Contacts of the helix formed by residues 92 - 110 (chain C) in PDB entry 1WOH
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C PRO* 3.9 11.2 - - + +
90C SER 3.3 14.1 - - - +
91C LEU* 1.3 80.2 - - - +
93C PRO* 1.3 73.5 - - - +
94C GLN 3.3 2.7 - - - -
95C LEU* 3.1 15.6 + - + +
96C ALA* 3.1 17.2 + - - +
93D PRO* 5.4 2.3 - - - +
154D ASP 3.4 24.5 - - - +
155D THR* 3.0 20.9 + - - -
156D LYS 4.5 0.9 + - - -
157D TRP* 4.2 12.6 + - - -
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Residues in contact with PRO 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C PHE* 4.8 7.4 - - + -
40C ILE* 5.3 0.2 - - + -
91C LEU* 3.3 6.3 - - + +
92C GLU* 1.3 87.6 - - - +
94C GLN* 1.3 58.3 + - + +
96C ALA* 3.2 7.0 + - + +
97C HIS* 2.9 44.3 + - - +
157C TRP* 4.3 25.1 - - + +
91D LEU* 4.4 31.2 - - + -
92D GLU* 5.4 1.8 - - - +
93D PRO* 4.9 15.7 - - + -
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Residues in contact with GLN 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C GLU 3.2 1.6 + - - -
93C PRO* 1.3 79.1 - - - +
95C LEU* 1.3 63.4 + - - +
97C HIS* 3.2 12.9 + - + +
98C ASP* 3.0 38.2 + - - +
157C TRP* 5.4 10.4 - - + +
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Residues in contact with LEU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C PRO* 3.8 16.6 - - + -
92C GLU* 3.1 20.9 + - + +
94C GLN* 1.3 77.4 - - - +
96C ALA* 1.3 67.3 + - - +
98C ASP* 3.2 10.5 + - + +
99C ARG* 2.9 55.9 + - + +
154D ASP* 3.7 33.0 - - + +
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Residues in contact with ALA 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C PHE* 3.8 28.7 - - + -
88C LEU* 4.1 11.2 - - + -
89C PRO* 4.0 22.4 - - + +
92C GLU 3.1 12.6 + - - +
93C PRO 3.4 8.3 - - - +
95C LEU* 1.3 77.9 - - - +
97C HIS* 1.3 57.1 + - + +
99C ARG* 3.2 3.1 + - - +
100C ILE* 2.9 37.8 + - + +
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Residues in contact with HIS 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C PHE* 4.9 10.7 - + - -
93C PRO* 2.9 30.7 + - + +
94C GLN* 3.3 12.1 - - + +
96C ALA* 1.3 79.9 - - + +
98C ASP* 1.3 63.7 + - - +
100C ILE* 3.2 5.0 + - + -
101C THR* 2.9 20.4 + - - -
122C SER* 4.9 9.9 + - - -
123C VAL* 6.2 0.2 - - - -
125C TYR* 4.2 15.6 - + - -
126C PRO* 3.4 29.7 - - + +
129C ARG* 3.2 21.9 + - - +
157C TRP* 3.6 50.9 + + + +
91D LEU* 5.9 0.2 - - - +
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Residues in contact with ASP 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C GLN* 3.0 38.1 + - - +
95C LEU* 3.2 12.6 + - + +
97C HIS* 1.3 75.6 - - - +
99C ARG* 1.3 63.9 + - + +
101C THR* 3.3 2.3 + - - -
102C GLU* 3.0 24.8 + - - +
129C ARG* 3.2 22.0 + - - +
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Residues in contact with ARG 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C VAL* 3.8 13.3 - - + +
87C ILE* 3.0 29.0 + - - +
88C LEU 4.0 1.0 - - - -
89C PRO* 3.7 22.7 - - - +
95C LEU* 2.9 44.2 + - + +
96C ALA* 3.7 4.9 - - - +
98C ASP* 1.3 76.1 - - + +
100C ILE* 1.3 62.4 + - - +
102C GLU* 3.9 5.1 - - - +
103C ALA* 3.0 27.2 + - - +
154D ASP* 2.8 31.3 + - - -
4F PRO* 3.7 30.5 - - - +
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Residues in contact with ILE 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C VAL* 3.5 34.8 - - + -
38C PHE* 5.0 4.9 - - + -
86C VAL* 3.9 11.0 - - + +
88C LEU* 4.0 15.7 - - + -
96C ALA* 2.9 30.0 + - + +
97C HIS* 3.5 7.9 - - + +
99C ARG* 1.3 76.7 - - - +
101C THR* 1.3 62.7 + - - +
103C ALA* 4.0 1.2 - - - +
104C ALA* 3.0 22.7 + - - +
123C VAL* 4.4 8.3 - - + +
126C PRO* 3.7 28.3 - - + -
127C LEU* 3.3 30.0 - - + +
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Residues in contact with THR 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C HIS 2.9 10.2 + - - -
98C ASP* 3.8 4.0 - - - -
100C ILE* 1.3 77.5 - - - +
102C GLU* 1.3 62.5 + - - +
