Contacts of the helix formed by residues 92 - 109 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93C PRO* 5.4 1.8 - - - +
154C ASP 3.4 24.8 - - - +
155C THR* 2.7 23.1 + - - -
156C LYS 4.4 0.5 + - - -
157C TRP* 3.8 15.2 + - - -
89D PRO* 3.9 7.3 - - + +
90D SER 3.3 14.6 - - - +
91D LEU* 1.3 80.0 - - - +
93D PRO* 1.3 73.6 - - - +
94D GLN* 3.2 3.4 - - - -
95D LEU* 3.1 18.6 + - + +
96D ALA* 2.9 18.4 + - - +
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Residues in contact with PRO 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LEU* 4.2 39.0 - - + -
92C GLU* 5.5 2.5 - - - +
93C PRO* 5.1 12.8 - - + -
38D PHE* 4.5 9.4 - - + -
40D ILE* 5.2 0.2 - - + -
91D LEU* 3.2 8.2 - - + +
92D GLU* 1.3 88.9 - - - +
94D GLN* 1.3 54.3 + - + +
96D ALA* 3.2 6.7 + - + +
97D HIS* 2.7 54.2 + - + +
157D TRP* 4.5 11.2 - - + +
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Residues in contact with GLN 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D GLU* 3.2 1.5 - - - -
93D PRO* 1.3 81.2 - - + +
95D LEU* 1.3 63.3 + - - +
97D HIS* 3.2 15.3 + - + +
98D ASP* 3.1 33.6 + - - +
157D TRP* 5.5 17.5 + - + +
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Residues in contact with LEU 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C ASP* 3.6 34.1 - - + +
89D PRO* 3.8 15.5 - - + -
92D GLU* 3.1 20.1 + - + +
94D GLN* 1.3 78.4 - - - +
96D ALA* 1.3 63.8 + - - +
98D ASP* 3.1 12.7 + - + +
99D ARG* 2.9 54.5 + - + +
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Residues in contact with ALA 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D PHE* 3.8 27.4 - - + -
88D LEU* 4.0 10.5 - - + -
89D PRO* 3.9 25.1 - - + +
91D LEU 4.6 0.7 - - - +
92D GLU 2.9 12.3 + - - +
93D PRO* 3.4 8.5 - - + +
95D LEU* 1.3 77.7 - - - +
97D HIS* 1.3 63.8 + - + +
99D ARG* 3.2 3.5 + - - +
100D ILE* 2.9 31.6 + - + +
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Residues in contact with HIS 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LEU* 5.8 0.2 - - - +
38D PHE* 5.0 9.1 - + - -
93D PRO* 2.7 37.7 + - + +
94D GLN* 3.2 12.8 + - + +
96D ALA* 1.3 75.2 - - + +
98D ASP* 1.3 58.5 + - - +
100D ILE* 3.3 4.5 + - + -
101D THR* 3.0 24.9 + - - -
122D SER* 5.1 8.2 + - - -
123D VAL* 6.3 0.2 - - - -
125D TYR* 4.3 10.7 - + - -
126D PRO* 3.3 30.7 - - + +
129D ARG* 3.1 23.9 + - - +
157D TRP* 3.6 57.6 + + + +
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Residues in contact with ASP 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D GLN* 3.1 23.0 + - - +
95D LEU* 3.1 14.5 + - + +
97D HIS* 1.3 74.8 - - - +
99D ARG* 1.3 66.0 + - - +
101D THR* 3.3 2.2 + - - -
102D GLU* 3.0 26.0 + - - +
129D ARG* 3.0 23.7 + - - +
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Residues in contact with ARG 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B PRO* 3.8 29.4 - - - +
154C ASP* 2.8 31.9 + - - -
86D VAL* 3.7 18.1 - - + +
87D ILE* 2.8 35.7 + - - +
88D LEU* 4.0 1.0 - - + -
89D PRO* 3.7 17.9 - - + +
95D LEU* 2.9 42.2 + - + +
96D ALA* 3.2 10.7 + - - +
98D ASP* 1.3 75.9 - - - +
100D ILE* 1.3 57.0 + - - +
102D GLU* 3.5 4.9 + - - +
103D ALA* 3.1 29.8 + - - +
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Residues in contact with ILE 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LEU* 4.9 0.2 - - - +
36D VAL* 3.4 34.1 - - + -
38D PHE* 4.9 5.2 - - + -
86D VAL* 4.0 10.6 - - + +
88D LEU* 3.9 17.0 - - + -
96D ALA* 2.9 27.0 + - + +
97D HIS* 3.5 8.1 - - + +
98D ASP 3.2 0.2 - - - -
99D ARG* 1.3 74.0 - - - +
101D THR* 1.3 65.0 + - - +
103D ALA* 3.4 2.3 + - - +
104D ALA* 2.9 22.9 + - - +
123D VAL* 4.4 8.7 - - + +
