +
98B ASP* 1.3 56.9 + - - +
100B ILE* 3.2 4.4 + - + -
101B THR* 2.9 33.6 + - - -
122B SER* 5.0 8.1 + - - -
123B VAL* 6.1 0.2 - - - -
125B TYR* 4.3 10.8 - + - -
126B PRO* 3.3 31.4 - - + +
129B ARG* 3.1 17.9 + - - +
157B TRP* 3.6 53.6 + + + +
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Residues in contact with ASP 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLN* 3.3 29.5 + - - +
95B LEU* 3.2 14.7 + - + +
97B HIS* 1.3 76.5 - - - +
99B ARG* 1.3 64.3 + - + +
101B THR* 3.5 2.2 + - - -
102B GLU* 3.0 25.9 + - - +
129B ARG* 3.2 22.0 + - - +
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Residues in contact with ARG 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B VAL* 3.7 14.9 - - + +
87B ILE* 2.8 32.3 + - - +
88B LEU* 3.9 1.8 - - + -
89B PRO* 3.8 19.6 - - - +
95B LEU* 3.1 36.7 + - + +
96B ALA* 3.8 7.2 - - - +
98B ASP* 1.3 77.0 - - + +
100B ILE* 1.3 57.8 + - - +
102B GLU* 3.8 6.0 - - - +
103B ALA* 3.0 31.0 + - - +
4D PRO* 3.8 27.8 - - - +
154E ASP* 2.6 34.4 + - - -
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Residues in contact with ILE 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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34B LEU* 4.9 0.3 - - - +
36B VAL* 3.6 32.5 - - + -
38B PHE* 5.2 3.8 - - + -
86B VAL* 4.0 10.1 - - + +
88B LEU* 4.1 13.5 - - + -
96B ALA* 2.9 36.3 + - + +
97B HIS* 3.4 9.0 - - + +
99B ARG* 1.3 78.5 - - - +
101B THR* 1.3 58.4 + - - +
103B ALA* 3.8 1.2 - - - +
104B ALA* 2.8 30.8 + - - +
123B VAL* 4.4 10.1 - - + +
126B PRO* 3.7 29.2 - - + -
127B LEU* 3.5 29.1 - - + +
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Residues in contact with THR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B HIS 2.9 7.3 + - - -
98B ASP* 3.9 3.4 - - - -
100B ILE* 1.3 77.8 - - - +
102B GLU* 1.3 51.8 + - - +
104B ALA* 3.1 4.4 + - - +
105B ARG* 2.8 71.5 + - - +
126B PRO 2.6 26.4 + - - +
129B ARG* 2.9 50.4 + - + +
130B ALA 3.9 1.3 - - - +
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Residues in contact with GLU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ASP 3.0 18.8 + - - +
99B ARG* 3.8 6.3 - - - +
101B THR* 1.3 76.5 - - - +
103B ALA* 1.3 62.4 + - - +
105B ARG* 3.3 25.0 + - - +
106B GLN* 3.0 57.9 + - - +
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Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PRO* 4.7 9.6 - - + -
34B LEU* 3.9 12.8 - - + -
86B VAL* 3.7 27.6 - - + -
99B ARG 3.0 18.6 + - - +
100B ILE 3.8 0.4 - - - +
102B GLU* 1.3 77.1 - - - +
104B ALA* 1.3 62.6 + - - +
106B GLN* 3.2 16.0 + - - +
107B VAL* 3.0 27.5 + - - +
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 3.9 10.0 - - + +
100B ILE 2.8 19.7 + - - +
101B THR* 3.4 7.0 - - - +
103B ALA* 1.3 77.1 - - - +
105B ARG* 1.3 55.5 + - - +
107B VAL* 3.4 1.6 + - - +
108B ARG* 2.8 33.8 + - - +
116B PHE* 3.9 23.9 - - + -
127B LEU* 4.2 12.8 - - + +
130B ALA* 3.6 17.9 - - + -
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Residues in contact with ARG 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B THR* 2.8 46.7 + - - +
102B GLU* 3.5 30.9 + - - +
103B ALA 3.2 0.2 - - - -
104B ALA* 1.3 74.0 - - - +
106B GLN* 1.3 58.7 + - + +
108B ARG* 3.3 5.6 + - - +
109B GLY* 3.0 26.2 + - - -
129B ARG* 4.2 14.5 + - - +
130B ALA* 3.7 21.4 - - + +
132B ALA* 6.2 0.6 - - - +
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Residues in contact with GLN 106 (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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23B PRO* 3.5 34.0 - - - +
24B ASP* 3.1 29.2 - - + +
102B GLU* 3.0 43.2 + - - +
103B ALA* 3.2 9.9 + - - +
105B ARG* 1.3 76.8 - - + +
107B VAL* 1.3 60.4 + - - +
109B GLY* 3.5 0.7 + - - -
110B ARG* 2.6 42.3 + - - +
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Residues in contact with VAL 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PRO* 4.3 10.1 - - + -
27B TRP* 4.1 9.4 - - + -
32B ALA* 3.5 37.0 - - + +
34B LEU* 4.1 23.6 - - + -
83B ALA* 3.7 27.4 - - + -
103B ALA 3.0 20.5 + - - +
104B ALA* 4.0 3.4 - - - +
106B GLN* 1.3 73.0 - - - +
108B ARG* 1.3 66.6 + - - +
110B ARG* 3.0 12.3 + - - +
111B CYS* 3.2 15.7 + - - -
114B PRO* 4.3 7.0 - - + -
116B PHE* 5.1 0.9 - - + -
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Residues in contact with ARG 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ALA 2.8 19.2 + - - +
105B ARG* 3.5 6.7 - - - +
107B VAL* 1.3 77.6 - - - +
109B GLY* 1.3 59.1 + - - +
111B CYS* 3.0 31.2 - - - +
114B PRO* 3.9 13.6 - - + +
116B PHE* 5.0 0.7 - - + -
130B ALA* 2.7 28.2 + - + +
131B PHE* 3.5 45.3 - - + +
133B ASP* 2.6 36.8 + - - -
134B VAL* 3.7 14.5 - - - +
268B VAL* 4.5 8.3 - - - +
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Residues in contact with GLY 109 (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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105B ARG 3.0 15.5 + - - -
106B GLN 3.5 2.0 + - - -
107B VAL 3.2 0.6 - - - -
108B ARG* 1.3 76.0 - - - +
110B ARG* 1.3 65.8 + - - +
111B CYS 3.6 0.9 - - - -
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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
------------------------------------------------------------
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