Contacts of the helix formed by residues 101 - 110 (chain B) in PDB entry 4BPK
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 TYR 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B PHE* 3.2 31.6 + + - +
98B GLU 3.6 3.8 - - - -
99B LEU 3.1 0.6 - - - -
100B ARG* 1.3 101.4 - - + +
102B ARG* 1.3 53.3 + - - +
103B ARG 3.2 3.0 + - - -
104B ALA* 3.3 9.7 + - + +
105B PHE* 2.7 36.6 + - + +
11D HR7 5.4 0.4 - - - -
12D MET* 3.5 54.3 - - + -
15D B3D 3.0 32.9 - - + +
16D LEU* 3.1 12.2 + - + -
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Residues in contact with ARG 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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20A LYS* 4.7 15.2 - - - +
95B ASP* 4.6 3.4 + - - +
98B GLU* 3.1 39.0 + - - +
99B LEU* 3.2 52.2 + - + +
100B ARG 3.5 1.2 + - - -
101B TYR* 1.3 75.4 - - - +
103B ARG* 1.3 56.0 + - - +
105B PHE* 4.0 5.9 - - - +
106B SER* 2.7 44.1 + - - +
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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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101B TYR 3.3 0.4 - - - -
102B ARG* 1.3 75.7 - - - +
104B ALA* 1.3 57.3 + - - +
106B SER* 3.2 4.8 + - - -
107B ASP* 2.6 59.9 + - - +
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Residues in contact with ALA 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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101B TYR* 3.3 13.1 + - + +
103B ARG* 1.3 82.0 - - + +
105B PHE* 1.3 63.1 + - - +
107B ASP* 3.4 10.7 - - - +
108B LEU* 3.0 34.5 + - + +
12D MET* 4.1 20.4 - - + -
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Residues in contact with PHE 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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97B PHE* 4.2 6.3 - + - -
98B GLU* 3.5 48.2 - - + +
101B TYR 2.7 26.2 + - - +
102B ARG* 4.0 6.5 - - - +
104B ALA* 1.3 73.0 - - - +
106B SER* 1.3 59.4 + - - +
108B LEU* 4.3 2.0 - - - +
109B THR* 2.5 54.8 + - + +
145B SER* 4.0 17.0 - - - -
149B ALA* 3.9 23.3 - - + -
9D AHP 4.0 25.4 - - + -
12D MET* 3.9 17.8 - - + +
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Residues in contact with SER 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 ARG* 2.7 32.3 + - - +
103B ARG* 3.8 4.0 - - - -
105B PHE* 1.3 81.4 - - - +
107B ASP* 1.3 66.2 + - - +
109B THR* 3.2 7.1 + - - -
110B SER* 3.2 24.8 + - - -
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Residues in contact with ASP 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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103B ARG* 2.6 52.8 + - - +
104B ALA* 3.4 9.8 - - - +
106B SER* 1.3 75.1 - - - +
108B LEU* 1.3 61.1 + - + +
110B SER* 2.7 24.2 + - - -
111B GLN* 3.6 11.0 + - - +
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Residues in contact with LEU 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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104B ALA* 3.0 26.3 + - + +
105B PHE 4.4 3.4 - - - +
107B ASP* 1.3 73.8 - - + +
109B THR* 1.3 62.8 + - - +
110B SER 3.2 1.8 - - - -
111B GLN* 3.0 27.7 + - - +
112B LEU* 3.6 10.3 + - - +
1D HT7 5.2 11.0 - - + -
5D ILE* 3.9 28.3 - - + +
8D B3Q 3.7 30.1 - - + -
9D AHP 3.6 40.2 - - + -
12D MET* 3.9 13.9 - - - -
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Residues in contact with THR 109 (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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105B PHE* 2.5 44.8 + - + +
106B SER* 3.2 15.1 + - - -
108B LEU* 1.3 77.1 - - + +
110B SER* 1.3 57.7 + - - +
111B GLN 3.1 0.4 - - - -
112B LEU* 3.1 25.0 + - + +
149B ALA* 3.8 28.5 - - + -
153B GLU* 2.8 26.4 - - - +
9D AHP 4.5 11.2 - - + -
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Residues in contact with SER 110 (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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106B SER 3.2 17.9 + - - -
107B ASP* 2.7 20.3 + - - -
109B THR* 1.3 76.0 + - - +
111B GLN* 1.3 67.6 + - - +
112B LEU 3.4 3.0 + - - +
153B GLU* 4.4 5.2 - - - -
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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