Contacts of the helix formed by residues 40 - 54 (chain B) in PDB entry 1BJJ
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 GLY 40 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B ASP* 1.3 78.2 + - - +
41B THR* 1.3 59.7 + - - +
43B ARG* 3.2 18.3 + - - +
44B CYS* 3.2 16.5 + - - -
105B CYS* 4.6 0.3 - - - -
109B ASN* 2.8 25.1 - - - +
112B THR* 5.0 5.9 + - - -
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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
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22B TYR* 3.8 30.9 + - + -
25B TYR* 3.7 28.9 - - + -
29B CYS* 3.9 1.7 - - - -
39B ASP* 3.3 8.2 + - - -
40B GLY* 1.3 75.2 - - - +
42B ASP* 1.3 58.2 + - - +
44B CYS* 2.9 32.2 + - - +
45B CYS 3.4 3.6 + - - -
106B PHE* 3.8 12.2 + - + -
109B ASN* 3.4 27.8 + - - +
112B THR* 5.3 0.2 + - - -
113B TYR* 4.0 13.4 - - + -
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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
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25B TYR* 3.7 5.8 - - + +
26B GLY* 3.3 7.8 - - - -
27B CYS* 2.6 27.0 + - - +
28B TYR* 2.8 27.6 + - - +
29B CYS* 3.4 13.3 + - - -
37B PRO* 3.5 8.2 - - - +
38B LYS* 2.9 30.8 + - + +
39B ASP* 2.9 19.7 + - - +
41B THR* 1.3 77.7 - - - +
43B ARG* 1.3 61.0 + - - +
44B CYS 3.3 0.2 - - - -
45B CYS* 3.5 2.0 + - - +
46B PHE* 3.2 16.6 + - - +
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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
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37B PRO* 3.7 26.9 + - + +
39B ASP 2.9 13.0 + - - +
40B GLY* 3.2 14.6 - - - +
41B THR 3.0 0.2 - - - -
42B ASP* 1.3 76.2 - - - +
44B CYS* 1.3 65.7 + - - +
45B CYS 3.1 0.7 - - - -
46B PHE* 3.0 17.1 + - + +
47B VAL* 2.9 40.1 + - + +
105B CYS* 5.2 0.4 - - - -
131B GLU* 2.7 43.0 + - - -
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Residues in contact with CYS 44 (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 GLY 3.3 14.4 - - - -
41B THR* 2.9 14.4 + - - +
43B ARG* 1.3 79.9 - - - +
45B CYS* 1.3 60.3 + - - +
47B VAL* 3.7 6.3 + - - +
48B HIS* 3.2 21.5 + - - +
102B ALA* 4.4 7.9 - - - +
105B CYS* 2.0 69.1 - - + -
106B PHE* 3.4 18.2 - - + -
109B ASN* 3.9 3.1 - - - -
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Residues in contact with CYS 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR 5.0 1.8 - - - -
28B TYR* 3.6 7.2 - - - +
29B CYS* 2.0 65.5 - - - +
41B THR 3.4 1.2 + - - -
42B ASP 3.7 3.4 - - - +
43B ARG 3.1 0.4 - - - -
44B CYS* 1.3 76.1 - - - +
46B PHE* 1.3 64.0 + - - +
48B HIS* 3.2 8.7 + - - +
49B ASP* 3.1 26.9 + - - +
106B PHE* 3.4 26.7 - - - -
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Residues in contact with PHE 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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28B TYR* 3.8 39.9 - + + +
37B PRO* 3.8 15.0 - - + -
42B ASP 3.2 11.3 + - - +
43B ARG* 3.0 26.2 + - - +
45B CYS* 1.3 80.0 - - - +
47B VAL* 1.3 71.8 + - + +
49B ASP* 3.3 7.9 + - + +
50B CYS* 3.2 42.0 + - - -
131B GLU* 3.7 37.5 - - + -
132B GLU 3.5 27.1 - - - -
133B CYS* 4.6 4.9 - - - -
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Residues in contact with VAL 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ARG* 2.9 28.3 + - + +
