Contacts of the helix formed by residues 92 - 109 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A PRO* 5.5 1.4 - - - +
154A ASP 3.3 24.6 - - - +
155A THR* 2.7 22.4 + - - -
156A LYS 4.5 0.9 + - - -
157A TRP* 4.0 14.2 + - - -
89F PRO* 3.9 11.1 - - + +
90F SER 3.3 14.6 - - - +
91F LEU* 1.3 80.5 - - - +
93F PRO* 1.3 72.1 - - - +
94F GLN* 3.2 3.4 - - - -
95F LEU* 3.1 15.8 + - + +
96F ALA* 3.0 17.8 + - - +
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Residues in contact with PRO 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 4.2 31.9 - - + -
92A GLU* 5.5 1.1 - - - +
93A PRO* 5.1 13.0 - - + -
38F PHE* 4.6 10.5 - - + -
40F ILE* 5.3 0.4 - - + -
91F LEU* 3.2 7.4 - - + +
92F GLU* 1.3 88.9 - - - +
94F GLN* 1.3 58.3 + - + +
96F ALA* 3.5 6.4 - - + +
97F HIS* 2.9 45.4 + - - +
157F TRP* 4.2 21.8 - - + +
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Residues in contact with GLN 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F GLU 3.2 1.0 - - - -
93F PRO* 1.3 81.6 - - + +
95F LEU* 1.3 63.1 + - - +
97F HIS* 3.3 12.8 + - + +
98F ASP* 3.1 37.8 + - - +
157F TRP* 4.7 20.1 + - + +
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Residues in contact with LEU 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ASP* 3.7 32.5 - - + +
89F PRO* 3.8 15.0 - - + -
92F GLU* 3.1 20.4 + - + +
94F GLN* 1.3 76.1 - - - +
96F ALA* 1.3 67.5 + - - +
98F ASP* 3.2 11.7 + - + +
99F ARG* 3.0 50.7 + - + +
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Residues in contact with ALA 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F PHE* 3.8 32.1 - - + -
88F LEU* 4.1 7.0 - - + -
89F PRO* 3.9 23.3 - - + +
91F LEU 4.7 0.2 - - - +
92F GLU 3.0 11.9 + - - +
93F PRO 3.5 7.9 - - - +
95F LEU* 1.3 77.3 - - - +
97F HIS* 1.3 63.7 + - + +
99F ARG* 3.2 4.1 + - - +
100F ILE* 2.9 31.9 + - + +
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Residues in contact with HIS 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 6.0 0.2 - - - +
38F PHE* 4.9 9.7 - + - -
93F PRO* 2.9 33.2 + - + +
94F GLN* 3.4 11.3 - - - +
95F LEU 3.2 0.2 - - - -
96F ALA* 1.3 81.2 - - + +
98F ASP* 1.3 58.1 + - - +
100F ILE* 3.2 4.4 + - + -
101F THR* 2.9 27.0 + - - -
122F SER* 4.9 10.5 + - - -
125F TYR* 4.3 12.4 - + + -
126F PRO* 3.3 31.6 - - + +
129F ARG* 3.1 21.9 + - - +
157F TRP* 3.7 52.4 + + + +
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Residues in contact with ASP 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F GLN* 3.1 26.4 + - - +
95F LEU* 3.7 14.5 - - + +
97F HIS* 1.3 75.1 - - - +
99F ARG* 1.3 58.5 + - + +
101F THR* 3.9 2.2 - - - -
102F GLU* 3.0 29.1 + - - +
105F ARG* 5.7 0.2 + - - -
129F ARG* 3.2 23.4 + - - +
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Residues in contact with ARG 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ASP* 2.7 32.9 + - - -
4C PRO* 3.5 32.7 - - - +
86F VAL* 3.8 15.2 - - + +
87F ILE* 3.1 27.0 + - - +
88F LEU 4.0 1.0 - - - -
89F PRO* 3.8 21.4 - - - +
95F LEU* 3.0 45.1 + - + +
96F ALA* 3.7 5.4 - - - +
98F ASP* 1.3 73.9 - - + +
100F ILE* 1.3 65.9 + - - +
102F GLU* 3.5 5.4 + - - +
103F ALA* 3.0 26.0 + - - +
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Residues in contact with ILE 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F VAL* 3.4 33.0 - - + -
38F PHE* 5.0 5.4 - - + -
86F VAL* 4.0 11.7 - - + +
88F LEU* 4.0 16.4 - - + -
96F ALA* 2.9 27.4 + - + +
97F HIS* 3.5 7.0 - - + +
99F ARG* 1.3 75.2 - - - +
101F THR* 1.3 60.9 + - - +
103F ALA* 3.3 1.2 + - - +
104F ALA* 2.9 29.1 + - - +
123F VAL* 4.4 9.6 - - + +
126F PRO* 3.7 28.9 - - + -
