Contacts of the helix formed by residues 40 - 55 (chain B) in PDB entry 2BHT
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 VAL 40 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B GLU* 3.5 39.9 + - + +
39B SER* 1.3 71.6 - - - +
41B LYS* 1.3 64.9 + - + +
42B ASP 2.8 6.6 + - - -
43B ARG* 3.2 21.5 + - - +
44B ALA* 4.3 1.2 + - - +
150B HIS* 4.5 8.5 - - + -
154B THR* 6.0 0.7 - - + -
178B THR* 4.3 27.8 - - + +
278B ILE* 4.4 3.6 - - + -
280B CYS* 2.7 27.4 + - + +
320B PLP 3.7 31.9 - - + +
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Residues in contact with LYS 41 (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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39B SER* 3.1 9.2 - - - +
40B VAL* 1.3 79.5 - - + +
42B ASP* 1.3 57.8 + - - +
43B ARG 3.3 0.7 - - - -
44B ALA* 4.3 11.4 - - + +
45B ALA* 3.0 18.9 + - - +
71B ASN* 4.0 16.4 - - + +
72B THR* 3.3 38.8 - - - +
75B ALA* 2.9 15.8 - - + +
140B GLN* 3.7 11.9 - - - +
146B ASN* 6.1 1.1 - - - +
175B THR* 3.9 3.9 - - - +
178B THR* 6.0 0.2 - - - +
208B GLY* 5.1 0.8 + - - -
320B PLP 1.5 95.4 + - + +
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Residues in contact with ASP 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 3.9 12.2 - - + +
35B ASN* 2.9 33.3 - - + +
36B PRO* 3.1 4.9 - - - +
37B ALA* 2.6 51.9 + - - +
39B SER* 3.4 3.7 + - - +
40B VAL 2.8 1.8 + - - -
41B LYS* 1.3 76.4 - - - +
43B ARG* 1.3 65.8 + - - +
46B LEU* 3.1 26.2 + - - +
75B ALA* 3.0 18.2 - - - +
78B MET* 3.8 9.9 - - + +
79B ILE* 3.6 3.0 - - - +
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Residues in contact with ARG 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 4.2 11.4 - - + -
9B GLY* 3.9 15.4 - - - -
10B ASN 3.9 1.2 - - - +
11B THR* 3.8 4.2 + - - -
32B GLU* 2.8 45.4 + - - +
35B ASN* 4.3 11.2 - - - +
40B VAL* 3.2 14.3 + - - +
42B ASP* 1.3 77.5 - - - +
44B ALA* 1.3 63.1 + - - +
46B LEU* 4.1 3.6 - - - +
47B SER* 3.1 23.2 + - - -
149B ALA* 3.8 15.7 - - + +
150B HIS* 4.9 4.9 - - + -
153B THR* 2.7 28.0 + - - +
154B THR* 2.7 31.1 + - - +
157B GLU* 2.6 43.8 + - - -
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Residues in contact with ALA 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL 4.3 0.8 + - - +
41B LYS* 4.0 16.2 + - + +
43B ARG* 1.3 75.5 - - - +
45B ALA* 1.3 60.4 + - - +
47B SER* 3.0 2.7 + - - -
48B MET* 2.8 44.1 + - + +
140B GLN* 5.9 2.0 - - + +
145B ASP 4.5 1.2 - - - +
146B ASN* 4.2 34.8 - - + +
149B ALA* 3.9 10.2 - - + +
150B HIS* 5.0 6.2 - - + +
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Residues in contact with ALA 45 (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 LYS 3.0 20.7 + - - +
42B ASP 3.9 0.4 - - - +
43B ARG 3.4 0.2 - - - -
44B ALA* 1.3 79.5 - - - +
46B LEU* 1.3 63.4 + - - +
48B MET* 3.5 6.3 - - + +
49B ILE* 3.1 25.3 + - - +
72B THR* 5.2 1.6 - - + +
75B ALA* 3.4 19.7 - - + -
76B LEU* 3.5 27.7 - - + +
79B ILE* 3.4 12.1 - - + -
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Residues in contact with LEU 46 (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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5B GLU* 3.5 23.6 - - + +
8B ILE* 4.1 21.3 - - + -
42B ASP 3.1 10.8 + - - +
43B ARG* 4.1 3.4 - - - +
45B ALA* 1.3 74.9 - - - +
47B SER* 1.3 53.5 + - - +
49B ILE* 3.3 1.2 + - - +
50B VAL* 2.5 50.0 + - + +
79B ILE* 3.0 30.9 - - + +
83B LYS* 3.0 41.7 - - - +
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Residues in contact with SER 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ARG 3.1 14.6 + - - -
44B ALA 3.0 7.1 + - - -
46B LEU* 1.3 75.4 - - - +
48B MET* 1.3 66.8 + - - +
