Contacts of the helix formed by residues 98 - 112 (chain E) in PDB entry 1O95
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 ILE 98 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96E ASP* 3.0 7.9 + - - +
97E ALA* 1.3 79.1 - - + +
99E VAL* 1.3 70.3 + - + +
100E VAL 3.0 0.7 - - - -
101E GLY 3.0 9.7 + - - -
102E ARG* 3.1 7.8 + - - +
129E SER* 5.2 2.9 - - - -
133E SER* 3.5 20.2 + - - +
137E TYR* 3.5 25.0 - - + +
226E MET* 4.3 27.8 - - + -
104F SER 4.3 1.6 - - - +
107F ALA* 3.3 38.6 - - + +
108F SER* 3.9 13.9 - - - +
114F PHE* 4.0 17.3 - - + -
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Residues in contact with VAL 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E SER* 3.3 24.2 - - - +
96E ASP* 2.4 44.5 + - - +
98E ILE* 1.3 71.9 - - + +
100E VAL* 1.3 61.3 + - - +
102E ARG* 3.2 7.8 + - + +
103E ILE* 3.0 21.1 + - + +
137E TYR* 5.8 0.4 - - - -
219E ASP 4.4 3.8 - - - +
220E VAL* 3.7 28.5 - - + -
221E GLY 4.1 2.0 - - - +
224E GLN* 4.0 35.0 - - + +
225E SER* 4.2 2.2 - - - +
226E MET* 5.8 1.3 - - - -
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Residues in contact with VAL 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E VAL* 4.9 10.5 - - + -
95E SER* 4.3 17.5 - - - +
96E ASP 2.7 21.2 + - - +
97E ALA* 4.3 2.0 - - - +
98E ILE 3.0 0.4 - - - -
99E VAL* 1.3 75.0 - - - +
101E GLY* 1.3 66.5 + - - +
102E ARG 3.1 0.2 + - - -
103E ILE* 3.1 6.8 + - - +
104E LEU* 2.8 48.3 + - + +
130E THR* 3.6 13.2 - - + +
1237E AMP 3.5 43.7 - - + +
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Residues in contact with GLY 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E ALA 3.9 4.4 + - - -
98E ILE 3.0 8.9 + - - -
100E VAL* 1.3 77.6 - - - +
102E ARG* 1.3 59.2 + - - +
104E LEU* 3.3 3.0 + - - +
105E THR* 2.7 37.5 + - - -
130E THR* 4.1 2.2 - - - +
133E SER* 3.8 14.1 - - - -
134E VAL* 3.7 23.3 - - - -
137E TYR* 4.1 2.2 - - - -
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Residues in contact with ARG 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E ILE 3.1 6.6 + - - +
99E VAL* 3.8 9.4 - - + +
100E VAL 3.1 0.6 - - - -
101E GLY* 1.3 78.3 - - - +
103E ILE* 1.3 68.1 + - + +
105E THR* 3.2 6.4 + - - -
106E GLU* 3.1 43.5 + - - +
137E TYR* 3.3 50.0 - - + +
214E GLY 5.4 1.4 + - - -
215E LEU* 3.5 32.5 - - + +
219E ASP* 4.2 20.4 + - + +
220E VAL* 6.4 0.7 - - + -
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Residues in contact with ILE 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E VAL* 3.6 34.5 - - + -
87E VAL* 3.7 18.4 - - + -
92E ALA* 5.0 4.7 - - + -
95E SER* 3.9 15.7 - - - +
99E VAL* 3.0 14.7 + - + +
100E VAL* 3.8 6.3 - - - +
102E ARG* 1.3 75.9 - - + +
104E LEU* 1.3 64.9 + - - +
106E GLU* 2.8 14.6 + - - +
107E VAL* 3.2 7.1 + - - +
210E LEU* 4.6 7.9 - - + -
213E ILE* 4.2 8.7 - - + +
215E LEU* 4.3 13.0 - - + -
220E VAL* 3.0 41.7 - - + -
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Residues in contact with LEU 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E LEU* 5.8 0.4 - - + -
6E ALA* 4.3 16.2 - - + -
62E VAL* 4.4 20.6 - - + -
64E VAL* 4.7 8.3 - - + +
87E VAL* 6.3 0.2 - - - -
100E VAL* 2.8 47.2 + - + +
101E GLY 3.4 3.6 - - - +
103E ILE* 1.3 72.7 - - - +
105E THR* 1.3 65.2 + - - +
107E VAL* 2.8 10.3 + - + +
108E ILE* 2.7 32.5 + - + +
130E THR* 3.6 18.8 - - + -
134E VAL* 3.6 19.1 - - + -
