Contacts of the helix formed by residues 89 - 105 (chain B) in PDB entry 2BKU
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 89 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B LEU* 3.6 13.0 - - - +
87B GLN 3.4 5.1 + - - -
88B VAL* 1.3 76.1 - - - +
90B PRO* 1.3 68.7 - - - +
91B GLU* 3.5 19.0 + - - +
92B ALA* 2.9 25.1 + - - +
93B LYS* 2.8 25.7 + - - +
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Residues in contact with PRO 90 (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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88B VAL 3.7 4.6 - - - +
89B SER* 1.3 82.2 - - - +
91B GLU* 1.3 73.6 + - - +
93B LYS* 3.9 13.9 - - + +
94B ASN* 3.3 22.5 + - - +
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Residues in contact with GLU 91 (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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89B SER* 3.0 15.4 - - - +
90B PRO* 1.3 97.7 - - - +
92B ALA* 1.3 61.3 + - - +
94B ASN* 3.8 3.8 + - - +
95B GLN* 3.3 26.9 + - - +
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Residues in contact with ALA 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 3.8 15.7 - - + +
42B GLY* 5.8 3.8 - - - -
88B VAL* 3.7 15.7 - - + -
89B SER* 2.9 20.6 + - - +
91B GLU* 1.3 75.2 - - - +
93B LYS* 1.3 56.2 + - - +
95B GLN* 3.5 6.6 - - - +
96B ILE* 2.8 44.2 + - + +
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Residues in contact with LYS 93 (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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84B TRP* 2.8 62.1 + - + +
85B ILE* 2.9 25.1 + - - +
88B VAL* 3.0 31.9 + - + +
89B SER 2.8 13.7 + - - +
90B PRO* 3.9 13.9 - - + +
92B ALA* 1.3 76.4 - - - +
94B ASN* 1.3 57.3 + - - +
96B ILE* 3.2 1.6 + - - +
97B LYS* 2.9 44.2 + - - +
126B GLU* 3.4 16.4 - - - +
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Residues in contact with ASN 94 (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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90B PRO 3.3 14.1 + - - +
91B GLU* 4.1 4.5 - - - +
92B ALA 3.3 0.4 - - - -
93B LYS* 1.3 77.3 - - - +
95B GLN* 1.3 57.1 + - - +
97B LYS* 3.9 12.6 - - - +
98B THR* 2.7 48.5 + - - -
134B GLU* 5.4 5.5 + - - -
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Residues in contact with GLN 95 (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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45B SER* 5.6 0.9 - - - +
91B GLU 3.3 16.7 + - - +
92B ALA* 3.1 12.2 + - - +
94B ASN* 1.3 80.0 - - + +
96B ILE* 1.3 59.9 + - + +
98B THR* 3.8 5.9 - - - +
99B ASN* 3.1 46.8 + - - +
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Residues in contact with ILE 96 (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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41B ALA* 3.5 37.5 - - + +
42B GLY* 4.1 6.7 - - - +
45B SER* 3.8 28.8 - - - +
65B LEU* 4.4 11.9 - - + -
84B TRP* 3.6 22.7 - - + -
88B VAL* 4.3 4.9 - - + -
92B ALA* 2.8 29.1 + - + +
93B LYS 3.6 3.1 - - - +
95B GLN* 1.3 71.7 - - + +
97B LYS* 1.3 59.9 + - - +
99B ASN* 3.2 4.7 + - - +
100B ALA* 2.9 26.3 + - - +
118B LEU* 5.1 3.6 - - + -
122B ILE* 4.0 23.8 - - + -
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Residues in contact with LYS 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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84B TRP* 4.6 1.8 - - + -
93B LYS* 2.9 32.2 + - - +
94B ASN* 3.9 11.9 - - - +
96B ILE* 1.3 76.3 - - - +
98B THR* 1.3 58.6 + - - +
100B ALA* 3.2 8.3 + - - +
101B LEU* 3.0 37.4 + - + +
122B ILE* 4.3 13.0 - - + -
126B GLU* 2.5 41.8 + - - -
131B ALA* 5.3 0.4 - - - +
132B TRP* 3.4 60.4 - - + +
134B GLU* 4.9 2.1 + - - +
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Residues in contact with THR 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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94B ASN* 2.7 37.8 + - - -
