Contacts of the helix formed by residues 90 - 101 (chain E) in PDB entry 1QO0
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 SER 90 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109B GLU* 4.3 14.9 - - - +
111B PHE* 3.9 13.7 - - - +
155B GLU* 2.5 37.8 + - - +
88E TYR* 3.4 21.6 - - - +
89E GLU* 1.3 80.2 - - - +
91E PRO* 1.3 70.0 - - - +
93E VAL* 3.1 4.2 + - - -
94E LEU* 2.9 26.2 + - - +
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Residues in contact with PRO 91 (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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109B GLU 5.5 0.7 - - - +
111B PHE* 3.4 39.3 - - + -
155B GLU* 3.7 6.1 - - + +
158B HIS* 3.8 23.3 - - + +
159B VAL* 5.5 9.0 - - + -
368B VAL* 5.1 11.9 - - + -
7D LEU* 3.8 19.4 - - + +
89E GLU 4.1 0.2 - - - -
90E SER* 1.3 87.7 - - - -
92E ALA* 1.3 57.4 + - - +
94E LEU* 4.8 1.3 - - + -
95E SER* 2.8 36.2 + - - -
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Residues in contact with ALA 92 (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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151B ILE* 5.7 0.2 - - + -
154B ARG* 4.7 7.2 - - + +
155B GLU* 2.8 29.1 + - + +
158B HIS* 3.7 31.8 - - + +
62E GLN* 5.0 13.1 + - + +
91E PRO* 1.3 72.3 - - - +
93E VAL* 1.3 60.7 + - + +
95E SER* 3.9 2.2 - - - -
96E GLN* 3.5 19.2 + - - +
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Residues in contact with VAL 93 (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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151B ILE* 3.7 14.6 - - + -
155B GLU* 3.2 11.6 + - - +
60E ILE* 4.2 14.4 - - + +
62E GLN* 3.5 26.2 - - - +
86E VAL* 4.4 4.0 - - + -
87E GLU 5.3 1.8 - - - +
88E TYR* 3.6 40.2 - - + +
90E SER 3.1 8.9 + - - +
92E ALA* 1.3 74.1 - - - +
94E LEU* 1.3 67.4 + - - +
96E GLN* 3.3 11.1 + - - +
97E ILE* 3.4 27.2 + - + +
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Residues in contact with LEU 94 (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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111B PHE* 6.2 0.4 - - + -
7D LEU* 4.1 18.4 - - + -
116D LEU* 3.8 25.1 - - + -
117D PRO* 4.1 25.4 - - + +
120D VAL* 3.9 21.5 - - + -
86E VAL* 4.6 0.2 - - + -
88E TYR 4.2 14.8 - - - +
89E GLU* 3.2 25.1 - - - +
90E SER 2.9 17.5 + - - +
91E PRO 4.1 2.0 - - - +
93E VAL* 1.3 75.0 - - - +
95E SER* 1.3 66.7 + - - +
97E ILE* 3.3 20.5 + - + +
98E ILE* 3.1 28.5 + - - +
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Residues in contact with SER 95 (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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158B HIS* 4.0 14.0 + - - -
3D ALA* 3.7 23.3 - - - +
4D ASN* 4.6 1.9 + - - +
7D LEU* 3.4 15.8 - - - +
91E PRO 2.8 20.3 + - - -
92E ALA* 3.9 7.9 - - - -
94E LEU* 1.3 79.1 - - - +
96E GLN* 1.4 57.4 + - - +
98E ILE* 3.3 4.5 + - - +
99E GLU* 2.9 42.9 + - - +
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Residues in contact with GLN 96 (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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59E SER 5.3 0.4 + - - -
60E ILE* 3.7 24.1 - - + +
61E PHE 2.8 29.7 + - - +
62E GLN* 4.5 3.6 + - - +
66E HIS* 3.2 47.1 + - + +
69E ILE* 5.1 6.1 - - - +
92E ALA 3.5 11.3 + - - +
93E VAL 3.3 8.7 + - - +
94E LEU 3.2 0.8 - - - -
95E SER* 1.4 75.6 - - - +
97E ILE* 1.3 60.9 + - - +
99E GLU* 3.4 10.3 + - + +
100E LEU* 2.9 51.4 + - + +
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Residues in contact with ILE 97 (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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117D PRO* 5.7 1.1 - - + +
120D VAL* 5.6 1.6 - - + -
121D SER* 4.6 12.6 - - - +
124D ARG* 4.8 1.3 - - - -
60E ILE* 3.7 28.7 - - + -
84E ALA* 4.0 7.6 - - + -
86E VAL* 3.5 39.5 - - + -
93E VAL* 3.4 17.4 + - + +
94E LEU* 3.6 18.6 - - + +
95E SER 3.3 0.4 - - - -
96E GLN* 1.3 80.5 - - - +
98E ILE* 1.3 64.4 + - + +
100E LEU* 3.6 0.6 + - - -
101E GLU 3.3 15.6 + - - -
102E CYS* 3.4 23.1 + - + -
105E VAL* 4.3 17.9 - - + -
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Residues in contact with ILE 98 (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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2D SER* 5.0 1.8 - - - +
3D ALA* 3.7 40.2 - - + +
6D LEU* 3.5 21.5 - - + -
7D LEU* 4.4 5.6 - - + -
120D VAL* 3.5 31.9 - - + -
121D SER* 5.8 0.4 - - - -
124D ARG* 3.6 29.4 - - + +
94E LEU 3.1 15.8 + - - +
95E SER 3.4 6.7 - - - +
97E ILE* 1.3 77.4 - - + +
99E GLU* 1.3 58.5 + - + +
101E GLU* 2.9 26.0 + - - +
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Residues in contact with GLU 99 (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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3D ALA* 4.3 10.9 - - + +
66E HIS* 4.4 14.9 + - - -
95E SER* 2.9 34.6 + - - +
96E GLN* 3.8 14.1 - - + +
98E ILE* 1.3 77.3 - - + +
100E LEU* 1.3 60.0 + - + +
101E GLU* 3.5 11.2 + - - +
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Residues in contact with LEU 100 (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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58E THR* 4.5 9.4 - - + -
60E ILE* 3.7 28.9 - - + -
66E HIS* 5.6 0.4 - - + +
69E ILE* 4.6 3.8 - - + -
70E ALA* 4.0 35.7 - - + +
73E LEU* 4.5 15.4 - - + +
82E LEU* 3.7 23.3 - - + +
96E GLN* 2.9 35.6 + - + +
97E ILE 3.9 4.3 - - - +
98E ILE 3.3 0.2 - - - -
99E GLU* 1.3 76.0 - - + +
101E GLU* 1.3 71.5 + - - +
102E CYS* 3.6 8.2 + - - -
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Residues in contact with GLU 101 (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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124D ARG* 3.5 31.2 + - - +
128D GLU* 5.7 5.7 - - - +
82E LEU* 4.5 1.7 - - - +
97E ILE 3.3 1.4 + - - -
98E ILE 2.9 21.1 + - - +
99E GLU 3.9 8.1 - - - +
100E LEU* 1.3 82.1 - - - +
102E CYS* 1.3 70.0 + - - +
103E HIS* 3.7 17.0 + - - +
133E LYS* 5.4 5.9 + - - -
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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