Contacts of the helix formed by residues 24 - 40 (chain B) in PDB entry 1B3U
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 VAL 24 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B GLU 3.2 4.7 + - - +
23B ASP* 1.3 72.7 + - - +
25B GLN* 1.3 62.1 + - - +
27B ARG* 3.1 39.4 + - - +
28B LEU* 3.0 24.5 + - + +
61B GLU* 4.7 14.6 - - + -
63B GLU* 5.3 13.7 - - + +
64B VAL* 4.4 14.1 - - + +
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Residues in contact with GLN 25 (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 ASP* 3.2 17.7 + - - +
24B VAL* 1.3 78.8 - - - +
26B LEU* 1.3 55.5 + - + +
28B LEU* 3.5 27.5 - - - +
29B ASN* 2.7 53.5 + - - +
32B LYS* 5.3 3.6 - - - +
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Residues in contact with LEU 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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18B GLU* 5.1 1.7 - - - +
21B ASN* 2.9 34.3 - - + +
23B ASP* 2.9 32.2 + - + +
25B GLN* 1.3 75.4 - - + +
27B ARG* 1.3 67.0 + - - +
29B ASN* 3.1 19.1 + - + +
30B SER* 3.0 21.0 + - - -
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Residues in contact with ARG 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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18B GLU 3.5 23.8 + - - +
19B LEU* 3.9 24.0 + - + +
21B ASN* 2.9 23.2 + - + +
22B GLU* 3.2 24.0 + - - +
23B ASP 3.2 10.3 + - - +
24B VAL* 3.1 32.1 + - - +
26B LEU* 1.3 78.3 - - - +
28B LEU* 1.3 62.8 + - - +
30B SER* 3.2 19.0 - - - -
31B ILE* 3.2 13.9 + - - +
60B ASP* 2.8 40.1 + - - +
61B GLU* 3.8 12.3 + - - +
64B VAL* 4.6 5.6 - - + -
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Residues in contact with LEU 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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24B VAL* 3.0 13.9 + - + +
25B GLN* 3.5 34.3 - - - +
27B ARG* 1.3 74.0 - - - +
29B ASN* 1.3 65.7 + - - +
31B ILE* 3.0 9.1 + - - +
32B LYS* 3.0 55.1 + - + +
63B GLU* 4.5 31.9 - - + +
64B VAL* 4.7 9.1 - - + +
67B ALA* 4.3 13.0 - - + -
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Residues in contact with ASN 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLN* 2.7 44.1 + - - +
26B LEU* 3.1 19.8 + - + +
28B LEU* 1.3 75.5 - - - +
30B SER* 1.3 64.9 + - - +
32B LYS* 3.2 28.4 + - - +
33B LYS* 3.3 24.4 + - - +
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Residues in contact with SER 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU* 3.6 11.5 - - - +
18B GLU* 2.8 52.7 + - - +
19B LEU* 4.4 4.0 - - - +
26B LEU 3.0 11.5 + - - -
27B ARG* 3.2 14.1 - - - -
28B LEU 3.1 0.2 - - - -
29B ASN* 1.3 76.5 - - - +
31B ILE* 1.3 62.3 + - - +
33B LYS* 2.9 19.0 + - - +
34B LEU* 3.3 8.5 + - - -
37B ILE* 5.1 1.7 - - - +
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Residues in contact with ILE 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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15B LEU* 5.1 7.0 - - + -
19B LEU* 4.5 20.2 - - + -
27B ARG 3.2 12.1 + - - +
28B LEU* 3.0 9.0 + - - +
30B SER* 1.3 72.3 - - - +
32B LYS* 1.3 57.4 + - - +
33B LYS 2.9 4.9 - - - -
34B LEU* 2.7 40.5 + - + +
54B LEU* 5.9 2.9 - - + -
58B ILE* 5.9 4.3 - - + -
64B VAL* 3.7 26.5 - - + -
67B ALA* 3.7 16.2 - - + +
68B LEU* 3.6 50.5 - - + +
71B GLN* 3.9 6.8 - - + +
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Residues in contact with LYS 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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25B GLN* 5.3 3.0 - - - +
28B LEU* 3.0 43.7 + - + +
29B ASN* 3.2 22.4 + - - +
31B ILE* 1.3 75.9 - - - +
33B LYS* 1.3 61.9 + - + +
34B LEU 3.5 0.6 + - - -
