Contacts of the helix formed by residues 31 - 51 (chain B) in PDB entry 1BT8
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 HIS 31 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A GLU* 3.9 8.5 - - - -
168A TYR* 2.9 31.1 + + - -
173A ASN* 4.1 14.0 - - + +
26B LEU 3.2 16.7 + - - -
27B HIS* 3.1 29.6 - + + +
30B LYS* 1.3 79.8 - - + +
32B HIS* 1.3 67.7 + - - +
34B ALA* 3.0 20.3 + - - +
35B TYR* 3.3 28.1 + - + +
165B HIS* 3.6 35.7 + + + +
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Residues in contact with HIS 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 3.6 15.8 - - + +
6B PRO* 3.9 13.2 - - + -
27B HIS 3.0 15.2 + - - +
28B HIS* 3.5 15.0 + - - +
31B HIS* 1.3 72.4 - - - +
33B LYS* 1.3 63.8 + - - +
35B TYR* 3.1 19.9 + + - +
36B VAL* 3.3 9.6 + - + +
72B HIS* 3.0 41.5 + - - -
75B HIS* 3.5 19.7 - - + +
76B SER* 3.6 17.9 - - - -
79B TRP* 2.8 34.5 + - + -
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Residues in contact with LYS 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 4.2 32.0 - - + +
28B HIS 3.5 4.5 + - - +
29B ASP* 3.3 44.8 + - - +
30B LYS 4.0 2.7 - - - +
31B HIS 3.2 0.4 - - - -
32B HIS* 1.3 77.9 - - - +
34B ALA* 1.3 62.0 + - - +
36B VAL* 3.3 5.9 + - + +
37B ASP* 3.2 36.9 + - - +
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Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LYS 3.4 12.7 + - - +
31B HIS* 3.0 13.1 + - - +
33B LYS* 1.3 80.4 - - - +
35B TYR* 1.3 63.0 + - + +
37B ASP* 3.5 7.2 + - - +
38B GLY* 2.9 24.9 + - - -
68B ASN* 3.9 3.3 - - - +
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Residues in contact with TYR 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B HIS* 3.3 34.1 + - + -
32B HIS* 3.1 14.0 + + - +
34B ALA* 1.3 77.8 - - + +
36B VAL* 1.3 61.5 + - - +
39B ALA* 3.0 30.7 + - - +
67B PHE* 4.0 15.9 - + - -
68B ASN* 3.4 41.0 - - - +
71B GLY* 3.9 9.0 - - - -
72B HIS* 3.8 9.1 - - - +
75B HIS* 3.3 32.8 - + - -
146B HIS* 3.0 30.7 + + - -
163B TRP* 4.5 5.9 - - - -
165B HIS* 4.3 14.4 - - - -
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Residues in contact with VAL 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B TYR* 3.5 33.8 - - + +
4B THR* 4.0 7.4 - - - -
5B LEU* 4.0 26.2 - - + +
32B HIS* 3.3 15.8 + - + +
33B LYS* 3.7 7.9 - - + +
34B ALA 3.3 0.2 - - - -
35B TYR* 1.3 76.5 - - - +
37B ASP* 1.3 68.8 + - - +
39B ALA* 3.4 5.3 + - - +
40B ASN* 3.1 32.9 + - - +
72B HIS* 4.0 26.9 - - + +
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Residues in contact with ASP 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LYS* 3.2 29.0 + - - +
34B ALA* 3.8 6.1 - - - +
36B VAL* 1.3 82.6 - - - +
38B GLY* 1.3 58.8 + - - +
40B ASN* 3.6 7.0 + - - +
41B THR* 2.9 34.2 + - - +
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Residues in contact with GLY 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ALA 2.9 17.4 + - - -
37B ASP* 1.3 76.1 - - - +
39B ALA* 1.3 59.3 + - - +
41B THR* 3.4 6.2 + - - -
42B ALA* 3.0 28.8 + - - +
64B ASP* 5.4 0.7 - - - +
68B ASN* 3.7 23.3 + - - -
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Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B TYR* 3.7 28.7 - - + -
35B TYR 3.0 19.2 + - - +
36B VAL* 3.8 3.4 - - - +
38B GLY* 1.3 76.1 - - - +
40B ASN* 1.3 62.1 + - - +
42B ALA* 3.5 7.6 + - - +
43B LEU* 3.3 26.0 + - - +
65B LEU* 4.3 4.8 - - + +
68B ASN* 3.5 11.6 - - + +
69B LEU* 4.2 18.2 - - + +
72B HIS* 5.4 1.8 - - + -
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Residues in contact with ASN 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ALA* 3.4 24.2 - - + +
2B VAL* 3.1 10.2 + - - +
3B TYR* 2.9 52.5 + - - +
36B VAL* 3.1 24.1 + - - +
37B ASP* 4.0 7.0 + - - +
39B ALA* 1.3 74.6 - - - +
41B THR* 1.3 65.5 + - - +
43B LEU* 3.2 8.0 + - - +
