Contacts of the helix formed by residues 41 - 52 (chain A) in PDB entry 1BL0
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 LYS 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A GLU* 4.3 22.4 - - + +
32A LYS* 4.0 28.4 - - - +
35A GLU* 3.6 36.7 + - + +
39A TYR 4.1 0.8 + - - -
40A SER* 1.3 71.5 - - - +
42A TRP* 1.3 107.4 + - + +
44A LEU* 3.6 5.8 + - - +
45A GLN* 2.8 38.0 + - - +
416B C 6.0 0.9 - - - +
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Residues in contact with TRP 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A SER* 3.1 21.4 - - - -
41A LYS* 1.3 105.9 - - + +
43A HIS* 1.3 57.9 + - - +
45A GLN* 3.4 12.6 - - - +
46A ARG* 3.0 28.1 + - - +
417B G 5.0 1.8 + - - -
418B T 3.2 27.4 + - + +
419B G 5.1 0.2 - - - +
431C C 3.1 72.0 - + + +
432C C 3.1 46.5 - + - +
433C A 3.9 3.8 - - - +
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Residues in contact with HIS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A TYR* 3.1 33.7 - + + -
40A SER* 2.9 12.0 + - - +
42A TRP* 1.3 74.9 - - - +
44A LEU* 1.3 58.9 + - - +
45A GLN 2.9 1.1 - - - -
46A ARG* 2.6 41.0 + - - +
47A MET* 2.8 41.4 + - + +
428C A 4.5 4.9 - - + -
429C T 3.0 59.6 + + + +
430C G 3.0 24.8 + - + +
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Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A THR* 5.9 2.0 - - - +
13A ILE* 3.8 22.2 - - + -
16A ILE* 4.5 17.9 - - + -
31A GLU 5.2 0.9 - - - +
34A SER* 3.3 40.4 - - - +
35A GLU* 4.0 8.7 - - - +
37A SER 4.0 11.2 - - - +
38A GLY* 6.0 0.2 - - - -
39A TYR* 4.6 12.2 - - + +
40A SER 2.9 17.5 + - - +
41A LYS* 3.8 5.2 - - - +
43A HIS* 1.3 73.9 - - - +
45A GLN* 1.3 61.7 + - + +
47A MET* 3.5 13.8 + - + +
48A PHE* 3.0 28.4 + - + +
56A LEU* 4.7 13.9 - - + -
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Residues in contact with GLN 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLU* 3.8 32.1 + - + +
41A LYS* 2.8 37.6 + - - +
42A TRP* 3.4 11.2 - - - +
43A HIS 2.9 0.6 - - - -
44A LEU* 1.3 78.1 - - + +
46A ARG* 1.3 61.7 + - - +
48A PHE* 3.8 4.1 - - - +
49A LYS* 2.9 27.3 + - - +
56A LEU* 4.7 12.8 + - + +
416B C 5.3 0.6 - - - +
417B G 3.2 45.4 + - - +
418B T 3.6 21.9 - - + +
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Residues in contact with ARG 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A TRP* 3.0 12.9 + - - +
43A HIS* 2.6 28.8 + - + +
45A GLN* 1.3 74.9 - - - +
47A MET* 1.4 63.9 + - - +
49A LYS* 3.7 4.3 - - - +
50A LYS* 3.0 29.7 + - + +
418B T 5.6 0.6 - - - +
419B G 4.1 16.7 + - - -
420B G 2.7 19.6 + - - -
421B C 4.1 3.7 - - - +
429C T 4.3 22.2 - - - +
430C G 2.9 14.8 + - - -
431C C 2.5 35.0 - - - +
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Residues in contact with MET 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ASP* 3.6 25.8 - - + +
12A THR* 3.2 36.8 - - + +
13A ILE* 3.6 15.5 - - + -
39A TYR* 3.9 20.0 - - + -
43A HIS* 2.8 55.2 + - + +
44A LEU* 3.8 11.4 - - + +
46A ARG* 1.4 71.0 - - - +
48A PHE* 1.3 52.7 + - - +
50A LYS* 3.0 16.6 - - + +
51A GLU* 2.6 39.2 + - - +
429C T 4.3 3.1 - - - -
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Residues in contact with PHE 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ILE* 3.5 29.3 - - + +
16A ILE* 3.9 11.4 - - + -
17A LEU* 3.2 34.8 - - + -
20A ILE* 4.5 0.2 - - + -
44A LEU* 3.0 18.2 + - + +
45A GLN* 3.8 3.4 - - - +
47A MET* 1.3 74.9 - - - +
49A LYS* 1.3 60.3 + - - +
51A GLU* 3.9 1.3 - - - -
52A THR* 2.8 49.5 + - + +
54A HIS* 3.1 34.1 - - + -
55A SER 4.2 0.4 - - - -
56A LEU* 3.2 49.4 - - + -
59A TYR* 3.7 15.7 - + + -
124A LEU 5.0 0.2 - - - -
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Residues in contact with LYS 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLN 2.9 19.9 + - - +
46A ARG* 3.7 5.4 - - - +
48A PHE* 1.3 73.6 - - - +
50A LYS* 1.3 64.0 + - - +
53A GLY* 2.5 64.6 + - - -
54A HIS 3.5 11.9 - - - +
55A SER* 4.0 11.9 + - - +
418B T 2.5 49.1 + - - +
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Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ASP* 3.1 28.7 - - - +
46A ARG* 3.0 13.8 + - + +
47A MET* 3.0 23.3 - - + +
49A LYS* 1.3 82.1 - - - +
51A GLU* 1.3 64.0 + - - +
53A GLY 4.6 1.0 + - - -
428C A 5.9 1.0 + - - -
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Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ASP* 3.1 24.8 + - + +
10A ALA* 3.2 34.0 + - - +
13A ILE* 3.5 36.6 - - + -
14A HIS* 4.4 11.3 - - - -
47A MET 2.6 22.6 + - - +
48A PHE 3.7 4.3 - - - +
50A LYS* 1.3 81.3 - - - +
52A THR* 1.4 58.2 + - - +
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Residues in contact with THR 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ILE* 4.0 20.4 - - + -
14A HIS* 5.9 2.9 - - + +
17A LEU* 4.4 10.1 - - + -
48A PHE* 2.8 44.2 + - + +
51A GLU* 1.4 74.2 - - - +
53A GLY* 1.4 56.4 + - - +
54A HIS* 3.0 38.4 + - - +
124A LEU 4.7 12.3 - - - +
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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