Contacts of the helix formed by residues 29 - 44 (chain C) in PDB entry 1BQ4
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 ALA 29 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12C GLU* 5.7 0.2 + - - -
15C GLU* 4.9 3.5 + - - +
28C SER* 1.3 73.0 - - - +
30C LYS* 1.3 61.7 + - - +
31C GLY 3.4 0.3 + - - -
32C GLN* 3.6 16.4 + - - +
33C GLN* 3.6 19.6 + - - +
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Residues in contact with LYS 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C GLN* 3.7 35.9 - - + +
15C GLU* 4.9 4.6 + - - +
28C SER* 3.2 7.5 + - - +
29C ALA* 1.3 78.6 - - - +
31C GLY* 1.3 59.2 + - - +
33C GLN* 3.5 21.9 + - - +
34C GLU* 3.0 57.8 + - - +
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Residues in contact with GLY 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C GLY* 3.9 25.9 + - - -
10C GLN* 3.9 9.6 - - - +
27C LEU* 4.0 11.0 - - - +
28C SER* 2.7 20.0 + - - -
30C LYS* 1.3 69.8 - - - +
32C GLN* 1.3 62.6 + - - -
33C GLN 3.1 2.2 - - - -
34C GLU* 3.3 6.4 + - - +
35C ALA* 3.0 19.9 + - - +
63C THR* 5.8 0.2 - - - +
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Residues in contact with GLN 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C LYS* 4.7 9.9 - - - +
27C LEU* 3.8 33.6 + - + +
28C SER 2.9 24.9 + - - +
29C ALA* 3.6 12.4 + - - +
31C GLY* 1.3 73.9 - - - +
33C GLN* 1.3 57.7 + - - +
35C ALA* 3.1 23.4 - - - +
36C ALA* 3.2 7.6 + - - +
62C GLN* 4.6 14.0 + - - +
66C ILE* 3.8 22.6 - - + +
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Residues in contact with GLN 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ALA 3.6 10.1 + - - +
30C LYS* 3.5 29.5 + - - +
32C GLN* 1.3 75.1 - - - +
34C GLU* 1.3 61.8 + - - +
35C ALA 3.0 1.6 - - - -
36C ALA* 3.2 9.6 + - + +
37C ARG* 2.8 27.9 + - + +
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Residues in contact with GLU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C GLY* 3.8 14.5 - - - +
10C GLN* 4.2 5.7 + - - +
30C LYS* 3.0 42.9 + - - +
31C GLY* 3.3 9.5 + - - +
33C GLN* 1.3 78.6 - - + +
35C ALA* 1.3 56.5 + - - +
37C ARG* 3.6 10.8 - - - +
38C ALA* 3.0 25.5 + - - +
207C THR* 2.9 39.7 + - - +
208C GLY* 3.6 16.0 - - - -
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Residues in contact with ALA 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C LEU* 4.8 0.4 - - + -
31C GLY 3.0 12.0 + - - +
32C GLN* 3.1 15.9 - - - +
34C GLU* 1.3 75.6 - - - +
36C ALA* 1.3 60.0 + - - +
38C ALA* 3.1 10.4 - - - +
39C GLY 3.0 22.0 + - - -
63C THR* 3.8 36.3 - - + +
66C ILE* 3.8 17.0 - - + -
67C ALA* 3.4 8.5 - - - +
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Residues in contact with ALA 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C GLN 3.2 8.9 + - - +
33C GLN* 3.4 12.6 - - + +
35C ALA* 1.3 77.2 - - - +
37C ARG* 1.3 64.3 + - - +
39C GLY* 2.9 12.0 + - - -
40C GLU* 3.2 21.7 + - - +
66C ILE* 3.9 7.1 - - + +
70C LYS* 3.8 30.8 - - - +
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Residues in contact with ARG 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C GLN* 2.8 17.8 + - + +
