Contacts of the helix formed by residues 18 - 36 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B SER* 3.3 8.2 + - - +
17B PRO* 1.3 78.7 - - + +
19B GLN* 1.3 63.9 + - - +
20B ASN* 2.6 48.0 + - - +
21B ILE* 3.1 29.2 + - + +
22B ARG* 3.2 20.5 + - - +
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Residues in contact with GLN 19 (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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47A VAL 5.0 8.0 - - - +
48A HIS* 5.7 4.0 - - - -
17B PRO 3.4 5.2 + - - +
18B ASP* 1.3 73.2 + - - +
20B ASN* 1.3 78.9 + - - +
22B ARG* 3.3 34.3 + - - +
23B LEU* 3.1 27.5 + - - +
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Residues in contact with ASN 20 (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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18B ASP* 2.6 26.1 + - - +
19B GLN* 1.3 91.4 + - - +
21B ILE* 1.3 57.8 + - + +
23B LEU* 3.6 8.5 + - - +
24B THR* 2.7 39.1 + - - +
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Residues in contact with ILE 21 (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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12B ASN* 3.8 19.5 - - + +
16B SER* 3.2 25.4 - - - +
18B ASP* 3.1 28.8 + - + +
20B ASN* 1.3 77.0 - - + +
22B ARG* 1.3 53.2 + - - +
24B THR* 3.1 6.8 + - - -
25B SER* 2.8 49.2 + - - +
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Residues in contact with ARG 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 5.8 3.4 + - - +
47A VAL* 3.5 46.9 + - - +
64A TRP* 4.1 17.6 - - - -
12B ASN 3.4 23.6 - - - +
13B SER* 3.8 20.5 - - - +
14B ILE 4.6 1.8 - - - -
16B SER* 3.4 29.5 + - - +
17B PRO* 3.7 11.7 + - - +
18B ASP 3.2 5.3 + - - +
19B GLN* 3.3 39.3 + - - +
21B ILE* 1.3 79.5 - - - +
23B LEU* 1.3 63.0 + - - +
25B SER* 3.7 1.2 - - - -
26B GLU* 3.0 28.0 + - - +
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Residues in contact with LEU 23 (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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43A LEU 5.9 2.9 - - - +
19B GLN 3.1 13.8 + - - +
20B ASN* 3.8 8.7 - - - +
21B ILE 3.3 0.2 - - - -
22B ARG* 1.3 78.4 - - - +
24B THR* 1.3 58.2 + - - +
26B GLU* 3.4 11.9 + - + +
27B THR* 2.5 39.7 + - - +
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Residues in contact with THR 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 6.4 0.7 - - + -
20B ASN* 2.7 25.8 + - - +
21B ILE* 3.5 6.8 - - - +
23B LEU* 1.3 77.7 - - - +
25B SER* 1.3 58.1 + - - +
27B THR* 3.1 9.7 + - - -
28B GLN* 2.9 30.3 + - + +
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Residues in contact with SER 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 3.4 41.0 - - - +
12B ASN* 3.2 23.9 + - - +
13B SER* 3.7 6.7 - - - -
21B ILE* 2.8 31.2 + - - +
22B ARG 3.7 3.1 - - - -
24B THR* 1.3 74.2 - - - +
26B GLU* 1.3 61.7 + - - +
28B GLN* 3.3 2.8 + - - +
29B LEU* 3.0 27.4 + - - +
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Residues in contact with GLU 26 (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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44A GLY* 4.5 3.7 - - - -
45A VAL* 4.9 3.8 - - - +
74A GLY* 3.1 20.2 - - - -
75A LEU* 3.3 24.1 + - + +
79A TYR* 2.8 35.6 + - - -
13B SER* 3.8 14.0 + - - +
22B ARG 3.0 18.4 + - - +
23B LEU* 3.7 11.2 - - + +
25B SER* 1.3 75.4 - - - +
27B THR* 1.3 61.3 + - - +
29B LEU* 3.4 6.8 + - - +
30B LYS* 3.1 23.9 + - + +
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Residues in contact with THR 27 (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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23B LEU* 2.5 34.9 + - - +
24B THR* 3.3 9.5 - - - -
26B GLU* 1.3 76.6 - - - +
28B GLN* 1.3 61.9 + - - +
30B LYS* 3.2 7.9 + - + +
31B LYS* 3.2 24.7 + - + +
