Contacts of the helix formed by residues 18 - 36 (chain D) in PDB entry 2BKU
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 ASP 18 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D SER* 3.2 5.4 + - - +
17D PRO* 1.3 79.3 - - + +
19D GLN* 1.3 65.4 + - - +
20D ASN* 2.6 47.0 + - - +
21D ILE* 3.0 32.4 + - + +
22D ARG* 3.2 21.5 + - - +
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Residues in contact with GLN 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C VAL 5.9 0.9 - - - +
17D PRO 3.5 5.0 + - - +
18D ASP* 1.3 74.3 + - - +
20D ASN* 1.3 78.0 + - - +
22D ARG* 3.3 32.6 + - - +
23D LEU* 3.1 27.4 + - - +
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Residues in contact with ASN 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ASP* 2.6 23.4 + - - +
19D GLN* 1.3 90.2 + - - +
21D ILE* 1.3 64.9 + - + +
23D LEU* 3.9 10.3 - - - +
24D THR* 2.9 31.0 + - - +
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Residues in contact with ILE 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ASN* 3.4 29.2 - - + +
16D SER* 3.2 24.2 - - - +
18D ASP* 3.0 29.7 + - + +
20D ASN* 1.3 77.8 - - + +
22D ARG* 1.3 53.3 + - - +
24D THR* 3.1 8.2 + - - -
25D SER* 2.7 43.0 + - - +
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Residues in contact with ARG 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C VAL* 5.6 4.0 + - - +
47C VAL* 3.4 47.1 + - - +
64C TRP* 4.1 17.8 - - - -
12D ASN 3.4 22.9 - - - +
13D SER* 3.6 20.7 - - - +
14D ILE 4.6 1.8 - - - -
16D SER* 3.3 29.8 + - - +
17D PRO* 3.5 18.0 + - - +
18D ASP 3.2 4.8 + - - +
19D GLN* 3.3 37.8 + - - +
20D ASN 3.4 0.2 - - - -
21D ILE* 1.3 79.0 - - - +
23D LEU* 1.3 57.2 + - - +
25D SER* 3.7 1.4 - - - -
26D GLU* 2.9 33.1 + - - +
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Residues in contact with LEU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C LEU* 5.4 10.1 - - + +
19D GLN 3.1 14.7 + - - +
20D ASN* 3.9 10.1 - - - +
22D ARG* 1.3 78.8 - - - +
24D THR* 1.3 53.9 + - - +
26D GLU* 3.3 12.6 + - + +
27D THR* 2.5 44.4 + - - +
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Residues in contact with THR 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LEU* 6.0 2.0 - - + -
20D ASN* 2.9 24.1 + - - +
21D ILE* 3.5 6.5 - - - -
23D LEU* 1.3 76.1 - - - +
25D SER* 1.3 59.0 + - - +
27D THR* 3.2 8.8 + - - -
28D GLN* 2.9 31.7 + - + +
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Residues in contact with SER 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D LEU* 3.5 41.2 - - - +
12D ASN* 3.3 18.9 + - - +
13D SER* 3.6 11.2 - - - -
21D ILE* 2.7 31.0 + - - +
22D ARG 3.7 2.9 - - - -
24D THR* 1.3 71.2 - - - +
26D GLU* 1.3 65.3 + - - +
28D GLN* 3.5 2.1 + - - +
29D LEU* 3.1 29.3 + - - +
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Residues in contact with GLU 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C LEU 5.3 0.3 - - - +
44C GLY* 4.3 5.3 - - - -
45C VAL* 4.8 3.6 + - - +
74C GLY* 3.1 18.2 - - - -
75C LEU* 3.9 25.1 - - + +
79C TYR* 2.8 35.7 + - - -
13D SER* 3.6 11.7 + - - +
22D ARG 2.9 18.1 + - - +
23D LEU* 3.6 12.6 - - - +
25D SER* 1.3 73.4 - - - +
27D THR* 1.3 65.8 + - - +
29D LEU* 3.4 6.9 + - - +
30D LYS* 3.1 23.2 + - + +
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Residues in contact with THR 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU* 2.5 33.7 + - - +
24D THR* 3.2 10.1 + - - -
26D GLU* 1.3 76.5 - - - +