44B CYS* 4.1 5.8 - - - +
46B PHE* 1.3 83.9 - - + +
48B HIS* 1.3 61.6 + - - +
50B CYS* 3.2 9.3 + - + +
51B CYS* 2.8 28.8 + - + +
54B ARG* 5.2 9.0 - - - +
101B VAL* 6.2 4.7 - - + -
105B CYS* 6.2 1.1 - - - -
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Residues in contact with HIS 48 (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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2B LEU* 5.8 0.4 - - - +
5B PHE* 3.4 29.3 - + - -
44B CYS 3.2 16.1 + - - +
45B CYS* 3.2 14.3 + - - +
47B VAL* 1.3 75.6 - - - +
49B ASP* 1.3 64.2 + - - +
51B CYS* 3.1 8.2 - - - +
52B TYR* 2.9 63.3 + + - +
98B CYS* 3.4 21.6 + - - +
99B ASP* 3.0 26.7 - - - -
102B ALA* 3.7 12.8 - - + +
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Residues in contact with ASP 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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28B TYR* 3.7 20.6 - - + -
32B GLY* 4.7 1.0 - - - -
33B GLY 4.7 4.5 + - - -
45B CYS 3.1 13.5 + - - +
46B PHE* 3.3 11.0 - - + +
48B HIS* 1.3 84.2 - - - +
50B CYS* 1.3 52.1 + - - +
52B TYR* 3.2 7.6 + - - +
53B GLY* 2.7 33.3 + - - -
133B CYS* 5.0 1.8 - - - -
134B CA 3.1 27.0 - - - -
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Residues in contact with CYS 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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46B PHE* 3.2 30.5 + - - -
47B VAL* 3.2 11.6 + - + +
49B ASP* 1.3 78.9 - - - +
51B CYS* 1.3 60.0 + - - +
53B GLY* 2.8 18.2 + - - +
54B ARG* 3.0 33.3 + - - +
133B CYS* 2.0 63.3 - - + +
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Residues in contact with CYS 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 VAL* 2.8 14.6 + - + +
48B HIS* 3.1 12.8 - - - +
50B CYS* 1.3 76.2 - - - +
52B TYR* 1.3 63.5 + - - +
54B ARG* 3.0 39.1 + - - +
55B LEU* 3.7 10.7 - - - +
97B GLU* 5.0 1.1 - - - -
98B CYS* 2.0 55.0 - - + -
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Residues in contact with TYR 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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2B LEU* 4.4 14.8 + - + +
5B PHE* 4.7 0.7 - - - -
48B HIS* 2.9 49.0 + + - +
49B ASP* 3.6 9.2 - - - +
51B CYS* 1.3 72.7 - - - +
53B GLY* 1.3 58.9 + - - +
55B LEU* 2.9 30.0 + - + +
56B VAL* 5.2 0.2 - - - -
68B THR* 3.4 55.7 + - + +
69B LYS* 4.4 12.3 - - + -
95B ILE* 3.9 9.9 - - + +
98B CYS* 3.5 21.1 - - + -
99B ASP* 2.5 28.2 + - - -
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Residues in contact with GLY 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 ASP 2.7 19.5 + - - -
50B CYS* 2.8 8.9 + - - -
52B TYR* 1.3 74.6 - - - +
54B ARG* 1.3 59.0 + - - +
55B LEU 3.3 0.7 + - - -
56B VAL* 4.1 12.0 + - - +
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Residues in contact with ARG 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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47B VAL* 4.7 8.5 + - - +
50B CYS* 3.0 24.6 + - - +
51B CYS* 3.0 41.5 + - - +
53B GLY* 1.3 76.0 - - - +
55B LEU* 1.3 68.3 + - + +
56B VAL* 3.4 15.3 + - - +
133B CYS* 5.3 8.1 + - - +
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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