50B VAL* 2.8 10.9 + - - -
51B GLU* 2.6 43.2 + - - +
145B ASP* 2.6 32.3 + - - +
148B LYS* 4.7 2.5 - - - +
149B ALA* 4.2 12.1 + - - -
152B THR* 6.3 0.4 - - - -
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Residues in contact with MET 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ALA* 2.8 17.1 + - + +
45B ALA* 3.5 12.1 - - - +
47B SER* 1.3 76.7 + - - +
49B ILE* 1.3 61.0 + - - +
51B GLU 4.4 0.3 - - - -
52B ALA* 3.4 20.1 + - - +
72B THR* 5.1 3.4 - - + -
76B LEU* 3.4 33.9 - - + -
138B LEU* 3.4 27.9 - - + +
140B GLN* 3.8 34.8 - - + -
143B ASN* 3.0 33.1 + - - +
145B ASP* 3.9 13.7 - - + +
146B ASN* 5.3 7.6 - - - -
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Residues in contact with ILE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ALA 3.1 13.2 + - - +
46B LEU 3.8 1.8 - - - +
47B SER 3.0 0.8 - - - -
48B MET* 1.3 77.9 - - - +
50B VAL* 1.3 70.0 + - - +
52B ALA* 2.9 21.4 + - - +
53B GLU* 3.9 2.6 - - - +
58B ILE* 3.5 19.0 - - + +
64B LEU* 3.9 13.5 - - + -
76B LEU* 4.2 4.3 - - + +
79B ILE* 3.3 34.3 - - + -
80B ALA* 4.2 4.3 - - - +
83B LYS* 4.4 6.7 - - + -
85B TYR* 4.1 17.0 - - + -
87B MET* 3.9 28.3 - - + -
138B LEU* 4.0 17.5 - - + -
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Residues in contact with VAL 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 2.5 43.8 + - + +
47B SER* 2.8 5.6 + - - +
49B ILE* 1.3 71.8 - - - +
51B GLU* 1.3 66.7 + - + +
53B GLU* 3.2 35.5 + - - +
54B LYS* 3.6 4.9 + - + +
83B LYS* 3.2 32.8 - - - +
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Residues in contact with GLU 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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47B SER* 2.6 25.1 + - - +
50B VAL* 1.3 77.6 - - + +
52B ALA* 1.3 54.8 + - - +
53B GLU 3.0 8.3 + - - -
54B LYS* 3.1 21.0 - - - +
55B ARG* 2.8 50.1 + - - +
145B ASP* 3.1 28.3 - - - +
148B LYS* 2.8 40.2 + - - +
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Residues in contact with ALA 52 (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 MET 3.4 16.0 + - - +
49B ILE* 2.9 11.5 + - - +
51B GLU* 1.3 75.4 - - - +
53B GLU* 1.3 58.9 + - - +
55B ARG* 3.5 13.7 - - - +
57B ARG* 3.7 8.6 + - + -
58B ILE* 2.8 49.4 + - + +
138B LEU* 5.4 5.2 - - + -
145B ASP* 4.7 0.4 + - - -
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Residues in contact with GLU 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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49B ILE* 3.9 8.9 - - - +
50B VAL* 3.3 24.6 - - - +
51B GLU 3.0 1.0 + - - -
52B ALA* 1.3 83.6 - - - +
54B LYS* 1.3 70.0 + - - +
55B ARG 3.0 4.7 + - - -
56B GLY* 3.1 18.1 + - - +
58B ILE* 3.9 6.5 - - + +
60B PRO* 5.0 3.3 - - - +
83B LYS* 4.8 7.6 + - - +
85B TYR* 2.3 41.5 + - - +
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Residues in contact with LYS 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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50B VAL 3.6 4.7 + - - +
51B GLU* 3.1 31.9 - - - +
53B GLU* 1.3 76.9 - - - +
55B ARG* 1.3 65.7 + - - +
56B GLY 3.8 1.2 + - - -
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Residues in contact with ARG 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 GLU* 2.8 45.9 + - - +
52B ALA* 3.5 10.0 - - - -
53B GLU 3.4 1.8 - - - -
54B LYS* 1.3 81.6 - - - +
56B GLY* 1.3 67.7 + - - +
57B ARG* 2.9 37.1 + - + +
145B ASP* 3.0 32.1 + - - -
148B LYS* 3.6 15.2 - - - +
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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
------------------------------------------------------------
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