35B SER* 5.0 1.9 + - - -
67B ALA* 4.9 9.2 - - + -
70B GLU* 5.8 5.6 - - - +
71B GLN* 3.7 18.5 + - - +
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Residues in contact with LYS 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 ASN* 3.6 17.9 - - - +
30B SER* 2.9 12.4 + - - +
31B ILE 2.9 0.8 - - - -
32B LYS* 1.3 81.8 - - + +
34B LEU* 1.3 65.5 + - - +
35B SER* 3.0 8.3 - - - -
36B THR* 2.8 32.1 + - - +
37B ILE* 3.5 5.3 - - + +
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Residues in contact with LEU 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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15B LEU* 4.0 33.4 - - + -
30B SER 3.3 3.6 + - - -
31B ILE* 2.7 24.1 + - + +
32B LYS 3.5 0.8 - - - -
33B LYS* 1.3 76.7 - - - +
35B SER* 1.3 62.2 + - - +
37B ILE* 3.0 22.0 + - + +
38B ALA* 3.3 8.3 + - - +
50B LEU* 4.5 12.8 - - + -
54B LEU* 4.0 14.8 - - + -
68B LEU* 3.5 32.1 - - + -
71B GLN* 3.9 17.4 - - + +
72B LEU* 5.1 2.2 - - + -
75B PHE* 3.6 22.4 - - + -
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Residues in contact with SER 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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32B LYS 5.0 1.6 + - - -
33B LYS* 4.0 6.9 + - - -
34B LEU* 1.3 76.9 - - - +
36B THR* 1.3 62.0 + - - +
38B ALA* 3.3 2.1 + - - +
39B LEU* 2.8 33.7 + - - +
71B GLN* 4.6 10.5 + - - +
75B PHE* 3.8 17.2 - - - -
78B LEU* 3.7 21.7 - - - +
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Residues in contact with THR 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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33B LYS* 2.8 25.8 + - - +
35B SER* 1.3 81.9 + - - +
37B ILE* 1.3 61.9 + - + +
39B LEU* 3.2 10.2 + - + +
40B ALA* 2.8 30.8 + - + +
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Residues in contact with ILE 37 (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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11B PRO* 3.9 31.6 - - + +
12B ILE* 4.5 3.4 - - + +
14B VAL* 5.9 2.7 - - + -
15B LEU* 4.1 17.9 - - + -
18B GLU* 4.3 15.5 - - - +
30B SER 5.1 1.1 - - - +
33B LYS* 3.5 20.4 - - + +
34B LEU* 3.0 19.5 + - + +
36B THR* 1.3 80.5 - - + +
38B ALA* 1.3 64.1 + - - +
40B ALA* 3.0 8.5 + - - +
41B LEU* 2.9 40.1 + - + +
50B LEU* 4.5 15.9 - - + -
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Residues in contact with ALA 38 (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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34B LEU 3.3 2.9 + - - +
35B SER 3.3 7.7 + - - +
37B ILE* 1.3 78.7 - - - +
39B LEU* 1.3 53.1 + - - +
41B LEU* 2.4 34.5 + - - +
42B GLY 4.5 0.5 - - - -
46B THR* 3.2 31.4 + - + +
50B LEU* 4.4 4.7 - - + +
75B PHE* 4.0 26.5 - - + -
78B LEU* 4.3 17.8 - - + +
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Residues in contact with LEU 39 (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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35B SER* 2.8 20.0 + - - +
36B THR* 3.5 9.2 - - - +
38B ALA* 1.3 77.1 - - - +
40B ALA* 1.3 60.2 + - - +
41B LEU 3.2 6.3 - - - +
78B LEU* 4.2 19.4 - - + +
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Residues in contact with ALA 40 (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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4B ASP* 5.5 2.6 - - - +
7B ASP* 5.6 1.6 - - - +
11B PRO* 3.9 23.1 - - + +
36B THR* 2.8 16.7 + - + +
37B ILE* 3.0 8.7 + - - +
39B LEU* 1.3 77.7 - - - +
41B LEU* 1.3 59.2 + - - +
42B GLY 4.1 0.3 + - - -
45B ARG* 5.3 2.9 + - - -
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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