Contacts of the helix formed by residues 3 - 19 (chain B) in PDB entry 1BT6
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 GLN 3 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A THR* 4.0 32.6 + - + +
14A THR* 4.9 8.3 + - - +
17A LYS* 5.9 2.3 + - - +
37A GLU* 3.3 12.6 + - - +
2B SER* 1.3 75.6 - - - +
4B MET* 1.3 57.6 + - - +
6B HIS* 3.1 8.6 + - - +
7B ALA* 2.8 30.1 + - - +
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Residues in contact with MET 4 (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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10A THR* 4.9 1.3 - - - -
11A MET* 3.5 36.8 - - + -
14A THR* 3.8 28.5 - - + +
33A LEU* 5.0 1.6 - - + -
37A GLU* 2.9 39.8 + - + +
38A PHE* 3.9 15.5 - - + -
71A PHE* 3.6 13.9 - - + -
75A ILE* 3.5 37.0 - - + -
2B SER* 3.7 2.5 - - - +
3B GLN* 1.3 75.4 - - - +
5B GLU* 1.3 57.2 + - - +
7B ALA* 3.2 4.0 + - - +
8B MET* 2.9 35.2 + - + +
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Residues in contact with GLU 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PHE* 4.0 31.9 - - + -
39A PRO* 4.9 0.9 - - - +
40A GLY 5.2 0.3 + - - -
1B PRO* 2.9 9.1 - - + +
2B SER* 2.8 39.1 + - - +
4B MET* 1.3 76.0 - - - +
6B HIS* 1.4 56.7 + - - +
8B MET* 3.2 4.0 + - - +
9B GLU* 2.9 29.6 + - - +
0D ACE 3.8 14.8 - - - +
3D VAL* 3.9 18.0 - - + +
4D HIS* 2.4 47.5 + - - +
7D LEU* 4.0 6.5 - - + +
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Residues in contact with HIS 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B PRO* 3.9 16.4 + - + +
2B SER 3.0 28.8 + - - -
3B GLN* 3.6 8.7 - - - +
5B GLU* 1.4 71.1 - - - +
7B ALA* 1.3 67.4 + - - +
9B GLU* 3.4 4.2 + - - +
10B THR* 2.9 33.3 + - + +
0D ACE 3.4 28.0 - - + +
1D SER* 5.8 1.6 - - - -
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Residues in contact with ALA 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ALA* 3.7 36.2 - - + +
10A THR* 4.0 12.1 - - + +
11A MET* 4.1 14.4 - - + -
3B GLN 2.8 17.4 + - - +
4B MET* 3.2 5.6 + - - +
6B HIS* 1.3 80.9 - - - +
8B MET* 1.3 57.9 + - - +
10B THR* 3.4 1.7 + - - -
11B MET* 3.0 31.1 + - - +
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Residues in contact with MET 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A MET* 4.1 16.8 - - + -
38A PHE* 3.3 34.3 - - + -
75A ILE* 4.3 7.0 - - + -
78A LEU* 3.8 28.0 - - + +
79A THR* 3.6 38.3 - - + +
82A CYS* 4.4 4.3 - - - -
4B MET* 2.9 17.5 + - + +
5B GLU* 3.2 7.4 + - - +
7B ALA* 1.3 74.0 - - - +
9B GLU* 1.3 67.4 + - - +
11B MET* 3.4 4.8 + - - +
12B MET* 3.1 21.8 + - - +
3D VAL* 4.1 21.8 - - + -
7D LEU* 4.3 8.5 - - + -
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Residues in contact with GLU 9 (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 2.9 16.1 + - - +
6B HIS* 3.7 8.2 + - - +
8B MET* 1.3 76.7 - - - +
10B THR* 1.4 63.7 + - + +
12B MET* 2.9 6.0 + - + +
13B PHE* 2.8 66.5 + - + +
0D ACE 2.9 4.4 - - - +
1D SER* 2.4 36.6 + - - -
2D THR* 2.9 14.1 + - - +
3D VAL* 3.2 17.9 + - + +
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Residues in contact with THR 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLN* 3.6 33.1 + - + +
4A MET* 4.5 1.0 + - - -
7A ALA* 3.5 19.5 - - + +
6B HIS* 2.9 36.9 + - + +
7B ALA* 3.4 3.8 + - - -
8B MET 3.3 0.2 - - - -
9B GLU* 1.4 75.0 - - + +
11B MET* 1.3 53.9 + - - +
13B PHE* 3.4 5.6 + - - +
14B THR* 2.8 37.9 + - - -
17B LYS* 4.8 3.5 + - - +
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Residues in contact with MET 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A MET* 3.9 22.2 - - + -
7A ALA* 4.1 25.6 - - + -
8A MET* 4.1 9.6 - - + +
11A MET* 3.5 36.8 - - + -
72A PHE* 4.9 2.5 - - + -
79A THR* 5.4 1.8 - - + -
7B ALA 3.0 16.1 + - - +
8B MET* 3.9 5.2 - - - +
9B GLU 3.2 0.4 - - - -
10B THR* 1.3 73.9 - - - +