95B GLN* 3.8 9.2 - - - +
97B LYS* 1.3 77.8 - - - +
99B ASN* 1.3 58.4 + - - +
101B LEU* 3.5 11.1 + - - +
102B THR* 2.8 41.2 + - - +
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Residues in contact with ASN 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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45B SER* 2.7 46.3 + - - +
46B GLN* 4.2 10.3 - - - +
48B LEU* 4.7 2.0 - - + -
49B ILE* 3.1 29.1 - - + +
95B GLN* 3.1 29.8 + - - +
96B ILE 3.5 7.4 - - - +
98B THR* 1.3 79.0 - - - +
100B ALA* 1.3 59.5 + - - +
102B THR* 3.3 7.7 + - - -
103B ALA* 2.8 31.5 + - - +
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Residues in contact with ALA 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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45B SER* 5.7 0.2 - - - -
48B LEU* 4.3 7.6 - - + +
96B ILE 2.9 13.0 + - - +
97B LYS* 3.4 12.6 - - - +
99B ASN* 1.3 76.3 - - - +
101B LEU* 1.3 52.5 + - - +
103B ALA* 3.3 8.1 + - - +
104B LEU* 2.7 34.1 + - - +
115B ALA* 3.6 6.0 - - - +
118B LEU* 4.7 20.9 - - + -
119B ILE* 3.8 23.1 - - + +
122B ILE* 5.0 4.0 - - + -
132B TRP* 5.4 0.7 - - + -
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Residues in contact with LEU 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 LYS* 3.0 26.2 + - + +
98B THR* 3.9 9.0 - - - +
99B ASN 3.3 0.2 - - - -
100B ALA* 1.3 72.8 - - - +
102B THR* 1.3 68.0 + - - +
104B LEU* 3.3 18.9 - - + +
105B VAL* 3.4 13.5 + - - +
119B ILE* 3.9 11.4 - - + -
132B TRP* 4.0 28.0 - - + +
135B LEU* 4.4 2.7 - - + -
138B ILE* 4.2 24.0 - - + -
139B MET* 3.8 28.9 - - + -
142B ASN* 5.7 0.4 - - - +
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Residues in contact with THR 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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49B ILE* 4.2 17.2 - - + +
98B THR* 2.8 26.1 + - - +
99B ASN* 3.4 10.4 + - - -
101B LEU* 1.3 76.1 - - - +
103B ALA* 1.3 63.4 + - - +
105B VAL* 2.9 30.9 + - + +
106B SER* 3.3 4.7 + - - -
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Residues in contact with ALA 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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48B LEU* 3.5 37.5 - - + -
49B ILE* 4.0 8.7 - - + +
58B ARG* 6.1 0.7 - - - +
99B ASN 2.8 20.8 + - - +
100B ALA 3.5 3.6 - - - +
102B THR* 1.3 72.1 - - - +
104B LEU* 1.3 61.9 + - - +
106B SER* 3.0 23.2 + - - +
111B ILE* 3.8 8.2 - - + +
112B ALA* 3.4 10.4 + - - -
115B ALA* 3.6 8.7 - - + -
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Residues in contact with LEU 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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100B ALA 2.7 18.1 + - - +
101B LEU* 3.3 14.8 - - + +
103B ALA* 1.3 74.7 - - - +
105B VAL* 1.3 58.3 + - + +
106B SER 3.4 0.4 - - - +
112B ALA* 3.2 30.4 - - - +
115B ALA* 3.4 6.0 - - + +
116B ALA* 3.9 16.4 - - - -
119B ILE* 3.6 20.9 - - + -
139B MET* 3.6 28.0 - - + -
142B ASN* 4.3 5.8 - - - +
150B ASN 4.8 1.6 - - - +
151B VAL* 5.4 0.5 - - - -
154B ALA* 3.3 38.5 - - + +
155B SER* 3.9 14.8 - - - +
158B ALA* 4.2 2.0 - - + -
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Residues in contact with VAL 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 LEU 3.7 10.8 - - - +
102B THR* 2.9 32.7 + - + +
104B LEU* 1.3 80.0 - - + +
106B SER* 1.3 68.8 + - - +
107B ILE* 3.5 2.4 + - - +
142B ASN* 4.7 11.4 - - - +
150B ASN* 3.0 17.0 + - - +
151B VAL* 3.9 34.5 - - + +
155B SER* 5.5 0.4 - - - +
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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
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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