127F LEU* 3.4 28.8 - - + +
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Residues in contact with THR 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F HIS 2.9 10.9 + - - -
98F ASP* 3.9 3.6 - - - -
100F ILE* 1.3 76.9 - - - +
102F GLU* 1.3 56.3 + - - +
104F ALA* 3.2 3.8 + - - +
105F ARG* 2.8 63.7 + - - +
126F PRO 2.5 25.1 + - - +
129F ARG* 2.9 45.4 + - + +
130F ALA* 3.9 6.2 - - - +
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Residues in contact with GLU 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98F ASP 3.0 18.1 + - - +
99F ARG* 3.8 6.5 - - - +
101F THR* 1.3 77.5 - - - +
103F ALA* 1.3 62.7 + - - +
105F ARG* 3.3 25.8 + - - +
106F GLN* 3.1 56.8 + - - +
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Residues in contact with ALA 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F PRO* 4.5 9.4 - - + +
34F LEU* 3.8 13.0 - - + -
86F VAL* 3.7 27.8 - - + -
99F ARG 3.0 17.9 + - - +
100F ILE 3.8 0.2 - - - +
102F GLU* 1.3 76.0 - - - +
104F ALA* 1.3 63.7 + - - +
106F GLN* 3.2 14.8 + - - +
107F VAL* 3.0 27.9 + - - +
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Residues in contact with ALA 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F LEU* 3.9 9.3 - - - +
100F ILE 2.9 18.4 + - - +
101F THR* 3.5 5.8 - - - +
103F ALA* 1.3 77.4 - - - +
105F ARG* 1.3 56.3 + - - +
107F VAL* 4.0 0.7 - - - +
108F ARG* 2.9 34.1 + - - +
116F PHE* 3.9 24.0 - - + -
127F LEU* 3.9 15.9 - - + +
130F ALA* 3.7 15.9 - - + -
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Residues in contact with ARG 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F THR* 2.8 40.2 + - - +
102F GLU* 3.3 32.8 + - - +
104F ALA* 1.3 77.6 - - - +
106F GLN* 1.3 65.0 + - + +
108F ARG* 3.6 4.8 - - - +
109F GLY* 3.0 20.3 + - - -
129F ARG* 4.4 12.7 + - - +
130F ALA* 3.6 21.0 - - + +
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Residues in contact with GLN 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F PRO* 3.3 33.6 - - - +
24F ASP* 3.5 26.7 + - + +
102F GLU* 3.1 41.6 + - - +
103F ALA* 3.6 9.4 - - - +
105F ARG* 1.3 77.5 - - + +
107F VAL* 1.3 63.5 + - - +
109F GLY* 3.3 8.0 + - - -
110F ARG* 2.9 34.0 + - - +
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Residues in contact with VAL 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F PRO* 4.3 12.6 - - + -
27F TRP* 4.2 9.1 - - + -
32F ALA* 3.8 30.3 - - + +
34F LEU* 4.1 22.4 - - + -
83F ALA* 3.7 26.7 - - + -
103F ALA 3.0 19.0 + - - +
104F ALA* 4.0 3.6 - - - +
106F GLN* 1.3 72.3 - - - +
108F ARG* 1.3 67.4 + - - +
110F ARG* 2.9 13.7 + - - +
111F CYS* 3.3 11.4 + - - +
114F PRO* 4.2 17.0 - - + -
116F PHE* 4.9 2.0 - - + -
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Residues in contact with ARG 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F ALA 2.9 19.5 + - - +
105F ARG* 3.6 6.1 - - - +
107F VAL* 1.3 78.3 - - - +
109F GLY* 1.3 57.2 + - - +
110F ARG 3.2 0.2 - - - -
111F CYS* 3.2 26.6 - - - +
112F ARG 6.0 0.9 - - - -
114F PRO* 3.6 24.4 - - + +
116F PHE* 4.9 0.4 - - + -
130F ALA 3.0 26.3 + - - +
131F PHE* 3.5 34.9 - - + +
133F ASP* 2.6 33.7 + - - -
134F VAL* 3.6 17.8 - - - +
268F VAL* 4.4 10.1 - - - +
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Residues in contact with GLY 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F ARG 3.0 13.9 + - - -
106F GLN 3.3 3.3 + - - -
107F VAL 3.1 0.8 - - - -
108F ARG* 1.3 76.2 - - - +
110F ARG* 1.3 69.1 + - - +
111F CYS 4.9 0.4 - - - -
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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