12B MET* 1.3 60.4 + - - +
14B THR* 3.8 0.9 - - - -
15B PHE* 3.5 8.3 + - - +
68B PHE* 4.2 2.1 - - + -
71B PHE* 3.4 27.5 - - + -
72B PHE* 4.2 21.8 - - + -
75B ILE* 3.8 31.4 - - + -
79B THR* 5.1 0.2 - - - +
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Residues in contact with MET 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A THR* 4.8 3.4 - - + +
82A CYS* 4.1 13.9 - - - +
83A ASN* 3.8 44.4 - - + +
86A PHE* 3.5 38.8 - - + -
8B MET 3.1 12.2 + - - +
9B GLU* 2.9 10.4 + - + +
11B MET* 1.3 73.7 - - - +
13B PHE* 1.3 83.1 + - + +
15B PHE* 3.6 3.6 + - - +
16B HIS* 3.1 31.9 + - + -
68B PHE* 4.0 12.5 - - + -
2D THR* 4.3 9.0 - - - +
3D VAL* 4.4 14.1 - - + -
6D ILE* 5.2 3.1 - - + -
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Residues in contact with PHE 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PHE* 4.2 20.0 - + - -
9B GLU* 2.8 52.2 + - + +
10B THR* 4.0 4.5 - - - +
12B MET* 1.3 101.1 - - + +
14B THR* 1.3 55.9 + - - +
16B HIS* 3.3 6.4 + + + +
17B LYS* 3.0 48.5 + - - +
2D THR* 3.8 20.4 - - + -
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Residues in contact with THR 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLN* 5.4 2.3 - - - +
4A MET* 3.3 40.4 + - + +
10B THR* 2.8 23.0 + - - -
11B MET 3.8 3.6 - - - -
12B MET 3.3 0.4 - - - -
13B PHE* 1.3 70.7 - - - +
15B PHE* 1.3 68.7 + - - +
17B LYS* 3.1 31.0 + - + +
18B PHE* 3.1 35.7 - - + -
33B LEU* 4.1 11.2 - - + -
37B GLU* 4.1 9.1 + - + +
71B PHE* 4.7 2.9 - - + -
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Residues in contact with PHE 15 (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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83A ASN* 5.4 0.4 - - - -
11B MET 3.5 4.5 + - - +
12B MET 3.7 7.2 - - - +
14B THR* 1.3 81.7 - - - +
16B HIS* 1.3 86.6 + + - +
18B PHE* 3.3 2.3 + - - +
19B ALA* 3.0 32.8 + - + +
23B GLY 3.5 26.7 - - - -
24B TYR* 3.9 9.9 - - - -
25B LEU* 4.1 14.9 - - + +
33B LEU* 4.8 5.8 - - - -
66B VAL 4.0 7.2 - - - -
67B GLY 3.6 6.1 - - - -
68B PHE* 3.4 48.9 - + + -
71B PHE* 3.7 44.3 - + + -
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Residues in contact with HIS 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASN* 2.7 33.0 + - - -
86A PHE* 3.4 28.5 - + + -
87A VAL* 3.8 18.4 - - + -
91A LYS* 6.3 1.1 - - + -
12B MET* 3.1 27.3 + - + +
13B PHE* 3.3 9.6 + - + +
14B THR 3.2 0.2 - - - -
15B PHE* 1.3 101.0 - + - +
17B LYS* 1.3 61.4 + - - +
19B ALA* 4.4 2.1 - - - +
20B GLY* 3.0 32.1 + - - +
23B GLY* 5.3 8.0 - - - -
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Residues in contact with LYS 17 (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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3A GLN* 4.0 26.8 + - - +
10B THR* 4.8 4.0 + - - +
13B PHE* 3.0 37.0 + - - +
14B THR* 3.1 22.0 + - + +
16B HIS* 1.3 75.5 - - - +
18B PHE* 1.3 77.7 + - + +
20B GLY* 4.5 2.9 + - - -
37B GLU* 5.6 3.3 + - - +
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Residues in contact with PHE 18 (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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14B THR* 3.1 40.3 + - + +
15B PHE 4.2 1.6 - - - +
16B HIS 3.2 0.2 - - - -
17B LYS* 1.3 93.1 - - + +
19B ALA* 1.4 61.3 + - - +
25B LEU* 4.9 3.4 - - + -
29B ASP* 2.7 34.7 - - + +
32B VAL* 4.2 20.0 - - + -
33B LEU* 3.2 50.0 - - + -
36B LYS* 4.5 17.9 - - + -
37B GLU* 4.0 22.0 - - + -
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 3.0 31.5 + - + +
16B HIS* 3.0 5.3 + - - +
18B PHE* 1.4 80.7 - - - +
20B GLY* 1.3 64.3 + - - +
22B LYS* 3.0 30.0 - - - +
23B GLY* 4.1 2.4 + - - -
24B TYR 3.1 37.3 - - - +
25B LEU* 4.3 4.0 - - + +
29B ASP* 4.8 0.2 - - - -
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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