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Residues in contact with GLN 28 (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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1B MET* 4.1 16.6 - - + +
9B LEU* 3.5 33.2 - - + -
24B THR* 2.9 19.0 + - + +
25B SER 3.7 4.5 - - - +
27B THR* 1.3 74.2 - - - +
29B LEU* 1.3 64.4 + - - +
31B LYS* 3.4 24.4 + - - +
32B LEU* 3.2 22.9 + - - +
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Residues in contact with LEU 29 (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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75A LEU* 4.8 11.4 - - + -
6B PHE* 3.5 36.8 - - + -
9B LEU* 4.0 20.9 - - + +
10B LEU* 3.6 29.8 - - + -
13B SER* 3.2 29.6 - - - +
25B SER 3.0 15.6 + - - +
26B GLU* 3.6 7.9 - - - +
27B THR 3.3 0.2 - - - -
28B GLN* 1.3 75.7 - - - +
30B LYS* 1.3 62.5 - - - +
32B LEU* 3.6 3.9 + - - +
33B SER* 3.2 16.6 + - - -
40B PHE* 3.5 19.8 - - + -
64B THR* 5.8 1.8 - - + +
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Residues in contact with LYS 30 (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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74A GLY* 5.4 7.2 + - - +
76A ARG* 5.5 6.9 - - - +
26B GLU* 3.1 18.2 + - + +
27B THR* 3.2 8.3 + - + +
29B LEU* 1.3 78.5 - - - +
31B LYS* 1.3 61.6 + - - +
33B SER* 3.2 19.6 + - - -
34B ASN* 2.9 28.0 + - - +
68B GLU* 2.6 32.9 + - - +
80B PHE* 5.9 2.2 - - - -
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Residues in contact with LYS 31 (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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27B THR* 3.2 15.1 + - + +
28B GLN* 3.4 27.1 - - - +
30B LYS* 1.3 73.0 - - - +
32B LEU* 1.3 61.7 + - - +
34B ASN* 3.1 11.1 + - - +
35B ASP* 2.8 65.2 + - - +
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Residues in contact with LEU 32 (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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1B MET* 3.3 42.4 - - + -
6B PHE* 3.8 18.8 - - + -
9B LEU* 5.1 1.6 - - + -
28B GLN* 3.2 16.1 + - - +
29B LEU* 3.7 6.1 - - - +
31B LYS* 1.3 84.9 - - + +
33B SER* 1.3 60.4 + - - +
35B ASP* 4.9 2.7 - - - -
36B ASN* 3.2 29.2 + - + +
39B GLN* 3.3 24.0 - - - +
40B PHE* 3.9 21.5 - - + +
43B LEU* 4.8 1.1 - - + -
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Residues in contact with SER 33 (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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29B LEU 3.2 12.6 + - - -
30B LYS* 3.2 15.6 + - - -
31B LYS 3.2 0.4 - - - -
32B LEU* 1.3 76.6 - - - +
34B ASN* 1.3 63.4 + - - +
37B PHE* 3.4 34.7 - - - +
40B PHE* 3.9 20.9 - - - -
68B GLU* 3.0 40.2 + - - +
83B ARG* 3.9 5.1 + - - -
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Residues in contact with ASN 34 (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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30B LYS* 2.9 36.3 + - - +
31B LYS* 3.1 14.1 + - - +
33B SER* 1.3 79.3 - - - +
35B ASP* 1.3 71.6 + - - +
37B PHE* 4.7 2.3 + - - +
68B GLU* 5.4 1.6 - - - +
83B ARG* 5.1 7.7 + - - +
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Residues in contact with ASP 35 (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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31B LYS* 2.8 53.9 + - - +
32B LEU* 4.7 2.6 - - - +
34B ASN* 1.3 81.2 - - - +
36B ASN* 1.3 62.2 + - + +
37B PHE 4.0 0.4 - - - -
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Residues in contact with ASN 36 (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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32B LEU* 3.2 19.5 + - + +
35B ASP* 1.3 83.8 - - + +
37B PHE* 1.3 65.8 + - - +
38B LEU* 3.6 14.5 - - - +
39B GLN* 3.0 39.5 + - + +
40B PHE 3.0 17.7 + - - -
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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