44B ASP* 3.0 31.2 + - - +
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Residues in contact with THR 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASP* 2.9 23.4 + - - +
38B GLY* 3.8 6.3 - - - -
40B ASN* 1.3 72.9 - - - +
42B ALA* 1.3 62.1 + - - +
44B ASP* 3.4 10.1 + - + +
45B LYS* 3.0 54.2 + - + +
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLY 3.0 17.3 + - - +
39B ALA 3.6 6.7 - - - +
40B ASN 3.2 0.2 - - - -
41B THR* 1.3 78.3 - - - +
43B LEU* 1.3 56.9 + - - +
45B LYS* 3.4 7.0 + - - +
46B LEU* 3.0 34.5 + - - +
61B LEU* 4.4 6.3 - - - +
64B ASP* 4.3 11.0 - - + -
65B LEU* 3.8 37.7 - - + +
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B VAL* 3.8 28.0 - - + -
3B TYR* 3.6 31.4 - - + +
39B ALA 3.3 11.2 + - - +
40B ASN* 3.2 9.5 + - - +
42B ALA* 1.3 74.7 - - - +
44B ASP* 1.3 61.3 + - - +
46B LEU* 3.2 11.2 + - + +
47B ALA* 2.9 29.9 + - - +
50B ARG* 5.3 0.9 + - - -
65B LEU* 4.0 25.4 - - + -
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Residues in contact with ASP 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ALA* 5.1 10.7 - - - +
40B ASN* 3.0 17.7 + - - +
41B THR* 3.6 13.1 + - + +
43B LEU* 1.3 78.4 - - - +
45B LYS* 1.3 61.1 + - + +
47B ALA* 3.3 7.5 + - - +
48B GLU* 2.9 29.3 + - - +
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Residues in contact with LYS 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B THR* 3.0 43.6 + - + +
42B ALA* 3.5 3.8 - - - +
43B LEU 3.2 0.2 - - - -
44B ASP* 1.3 77.9 - - + +
46B LEU* 1.3 58.5 + - - +
48B GLU* 3.4 17.8 + - - +
49B ALA* 3.0 27.9 + - - +
60B LYS* 4.7 14.3 - - - +
61B LEU* 3.5 32.9 - - + +
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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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42B ALA 3.0 22.8 + - - +
43B LEU* 3.6 13.2 - - + +
45B LYS* 1.3 73.2 - - - +
47B ALA* 1.3 65.3 + - - +
49B ALA* 3.3 8.2 + - + +
50B ARG* 3.2 40.1 + - - +
55B PHE* 5.1 1.9 - - + -
58B ILE* 4.0 21.8 - - + -
61B LEU* 3.7 35.0 - - + +
62B GLU* 4.7 8.5 - - - +
65B LEU* 4.0 27.4 - - + -
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Residues in contact with ALA 47 (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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43B LEU 2.9 17.0 + - - +
44B ASP* 3.5 8.3 - - - +
46B LEU* 1.3 74.9 - - - +
48B GLU* 1.3 63.2 - - - +
50B ARG* 3.2 29.7 + - - +
51B ASP* 3.1 30.4 + - - +
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Residues in contact with GLU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ASP 2.9 16.8 + - - +
45B LYS* 3.7 18.9 - - - +
47B ALA* 1.3 73.7 - - - +
49B ALA* 1.3 64.5 + - - +
51B ASP* 3.4 8.7 + - - +
52B LYS* 3.2 51.6 + - + +
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Residues in contact with ALA 49 (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 LYS 3.0 15.0 + - - +
46B LEU* 3.4 14.8 - - + +
47B ALA 3.2 0.2 - - - -
48B GLU* 1.3 77.4 - - - +
50B ARG* 1.3 57.4 + - - +
53B ALA* 3.0 8.0 + - - -
54B ASP* 3.0 48.1 + - - +
55B PHE* 4.0 18.2 - - + -
58B ILE* 6.4 0.2 - - + -
61B LEU* 4.6 10.8 - - + -
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Residues in contact with ARG 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU 5.3 0.6 + - - -
46B LEU* 3.2 25.9 + - - +
47B ALA* 3.2 31.0 + - - +
49B ALA* 1.3 75.0 - - - +
51B ASP* 1.3 70.2 + - - +
53B ALA* 3.1 12.6 + - - +
55B PHE* 3.9 25.5 - - + -
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Residues in contact with ASP 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA* 3.1 17.5 + - - +
48B GLU* 3.4 11.1 + - - +
50B ARG* 1.3 79.7 - - - +
52B LYS* 1.3 69.5 + - + +
53B ALA* 3.3 1.6 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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