Contacts of the helix formed by residues 92 - 113 (chain X) in PDB entry 2OU0
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 ASP 92 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90X SER 4.1 0.6 + - - -
91X LEU* 1.3 74.9 - - - +
93X ALA* 1.3 58.9 + - - +
94X VAL* 3.1 16.5 + - - +
95X ARG* 3.0 60.4 + - - +
96X ARG* 2.9 28.5 + - - +
124X LYS* 4.9 2.8 + - - +
126X TRP* 4.8 2.1 - - - -
156X GLY* 4.5 2.9 - - - +
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Residues in contact with ALA 93 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92X ASP* 1.3 74.8 - - - +
94X VAL* 1.3 63.7 + - + +
96X ARG* 3.6 16.1 + - - +
97X ALA* 3.3 19.6 + - - +
158X TRP* 5.1 1.1 - - - -
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Residues in contact with VAL 94 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92X ASP* 3.1 10.2 + - - +
93X ALA* 1.3 76.8 - - + +
95X ARG* 1.3 62.0 + - - +
97X ALA* 3.1 19.8 + - - +
98X ALA 3.4 4.2 + - - -
152X THR* 3.7 15.4 - - + +
156X GLY 3.6 33.0 - - - +
157X THR* 3.7 18.4 - - - +
158X TRP* 3.7 34.5 - - + +
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Residues in contact with ARG 95 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91X LEU* 4.0 14.8 - - + -
92X ASP* 3.0 35.0 + - - +
94X VAL* 1.3 70.9 - - - +
96X ARG* 1.3 65.7 + - - +
98X ALA* 3.1 10.9 + - - +
99X ALA* 3.0 18.9 + - - +
126X TRP* 3.4 57.1 - - - +
152X THR 3.7 14.4 - - - +
153X PHE* 2.7 31.0 + - + +
154X ARG 3.3 14.1 + - - -
155X THR 3.3 24.0 + - - -
156X GLY* 3.6 13.8 - - - -
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Residues in contact with ARG 96 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88X TYR* 3.0 60.6 + - + +
89X ASP* 2.9 35.5 + - - +
91X LEU* 3.0 16.6 + - + +
92X ASP 2.9 23.3 + - - +
93X ALA* 3.6 12.9 - - - +
95X ARG* 1.3 74.9 - - - +
97X ALA* 1.3 57.2 + - - +
99X ALA* 3.3 7.3 + - - +
100X ILE* 2.9 34.3 + - + +
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Residues in contact with ALA 97 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3X ILE* 3.1 33.7 - - + +
6X MET* 4.1 2.5 - - - -
93X ALA 3.3 8.9 + - - +
94X VAL 3.1 12.6 + - - +
96X ARG* 1.3 73.6 - - - +
98X ALA* 1.3 59.9 + - - +
100X ILE* 3.3 6.2 + - + +
101X ASN* 2.8 26.9 + - - +
158X TRP* 3.4 29.2 - - + -
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Residues in contact with ALA 98 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X MET* 3.9 11.3 - - + +
94X VAL 3.4 2.8 + - - -
95X ARG 3.1 10.9 + - - +
97X ALA* 1.3 77.6 - - - +
99X ALA* 1.3 62.2 + - - +
101X ASN* 3.4 4.1 + - - +
102X MET* 3.1 26.9 + - - +
149X VAL* 3.7 10.5 - - + +
152X THR* 4.0 23.1 - - + -
153X PHE* 3.6 28.9 - - + -
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Residues in contact with ALA 99 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78X ILE* 4.2 2.2 - - - -
88X TYR* 4.1 10.5 - - + -
91X LEU* 4.2 3.6 - - + -
95X ARG 3.0 11.4 + - - +
96X ARG 3.3 8.9 + - - +
98X ALA* 1.3 74.3 - - - +
100X ILE* 1.3 64.8 + - - +
102X MET* 3.4 4.9 + - - +
103X VAL* 3.2 25.5 + - - +
153X PHE* 3.4 10.0 - - + -
303X MR3 3.4 42.5 - - + +
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Residues in contact with ILE 100 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3X ILE* 3.8 28.9 - - + -
7X LEU* 4.6 5.2 - - + -
71X VAL* 4.5 6.3 - - + +
74X ALA* 4.1 20.6 - - + -
75X VAL* 3.7 27.6 - - + -
78X ILE* 3.9 11.7 - - + -
88X TYR* 3.6 26.9 - - + +
96X ARG* 2.9 25.6 + - + +
97X ALA* 3.7 10.1 - - - +
99X ALA* 1.3 70.8 - - - +
101X ASN* 1.3 56.9 - - - +
103X VAL* 3.2 3.1 + - - +
104X PHE* 2.8 32.6 + - - +
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Residues in contact with ASN 101 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3X ILE* 3.8 2.4 - - + +
6X MET* 3.4 25.2 - - - +
7X LEU* 3.7 22.6 - - + +
10X ASP* 2.7 25.5 + - - -
97X ALA 2.8 14.2 + - - +
98X ALA* 3.4 11.0 - - - +
100X ILE* 1.3 76.3 - - - +
102X MET* 1.3 62.9 + - - +
104X PHE* 3.2 2.9 + - - +
105X GLN* 3.0 20.8 + - - +
145X ARG* 2.8 32.4 + - - -
149X VAL* 3.7 13.5 - - + +
161X TYR* 3.7 2.2 + - - -
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Residues in contact with MET 102 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98X ALA 3.1 14.1 + - - +
99X ALA 3.6 8.1 - - - +
100X ILE 3.3 0.2 - - - -
101X ASN* 1.3 78.1 + - - +
103X VAL* 1.3 56.6 + - - +
105X GLN* 3.2 7.2 + - - +
106X MET* 2.9 64.3 + - + +
111X VAL* 3.7 12.6 - - + -
114X PHE* 4.0 21.1 - - + -
133X LEU* 4.1 9.4 - - + -