1237E AMP 4.0 23.8 - - + +
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Residues in contact with THR 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E GLY 2.7 24.4 + - - -
102E ARG* 3.5 6.5 - - - -
103E ILE 3.0 0.2 + - - -
104E LEU* 1.3 72.9 - - - +
106E GLU* 1.3 64.0 + - - +
108E ILE* 2.7 25.4 + - - +
109E LYS* 2.9 30.4 + - - +
134E VAL* 3.2 24.3 + - - +
137E TYR* 3.5 16.8 - - + +
138E LEU* 3.8 30.1 - - + +
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Residues in contact with GLU 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E ARG* 3.1 36.3 + - - +
103E ILE 2.8 7.7 + - - +
105E THR* 1.3 80.5 - - - +
107E VAL* 1.3 62.4 + - - +
109E LYS* 3.7 34.5 + - - +
110E LYS* 3.5 16.5 + - - +
213E ILE* 3.5 33.6 - - + +
214E GLY 5.6 1.1 - - - -
215E LEU* 3.7 22.7 - - + -
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Residues in contact with VAL 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E LEU* 4.9 2.2 - - + -
62E VAL* 3.6 35.9 - - + -
85E VAL* 4.7 3.1 - - + -
87E VAL* 4.1 23.8 - - + -
103E ILE 3.2 6.4 + - - +
104E LEU* 2.8 11.7 + - + +
106E GLU* 1.3 77.9 - - - +
108E ILE* 1.3 72.2 + - + +
110E LYS* 2.9 45.5 + - + +
111E GLU* 3.0 15.4 + - + +
208E VAL* 4.1 9.0 - - + -
213E ILE* 4.2 4.2 - - + +
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Residues in contact with ILE 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E LEU* 4.0 28.9 - - + -
6E ALA* 6.0 0.7 - - + -
104E LEU* 2.7 27.2 + - + +
105E THR* 2.7 9.6 + - - +
107E VAL* 1.3 80.5 - - + +
109E LYS* 1.3 50.1 + - - +
111E GLU* 3.5 0.7 + - - -
112E ALA* 2.7 30.3 + - - -
113E PRO* 3.4 14.3 - - + +
116E VAL* 3.8 32.1 - - + -
134E VAL* 3.7 29.2 - - + -
138E LEU* 3.9 20.6 - - + -
140E TRP* 4.7 2.7 - - + -
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Residues in contact with LYS 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E THR* 2.9 32.6 + - - +
106E GLU* 3.8 33.3 + - - +
107E VAL 3.1 0.4 - - - -
108E ILE* 1.3 75.2 - - - +
110E LYS* 1.3 68.5 + - - +
112E ALA* 3.4 14.1 + - - +
137E TYR 5.0 7.4 + - - -
138E LEU* 4.6 15.0 - - + +
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Residues in contact with LYS 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E VAL* 4.2 13.5 - - - +
106E GLU 3.5 10.6 + - - +
107E VAL* 2.9 28.5 + - + +
109E LYS* 1.3 80.8 - - - +
111E GLU* 1.3 83.4 + - - +
112E ALA* 3.5 2.4 + - - +
206E GLU* 4.7 5.6 + - - -
208E VAL* 3.4 31.3 - - + +
212E ASP* 5.1 10.3 - - + +
213E ILE* 4.7 10.3 - - + -
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Residues in contact with GLU 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E LYS* 2.6 51.3 + - - +
4E LEU* 4.1 23.1 - - + -
60E VAL* 3.9 7.5 - - + +
62E VAL* 5.3 2.2 - - + -
83E ARG* 2.5 41.2 + - - -
85E VAL* 5.4 0.9 - - + -
107E VAL* 3.0 17.6 + - + +
108E ILE 3.8 3.1 - - - +
110E LYS* 1.3 97.6 + - - +
112E ALA* 1.3 74.5 + - - +
113E PRO* 4.8 0.4 - - + -
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Residues in contact with ALA 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E LYS* 4.1 5.0 - - - +
108E ILE 2.7 15.5 + - - -
109E LYS* 3.4 12.7 + - - +
110E LYS 3.3 4.1 - - - +
111E GLU* 1.3 80.5 - - - +
113E PRO* 1.3 68.2 - - - +
114E ASP* 5.3 1.0 - - - +
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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