Contacts of the helix formed by residues 49 - 58 (chain B) in PDB entry 2BKG
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 THR 49 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B LEU* 3.5 3.6 - - - -
40B VAL 4.7 1.1 - - - -
41B ASN* 4.1 23.6 - - + +
42B ALA 3.2 11.2 - - - +
43B GLU* 4.2 11.9 - - + +
47B GLY 4.4 1.3 - - - +
48B ASP* 1.3 74.4 - - - +
50B PRO* 1.3 74.7 - - - +
51B LEU* 3.5 10.4 + - - +
52B HIS* 3.0 29.4 + - + +
53B LEU* 2.9 21.3 + - - +
72B ASP 5.2 0.2 + - - -
75B ALA* 3.9 25.3 - - + +
83B PRO* 4.9 0.2 - - - +
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Residues in contact with PRO 50 (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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18B LEU* 3.9 24.9 - - + +
19B LEU* 3.6 18.4 - - + -
22B ALA* 3.8 19.9 - - + +
40B VAL 3.4 20.0 - - - +
42B ALA* 3.2 16.4 - - + +
49B THR* 1.3 87.6 - - - +
51B LEU* 1.3 54.9 + - - +
53B LEU* 3.2 3.9 + - + +
54B ALA* 2.9 31.7 + - - +
66B LEU* 3.4 23.0 - - + +
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Residues in contact with LEU 51 (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 VAL 5.0 1.0 + - - +
49B THR* 3.1 10.3 + - - +
50B PRO* 1.3 75.8 - - - +
52B HIS* 1.3 66.8 + - - +
54B ALA* 4.8 0.2 - - - -
55B ALA* 3.0 26.9 + - + +
63B VAL* 3.8 44.2 - - + +
66B LEU* 3.5 12.9 - - + +
67B LEU* 4.0 15.5 - - + -
71B ALA* 4.1 13.2 - - + -
72B ASP 3.7 24.5 - - - +
73B VAL* 3.8 15.9 - - - -
83B PRO* 3.8 15.7 - - + -
99B LEU* 4.1 10.5 - - + -
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Residues in contact with HIS 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLY 4.1 4.9 - - - -
48B ASP* 3.4 27.5 - - + +
49B THR* 3.0 34.2 + - - +
51B LEU* 1.3 78.0 - - - +
53B LEU* 1.4 63.1 + - - +
55B ALA* 3.8 1.2 - - - +
56B ARG* 3.0 25.8 + - - +
75B ALA* 2.9 39.3 + - + -
76B LEU 4.0 0.9 - - - -
77B ASP* 3.6 11.6 + - - -
81B SER 2.9 24.3 + - - -
83B PRO* 3.6 24.9 - - + +
86B LEU* 3.6 18.5 - - + +
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Residues in contact with LEU 53 (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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19B LEU* 3.4 44.6 - - + +
23B ARG* 4.2 40.8 - - + +
44B ASP* 3.8 9.9 - - + +
48B ASP* 3.6 21.5 - - + -
49B THR 2.9 16.4 + - - +
50B PRO* 3.8 5.2 - - + +
52B HIS* 1.4 75.8 - - - +
54B ALA* 1.3 62.9 + - - +
56B ARG* 3.2 33.1 + - - +
57B VAL* 3.1 26.5 + - - +
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Residues in contact with ALA 54 (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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22B ALA 4.2 7.8 + - - +
50B PRO 2.9 16.5 + - - +
51B LEU 4.1 1.1 - - - +
53B LEU* 1.3 78.7 - - - +
55B ALA* 1.3 57.2 + - - +
57B VAL* 4.2 7.0 - - - -
58B GLY* 2.9 25.5 + - - -
59B HIS* 3.1 12.2 + - + +
62B ILE* 3.7 32.1 - - + -
63B VAL* 3.8 18.4 - - + +
66B LEU* 4.5 1.8 - - + -
95B ILE* 4.0 1.0 - - - +
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Residues in contact with ALA 55 (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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51B LEU* 3.0 20.0 + - + +
52B HIS 3.8 2.7 - - - +
54B ALA* 1.3 78.9 - - - +
56B ARG* 1.3 59.8 + - - +
58B GLY 3.8 0.3 + - - -
63B VAL* 3.8 10.3 - - + +
83B PRO* 3.6 32.3 - - + +
86B LEU* 5.1 0.2 - - + -
87B ALA* 3.5 14.8 - - + +
92B HIS* 3.3 17.0 + - - -
95B ILE* 3.9 19.9 - - + +
99B LEU* 4.5 1.3 - - + -
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Residues in contact with ARG 56 (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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23B ARG* 5.8 2.4 - - - +
44B ASP* 4.9 1.8 + - - -
48B ASP* 3.8 22.8 + - - -
52B HIS 3.0 15.9 + - - +
53B LEU* 3.2 36.4 + - - +
55B ALA* 1.3 77.7 - - - +
57B VAL* 1.3 59.0 + - + +
77B ASP* 5.1 1.4 + - - -
86B LEU* 3.9 37.0 - - + +
90B ARG* 3.2 35.2 + - + +
92B HIS* 2.9 20.4 - - - -
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Residues in contact with VAL 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ARG* 3.6 19.3 - - + +
53B LEU 3.1 17.6 + - - +
54B ALA* 3.8 4.7 - - - +
56B ARG* 1.3 81.5 - - + +
58B GLY* 1.3 61.0 + - - +
59B HIS* 3.0 43.7 + - + +
90B ARG* 5.9 1.3 - - - +
92B HIS* 3.5 7.9 + - - -
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Residues in contact with GLY 58 (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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54B ALA 2.9 11.3 + - - -
56B ARG 3.3 2.6 - - - -
57B VAL* 1.3 78.5 - - - +
59B HIS* 1.3 60.9 + - - +
60B LEU* 3.2 7.3 + - - +
61B GLU* 4.9 0.3 - - - +
92B HIS* 3.5 25.7 + - - -
95B ILE* 3.5 13.7 - - - +
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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