28D GLN* 1.3 61.7 + - - +
30D LYS* 3.2 8.6 + - + +
31D LYS* 3.1 23.7 + - + +
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Residues in contact with GLN 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 4.4 15.3 - - + +
9D LEU* 3.6 31.0 - - + -
24D THR* 2.9 20.0 + - + +
25D SER 3.5 4.2 + - - +
26D GLU 3.4 0.2 - - - -
27D THR* 1.3 76.5 - - - +
29D LEU* 1.3 60.8 + - - +
31D LYS* 3.2 28.0 + - - +
32D LEU* 3.2 22.1 + - - +
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Residues in contact with LEU 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C LEU* 4.7 11.9 - - + -
6D PHE* 3.6 35.7 - - + -
9D LEU* 3.9 25.4 - - + +
10D LEU* 3.8 26.2 - - + -
13D SER* 3.3 27.8 - - - +
25D SER 3.1 16.3 + - - +
26D GLU* 3.6 7.4 - - - +
28D GLN* 1.3 73.8 - - - +
30D LYS* 1.3 65.9 + - - +
32D LEU* 3.7 2.4 + - + -
33D SER* 3.2 16.1 + - - -
40D PHE* 3.3 22.1 - - + -
64D THR* 5.7 2.2 - - - +
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Residues in contact with LYS 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C GLY 5.3 7.2 + - - +
76C ARG* 5.2 10.7 - - - +
26D GLU* 3.1 13.9 + - + +
27D THR* 3.2 11.9 + - + +
29D LEU* 1.3 75.4 - - - +
31D LYS* 1.3 64.2 + - - +
33D SER* 3.0 19.5 - - - -
34D ASN* 2.9 29.3 + - - +
67D ASN 5.6 0.4 + - - -
68D GLU* 2.6 35.3 + - - +
76D LYS* 6.1 1.2 - - - +
80D PHE* 5.7 3.2 - - - -
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Residues in contact with LYS 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D THR* 3.1 11.8 + - + +
28D GLN* 3.2 30.1 - - - +
30D LYS* 1.3 75.3 - - - +
32D LEU* 1.3 60.9 + - - +
34D ASN* 2.8 14.1 + - - +
35D ASP* 2.6 65.9 + - - +
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Residues in contact with LEU 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 3.3 41.7 - - + -
6D PHE* 3.8 21.8 - - + -
9D LEU* 5.3 1.6 - - + -
28D GLN* 3.2 17.1 + - - +
29D LEU* 3.9 5.4 - - - +
31D LYS* 1.3 84.2 - - + +
33D SER* 1.3 56.2 + - - +
35D ASP* 4.5 5.2 - - + +
36D ASN* 3.1 40.6 + - + +
39D GLN* 3.3 24.2 - - + +
40D PHE* 3.8 14.5 - - + +
43D LEU* 4.8 1.1 - - + -
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Residues in contact with SER 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D LEU 3.2 14.1 + - - -
30D LYS* 3.0 17.6 + - - -
32D LEU* 1.3 78.6 - - - +
34D ASN* 1.3 59.2 + - - +
37D PHE* 3.6 29.3 - - - +
40D PHE* 3.7 25.1 - - - -
68D GLU* 3.4 37.1 + - - +
83D ARG* 3.9 7.5 + - - -
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Residues in contact with ASN 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LYS* 2.9 41.4 + - - +
31D LYS* 2.8 15.5 + - - +
33D SER* 1.3 74.0 - - - +
35D ASP* 1.3 70.3 + - - +
36D ASN* 4.7 0.2 - - - -
37D PHE* 4.7 1.6 + - - +
68D GLU* 5.8 0.3 - - - +
83D ARG* 5.0 8.6 + - - +
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Residues in contact with ASP 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D LYS* 2.6 56.3 + - - +
32D LEU* 4.6 2.9 - - - +
34D ASN* 1.3 80.9 - - - +
36D ASN* 1.3 62.6 + - + +
37D PHE 4.1 0.2 - - - -
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Residues in contact with ASN 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D LEU* 3.1 23.7 + - + +
35D ASP* 1.3 83.7 - - + +
37D PHE* 1.3 65.7 + - - +
38D LEU* 3.9 10.6 - - - +
39D GLN* 3.2 40.5 + - - +
40D PHE 3.0 17.0 + - - -
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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