34C GLU* 3.6 10.8 - - - +
36C ALA* 1.3 74.3 - - - +
38C ALA* 1.3 67.1 + - - +
40C GLU* 3.3 15.1 + - - +
41C LEU* 2.9 61.6 + - + +
44C GLU* 4.6 7.9 + - - -
208C GLY 4.4 10.1 - - - +
209C ILE* 6.3 0.9 - - + -
229C ASP* 3.3 26.0 + - - -
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Residues in contact with ALA 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C VAL* 4.2 23.8 - - + -
34C GLU 3.0 16.8 + - - +
35C ALA* 3.1 13.7 - - - +
36C ALA 3.1 0.2 - - - -
37C ARG* 1.3 76.0 - - - +
39C GLY* 1.3 63.7 - - - +
41C LEU* 3.1 15.3 + - - +
42C LEU* 3.4 15.9 + - + +
63C THR* 5.4 0.7 - - + +
67C ALA* 4.3 8.3 - - + -
208C GLY* 3.8 15.9 - - - +
210C PRO* 4.3 8.7 - - + +
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Residues in contact with GLY 39 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C ALA 3.0 8.9 + - - -
36C ALA 2.9 9.6 + - - -
38C ALA* 1.3 75.8 - - - +
40C GLU* 1.3 61.5 + - - -
42C LEU* 3.0 20.1 + - - +
43C LYS* 3.4 10.4 + - - +
67C ALA* 3.3 27.8 - - - +
70C LYS* 3.7 11.7 - - - -
71C ALA* 4.0 3.8 - - - +
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Residues in contact with GLU 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ALA* 3.2 15.4 + - - +
37C ARG* 3.3 17.4 + - - +
39C GLY* 1.3 72.9 - - - +
41C LEU* 1.3 57.8 + - - +
43C LYS* 3.7 14.2 + - - +
44C GLU* 2.9 34.5 + - + +
70C LYS* 3.5 40.3 + - - +
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Residues in contact with LEU 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ARG* 2.9 57.7 + - + +
38C ALA* 3.1 9.8 + - - +
39C GLY 3.1 1.2 - - - -
40C GLU* 1.3 75.2 - - - +
42C LEU* 1.3 62.4 + - - +
44C GLU* 3.9 18.2 - - + +
45C LYS* 3.5 14.5 + - + +
208C GLY 4.5 7.6 - - - +
209C ILE* 4.9 3.1 - - + -
210C PRO* 4.3 20.6 - - + -
228C LEU* 3.0 42.7 - - + +
229C ASP* 3.8 25.4 - - + +
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Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C VAL* 3.8 21.8 - - + -
6C VAL* 5.5 2.2 - - + -
38C ALA* 3.4 13.9 + - + +
39C GLY* 3.0 11.5 + - - +
41C LEU* 1.3 77.3 - - - +
43C LYS* 1.3 61.6 + - - +
46C LYS* 3.3 2.8 + - - -
47C VAL* 3.0 66.6 + - + +
48C TYR* 4.4 1.0 - - - -
49C PRO* 4.4 10.3 - - + -
67C ALA* 5.1 7.4 - - + +
68C LEU* 5.1 3.4 - - + -
71C ALA* 4.3 18.8 - - + -
177C MET* 4.3 23.6 - - + -
210C PRO* 4.6 7.4 - - + -
228C LEU* 4.2 9.2 - - + -
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Residues in contact with LYS 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C GLY 3.4 8.2 + - - +
40C GLU* 3.7 15.2 + - - +
42C LEU* 1.3 80.9 - - - +
44C GLU* 1.3 64.5 + - - +
46C LYS* 3.4 18.0 + - - +
48C TYR* 4.0 17.3 + - - +
70C LYS 3.4 21.7 + - - +
71C ALA* 4.3 13.4 - - - +
72C ASP* 3.5 26.4 + - - +
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Residues in contact with GLU 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ARG* 4.6 6.9 + - - -
40C GLU* 2.9 21.1 + - + +
41C LEU* 4.1 23.3 - - - +
43C LYS* 1.3 78.7 - - - +
45C LYS* 1.3 90.5 + - + +
46C LYS* 3.2 12.0 + - - +
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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