104C ALA* 3.3 4.3 + - - +
105C ARG* 3.0 50.3 + - - +
126C PRO 2.5 25.6 + - - +
129C ARG* 3.0 45.2 + - + +
130C ALA* 4.0 7.6 - - - +
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Residues in contact with GLU 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ASP 3.0 17.5 + - - +
99C ARG* 3.9 5.6 - - - +
101C THR* 1.3 77.3 - - - +
103C ALA* 1.3 62.1 + - - +
105C ARG* 2.8 29.2 + - - +
106C GLN* 2.6 56.0 + - - +
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Residues in contact with ALA 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PRO* 4.1 13.8 - - + +
34C LEU* 3.9 9.9 - - + -
86C VAL* 3.9 25.8 - - + -
99C ARG 3.0 19.0 + - - +
100C ILE 4.0 0.2 - - - +
102C GLU* 1.3 76.4 - - - +
104C ALA* 1.3 63.0 + - - +
106C GLN* 3.4 13.2 + - - +
107C VAL* 3.0 27.9 + - - +
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Residues in contact with ALA 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 3.9 9.1 - - + +
100C ILE 3.0 19.0 + - - +
101C THR* 3.6 4.9 - - - +
103C ALA* 1.3 78.8 - - - +
105C ARG* 1.3 57.3 + - - +
107C VAL* 3.4 1.8 + - - +
108C ARG* 2.9 32.7 + - - +
116C PHE* 3.9 24.7 - - + -
127C LEU* 4.1 13.9 - - + +
130C ALA* 3.8 15.9 - - + -
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Residues in contact with ARG 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C THR* 3.0 32.8 + - - +
102C GLU* 2.8 43.4 + - - +
103C ALA 3.3 0.2 - - - -
104C ALA* 1.3 75.8 - - - +
106C GLN* 1.3 64.1 + - + +
108C ARG* 3.3 6.1 + - - +
109C GLY* 3.0 20.6 + - - -
129C ARG* 4.9 4.8 + - - +
130C ALA* 3.8 25.6 - - + +
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Residues in contact with GLN 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C PRO* 3.5 22.9 - - - +
24C ASP* 3.8 24.3 - - + +
102C GLU* 2.6 51.1 + - - +
103C ALA* 3.7 13.4 - - - +
105C ARG* 1.3 76.2 - - + +
107C VAL* 1.3 65.1 + - - +
109C GLY* 3.6 0.6 + - - -
110C ARG* 2.9 42.8 + - - +
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Residues in contact with VAL 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PRO* 4.0 13.9 - - + -
27C TRP* 4.0 8.5 - - + -
32C ALA* 3.6 35.7 - - + +
34C LEU* 4.4 18.4 - - + -
83C ALA* 3.8 25.8 - - + -
103C ALA 3.0 19.2 + - - +
104C ALA* 3.9 5.6 - - - +
106C GLN* 1.3 76.5 - - - +
108C ARG* 1.3 64.3 + - - +
110C ARG* 3.0 13.3 + - - +
111C CYS* 3.2 16.3 + - - +
114C PRO* 4.3 7.6 - - + -
116C PHE* 5.0 1.6 - - + -
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Residues in contact with ARG 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C ALA 2.9 19.6 + - - +
105C ARG* 3.5 7.9 - - - +
107C VAL* 1.3 77.8 - - - +
109C GLY* 1.3 58.3 + - - +
110C ARG 3.1 0.2 + - - -
111C CYS* 3.0 30.8 - - - +
112C ARG 6.0 0.4 - - - -
114C PRO* 3.7 21.5 - - + +
116C PHE* 4.8 0.4 - - + -
130C ALA 2.9 22.0 + - - +
131C PHE* 3.4 40.4 - - + +
133C ASP* 2.6 36.0 + - - -
134C VAL* 3.9 14.8 - - - +
268C VAL* 4.3 11.7 + - - +
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Residues in contact with GLY 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C GLN* 5.8 1.0 - - - +
105C ARG 3.0 15.7 + - - -
106C GLN 3.6 2.4 + - - -
107C VAL 3.3 0.4 - - - -
108C ARG* 1.3 75.8 - - - +
110C ARG* 1.3 64.0 + - - +
111C CYS 4.7 0.8 - - - +
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Residues in contact with ARG 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PRO 3.3 16.2 + - - -
24C ASP* 3.3 29.5 + - - +
25C GLY 2.8 19.4 + - - -
27C TRP* 3.5 46.8 - - + +
28C GLN* 3.3 16.1 - - + +
29C ALA 3.3 20.8 + - - +
106C GLN* 2.9 32.8 + - - +
107C VAL 3.0 3.7 + - - +
109C GLY* 1.3 82.8 - - - +
111C CYS* 1.3 57.8 + - - +
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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
------------------------------------------------------------
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