126D PRO* 3.8 28.0 - - + -
127D LEU* 3.3 29.7 - - + +
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Residues in contact with THR 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D HIS 3.0 9.9 + - - -
98D ASP* 3.8 3.6 - - - -
100D ILE* 1.3 75.1 - - - +
102D GLU* 1.3 59.2 + - - +
104D ALA* 3.2 4.6 + - - +
105D ARG* 2.9 53.7 + - - +
126D PRO 2.7 21.9 + - - +
129D ARG* 2.9 49.8 + - + +
130D ALA* 3.9 6.7 - - - +
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Residues in contact with GLU 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ASP 3.0 18.0 + - - +
99D ARG* 3.8 5.4 - - - +
101D THR* 1.3 77.6 - - - +
103D ALA* 1.3 63.2 + - - +
105D ARG* 3.2 23.2 + - - +
106D GLN* 2.6 60.1 + - - +
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Residues in contact with ALA 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D PRO* 4.8 7.0 - - + -
34D LEU* 3.8 13.2 - - + -
86D VAL* 3.7 27.8 - - + -
99D ARG 3.1 18.0 + - - +
100D ILE 3.9 0.4 - - - +
102D GLU* 1.3 77.3 - - - +
104D ALA* 1.3 62.2 + - - +
106D GLN* 3.3 16.0 + - - +
107D VAL* 3.0 28.8 + - - +
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Residues in contact with ALA 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LEU* 3.9 2.0 - - - +
100D ILE 2.9 17.7 + - - +
101D THR* 3.4 6.7 - - - +
103D ALA* 1.3 78.2 - - - +
105D ARG* 1.3 57.0 + - - +
107D VAL* 3.8 0.9 - - - +
108D ARG* 2.9 33.6 + - - +
116D PHE* 3.9 31.4 - - + -
127D LEU* 4.1 13.0 - - + +
130D ALA* 3.6 18.4 - - + -
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Residues in contact with ARG 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D THR* 2.9 32.4 + - - +
102D GLU* 3.2 23.9 + - - +
104D ALA* 1.3 77.5 - - - +
106D GLN* 1.3 62.2 + - + +
108D ARG* 3.4 4.4 + - - +
109D GLY* 3.2 18.9 + - - -
129D ARG* 4.5 10.1 + - - +
130D ALA* 3.8 23.2 - - + +
132D ALA* 6.1 1.6 - - - +
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Residues in contact with GLN 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D PRO* 3.3 35.0 - - - +
24D ASP* 3.8 23.5 + - + +
102D GLU* 2.6 46.4 + - - +
103D ALA* 3.6 11.8 - - - +
105D ARG* 1.3 77.2 - - + +
107D VAL* 1.3 61.9 + - - +
109D GLY* 3.3 9.2 + - - -
110D ARG* 2.7 33.0 + - - +
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Residues in contact with VAL 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D PRO* 4.2 10.1 - - + -
27D TRP* 4.2 7.6 - - + -
32D ALA* 3.6 31.2 - - + +
34D LEU* 4.2 23.1 - - + -
83D ALA* 3.8 26.7 - - + -
103D ALA 3.0 21.6 + - - +
104D ALA* 4.0 3.1 - - - +
106D GLN* 1.3 73.7 - - - +
108D ARG* 1.3 67.0 + - - +
110D ARG* 3.1 12.6 + - - +
111D CYS* 3.3 16.5 + - - +
114D PRO* 4.2 11.0 - - + -
116D PHE* 5.1 1.3 - - + -
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Residues in contact with ARG 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D ALA 2.9 19.5 + - - +
105D ARG* 3.7 6.5 - - - +
107D VAL* 1.3 77.2 - - - +
109D GLY* 1.3 58.7 + - - +
111D CYS* 3.1 27.7 - - - +
112D ARG 5.9 1.1 - - - -
114D PRO* 3.8 16.1 - - + +
116D PHE* 5.1 0.2 - - + -
130D ALA 2.7 28.7 + - - +
131D PHE* 3.3 44.6 - - + +
133D ASP* 2.6 37.3 + - - -
134D VAL* 3.6 14.5 - - - +
268D VAL* 4.5 7.5 - - - +
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Residues in contact with GLY 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D ARG 3.2 13.1 + - - -
106D GLN 3.3 3.8 + - - -
107D VAL 3.1 0.8 - - - -
108D ARG* 1.3 77.8 - - - +
110D ARG* 1.3 64.3 + - - +
111D CYS 3.7 0.7 - - - -
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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