138X TRP* 3.8 29.2 - - + -
149X VAL* 3.8 13.5 - - + -
153X PHE* 3.7 22.2 - - - -
303X MR3 3.8 13.9 - - - -
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Residues in contact with VAL 103 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74X ALA* 4.0 27.6 - - + +
77X GLY* 6.0 0.2 - - - -
78X ILE* 3.6 24.7 - - + -
84X LEU* 4.1 13.7 - - + -
99X ALA 3.2 11.8 + - - +
100X ILE 3.2 7.0 + - - +
102X MET* 1.3 71.2 - - - +
104X PHE* 1.3 64.1 + - - +
107X GLY* 2.8 27.1 + - - +
108X GLU* 4.0 23.6 - - + +
111X VAL* 3.8 20.4 - - + -
303X MR3 4.3 2.9 - - + -
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Residues in contact with PHE 104 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7X LEU* 3.7 25.6 - - + -
11X GLU* 3.6 34.5 - - + -
29X ILE 3.4 18.6 - - - -
30X GLY 3.5 21.0 - - - +
67X PHE* 4.1 20.0 - + - -
70X ASP* 3.5 42.8 - - + -
71X VAL* 4.2 3.8 - - + -
74X ALA* 4.4 9.5 - - + +
100X ILE 2.8 16.9 + - - +
101X ASN 3.3 9.4 - - - +
103X VAL* 1.3 74.3 - - - +
105X GLN* 1.3 60.4 + - - +
107X GLY 4.6 0.7 + - - -
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Residues in contact with GLN 105 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11X GLU* 4.6 2.7 - - - +
21X THR* 5.1 3.6 + - - +
101X ASN* 3.0 15.5 + - - +
102X MET* 3.2 4.9 + - - +
104X PHE* 1.3 83.6 - - - +
106X MET* 1.3 61.4 + - + +
107X GLY 3.7 0.2 - - - -
138X TRP* 2.9 30.6 + - - -
142X THR* 3.2 35.2 + - - +
145X ARG* 3.2 42.1 + - - +
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Residues in contact with MET 106 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102X MET* 2.9 49.1 + - + +
105X GLN* 1.3 77.8 - - + +
107X GLY* 1.3 64.9 + - - +
110X GLY* 4.1 12.8 + - - -
111X VAL* 3.3 26.2 - - + +
114X PHE* 3.6 25.1 - - - -
138X TRP* 3.6 38.8 - - + +
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Residues in contact with GLY 107 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103X VAL* 2.8 21.2 + - - -
104X PHE 4.6 0.8 + - - -
105X GLN 3.7 0.6 - - - -
106X MET* 1.3 84.1 - - - +
108X GLU* 1.3 65.9 + - - -
109X THR 3.3 3.1 - - - -
110X GLY 3.3 0.7 + - - -
111X VAL* 3.2 19.9 + - - +
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Residues in contact with GLU 108 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77X GLY* 3.0 35.7 - - - +
80X ARG* 5.2 1.2 - - - +
81X ASN* 2.7 31.7 + - - +
84X LEU* 3.8 19.4 - - + +
103X VAL* 4.0 19.7 - - + +
107X GLY* 1.3 69.7 - - - -
109X THR* 1.3 68.1 + - - +
111X VAL 4.5 0.2 - - - +
112X ALA* 3.0 30.5 + - - +
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Residues in contact with THR 109 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81X ASN* 5.6 1.3 - - - +
107X GLY 3.3 0.8 - - - -
108X GLU* 1.3 80.6 - - - +
110X GLY* 1.3 66.7 + - - +
112X ALA* 3.3 14.0 + - + +
113X GLY* 3.3 9.4 + - - -
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Residues in contact with GLY 110 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106X MET* 4.1 21.6 + - - -
107X GLY 3.3 8.8 + - - -
109X THR* 1.3 80.7 - - - +
111X VAL* 1.3 60.0 + - - +
113X GLY* 3.4 9.0 + - - -
114X PHE* 3.4 15.1 - - - -
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Residues in contact with VAL 111 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84X LEU* 4.0 5.8 - - + -
102X MET* 3.7 9.6 - - + -
103X VAL* 3.7 28.3 - - + +
106X MET* 3.3 27.8 - - + -
107X GLY 3.2 10.7 + - - +
108X GLU 4.0 3.6 - - - +
110X GLY* 1.3 71.2 - - - +
112X ALA* 1.3 59.4 + - - +
113X GLY 3.1 4.7 - - - -
114X PHE* 2.9 33.8 + - + +
118X LEU* 3.9 5.8 - - + +
303X MR3 3.6 42.8 - - + -
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Residues in contact with ALA 112 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81X ASN* 4.3 17.0 - - - +
83X LYS* 4.0 23.4 - - + +
84X LEU* 3.8 19.0 - - + +
108X GLU 3.0 19.5 + - - +
109X THR* 3.3 7.1 + - + +
111X VAL* 1.3 75.9 - - - +
113X GLY* 1.3 56.0 + - - +
114X PHE 3.2 2.8 + - - -
115X THR* 3.6 11.6 + - - -
118X LEU* 3.9 10.5 - - - +
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Residues in contact with GLY 113 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109X THR 3.3 10.8 + - - -
110X GLY 3.4 5.1 + - - -
111X VAL 3.1 1.6 - - - -
112X ALA* 1.3 73.3 - - - +
114X PHE* 1.3 59.8 + - - +
115X THR* 3.1 16.4 + - - -
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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
------------------------------------------------------------
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