Contacts of the helix formed by residues 96 - 108 (chain B) in PDB entry 2OTD
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 LEU 96 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B GLU* 4.2 23.8 - - + +
50B ILE 3.3 14.8 - - - +
73B TRP* 3.4 50.0 - - + +
77B LEU* 6.1 0.4 - - + -
95B PRO* 1.3 73.4 - - - +
97B LEU* 1.3 67.2 + - - +
98B SER* 4.0 18.4 - - - +
99B GLN* 2.8 37.9 + - + +
100B VAL* 3.1 10.8 + - - +
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B PHE* 3.6 31.6 - - + -
42B ALA* 4.5 4.7 - - + -
50B ILE* 2.8 33.8 + - + +
51B PHE* 4.3 1.0 - - - +
52B LEU* 4.4 9.8 - - + +
95B PRO 4.0 1.0 + - - -
96B LEU* 1.3 68.8 - - - +
98B SER* 1.3 50.5 + - - +
100B VAL* 2.8 12.8 + - + +
101B ALA* 2.8 33.1 + - - +
113B ILE* 4.0 22.7 - - + -
129B VAL* 4.6 6.3 - - + +
132B ALA* 4.0 25.4 - - + -
133B ALA* 4.2 9.2 - - - +
136B LEU* 4.1 10.8 - - + -
137B TRP* 4.1 14.1 - - + -
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Residues in contact with SER 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B LEU* 3.0 17.4 + - - +
97B LEU* 1.3 77.7 - - - +
99B GLN* 1.3 68.2 + - - +
101B ALA* 3.5 4.1 + - - +
102B GLU* 3.2 22.2 + - - +
136B LEU* 3.6 34.5 - - - +
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Residues in contact with GLN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LEU* 4.1 27.4 - - + +
73B TRP* 4.9 1.6 - - - -
94B LEU 4.7 2.6 + - - -
95B PRO* 3.7 6.5 - - - +
96B LEU* 2.8 52.5 + - + +
98B SER* 1.3 85.5 + - - +
100B VAL* 1.3 66.6 + - - +
102B GLU* 3.4 7.2 + - - +
103B ARG* 3.2 25.2 + - - +
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Residues in contact with VAL 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LEU* 4.2 18.6 - - + -
27B ILE* 4.0 15.0 - - + -
40B PHE* 3.6 37.2 - - + -
52B LEU* 3.6 34.5 - - + -
95B PRO* 4.4 2.5 - - + -
96B LEU 3.1 12.4 + - - +
97B LEU* 2.8 11.0 + - + +
99B GLN* 1.3 73.2 - - - +
101B ALA* 1.3 66.7 + - - +
103B ARG* 2.9 14.5 + - - +
104B CYS* 3.0 18.4 + - - -
137B TRP* 4.9 0.7 - - + -
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Residues in contact with ALA 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LEU 2.8 14.7 + - - +
98B SER* 3.6 10.1 - - - +
99B GLN 3.4 0.2 - - - -
100B VAL* 1.3 72.7 - - - +
102B GLU* 1.3 58.1 + - - +
104B CYS* 3.2 5.9 + - - +
105B ARG* 3.1 26.0 + - - +
136B LEU* 4.2 21.3 - - + +
137B TRP* 3.7 38.9 - - + -
140B MSE 4.6 8.6 - - + +
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Residues in contact with GLU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B SER 3.2 15.0 + - - +
99B GLN* 3.9 7.4 - - - +
100B VAL 3.2 0.4 - - - -
101B ALA* 1.3 76.4 - - - +
103B ARG* 1.3 59.5 + - - +
105B ARG* 2.9 45.3 + - - +
106B GLU* 3.1 44.3 + - - +
140B MSE 5.6 0.3 - - - +
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Residues in contact with ARG 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LEU* 3.7 42.3 + - + +
25B ALA 4.9 0.4 - - - +
27B ILE* 4.3 19.1 - - + -
28B ASP* 2.7 42.9 + - - -
99B GLN 3.2 13.8 + - - +
100B VAL* 2.9 12.2 + - - +
102B GLU* 1.3 75.0 - - - +
104B CYS* 1.3 64.8 + - - +
106B GLU* 3.1 23.3 + - - +
107B HIS* 2.9 37.1 + - - +
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Residues in contact with CYS 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ILE* 3.6 34.3 - - - -
100B VAL* 3.0 17.8 + - - -
101B ALA* 3.5 10.3 - - - +
103B ARG* 1.3 77.9 - - - +
105B ARG* 1.3 55.6 + - - +
107B HIS* 3.2 0.6 + - - -
108B GLY* 2.9 26.3 + - - -
109B MSE 2.9 40.8 + - - +
111B ALA* 4.3 16.8 - - - -
137B TRP* 4.6 10.1 - - + +
140B MSE 5.6 1.8 - - - -
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Residues in contact with ARG 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ALA 3.1 16.0 + - - +
102B GLU* 2.9 40.4 + - - +
104B CYS* 1.3 76.3 - - - +
106B GLU* 1.3 66.4 + - + +
107B HIS 2.9 1.6 + - - -
108B GLY* 3.2 9.1 + - - -
136B LEU 4.7 0.6 + - - -
138B ALA 3.9 12.9 + - - -
139B GLY 5.3 0.6 + - - -
140B MSE 3.0 50.5 - - - +
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Residues in contact with GLU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B GLU* 3.1 36.3 + - - +
103B ARG* 3.1 31.0 + - - +
105B ARG* 1.3 80.5 - - + +
107B HIS* 1.3 70.9 + - + +
108B GLY 4.1 0.2 + - - -
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Residues in contact with HIS 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ILE* 4.4 6.3 + - - +
28B ASP* 2.9 35.6 + - + -
31B ALA* 3.0 33.6 - - + +
35B HIS 5.1 1.4 - - - +
36B LYS* 5.0 5.5 + - - +
103B ARG* 2.9 19.2 + - - +
104B CYS 4.1 1.1 - - - +
106B GLU* 1.3 93.7 + - + +
108B GLY* 1.3 64.3 + - - +
109B MSE 3.3 26.3 + - - +
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Residues in contact with GLY 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LYS* 4.0 27.0 + - - +
104B CYS 2.9 7.1 + - - -
105B ARG* 3.2 8.1 + - - -
106B GLU 3.6 0.4 - - - -
107B HIS* 1.3 78.3 - - - +
109B MSE 1.3 57.4 + - - +
110B MSE 5.6 3.8 - - - +
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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
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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