Contacts of the helix formed by residues 30 - 46 (chain A) in PDB entry 2QB1
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 SER 30 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A TYR 3.6 1.7 + - - -
29A TRP* 1.3 75.7 - - - +
31A ARG* 1.3 67.8 + - - +
32A ASP* 3.3 14.3 + - - +
33A ASP* 2.7 35.0 + - - -
34A VAL* 3.1 10.2 + - - +
58A ASN* 3.9 6.5 - - - -
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Residues in contact with ARG 31 (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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30A SER* 1.3 72.3 - - - +
32A ASP* 1.3 56.6 + - - +
34A VAL* 3.4 6.1 - - - +
35A ALA* 3.3 22.2 + - - +
55A PHE 5.0 1.5 - - - +
56A GLU* 2.8 47.2 + - - +
57A MET* 3.2 33.4 - - - +
58A ASN* 3.6 7.6 - - + +
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Residues in contact with ASP 32 (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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30A SER* 2.8 9.6 + - - +
31A ARG* 1.3 77.2 - - - +
33A ASP* 1.3 65.8 + - - +
34A VAL 3.2 0.7 - - - -
35A ALA* 3.5 9.1 + - - +
36A GLN* 3.0 41.0 + - - +
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Residues in contact with ASP 33 (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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21A HIS 4.9 5.2 - - - +
22A LEU* 3.5 20.5 - - + +
24A LEU* 4.9 7.5 - - - +
28A TYR 4.0 2.6 - - - +
29A TRP* 3.3 30.9 - - + -
30A SER* 2.7 41.6 + - - +
32A ASP* 1.3 73.4 - - - +
34A VAL* 1.3 49.9 - - - +
36A GLN* 3.0 7.1 + - - +
37A TRP* 2.7 33.4 + - - +
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Residues in contact with VAL 34 (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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29A TRP* 4.4 11.2 - - + +
30A SER 3.1 9.7 + - - +
31A ARG 3.4 8.5 - - - +
33A ASP* 1.3 74.5 - - - +
35A ALA* 1.3 63.2 + - - +
37A TRP* 3.2 9.6 + - + +
38A LEU* 3.0 30.4 + - + +
55A PHE* 3.8 35.9 - - + +
57A MET 3.4 17.3 - - - +
58A ASN 3.8 2.5 - - - +
59A GLY* 3.7 24.0 - - - +
62A LEU* 4.3 17.5 - - + -
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Residues in contact with ALA 35 (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 ARG 3.3 11.0 + - - +
32A ASP* 3.8 17.0 - - - +
33A ASP 3.4 0.2 - - - -
34A VAL* 1.3 79.0 - - - +
36A GLN* 1.3 62.4 + - - +
38A LEU* 3.4 12.5 + - - +
39A LYS* 3.0 28.4 + - - +
52A SER* 4.6 27.4 - - - +
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Residues in contact with GLN 36 (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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21A HIS* 4.6 18.0 + - + +
22A LEU* 4.1 11.6 - - + +
32A ASP* 3.0 37.1 + - - +
33A ASP* 3.0 12.6 + - - +
35A ALA* 1.3 80.8 + - - +
37A TRP* 1.3 60.9 + - - +
39A LYS* 3.9 29.0 - - - +
40A TRP* 3.2 27.0 + - - +
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Residues in contact with TRP 37 (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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18A LEU* 4.0 17.9 - - + -
22A LEU* 3.8 12.7 - - + +
29A TRP* 3.5 35.2 - + + -
33A ASP 2.7 18.2 + - - +
34A VAL* 3.2 6.0 + - + +
36A GLN* 1.3 71.6 - - - +
38A LEU* 1.3 93.6 + - + +
40A TRP* 3.8 7.6 - + - +
41A ALA* 2.9 30.1 + - + +
62A LEU* 3.8 21.3 - - + -
70A PHE* 4.3 10.1 - + - -
81A LEU* 3.3 37.2 - - + -
84A LEU* 3.5 25.8 - - + +
85A LEU* 4.1 17.7 - - + -
88A ILE* 3.3 17.4 - - - +
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Residues in contact with LEU 38 (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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34A VAL* 3.0 31.4 + - + +
35A ALA* 3.7 6.3 - - - +
37A TRP* 1.3 96.3 - - + +
39A LYS* 1.3 65.5 + - - +
41A ALA* 4.0 3.2 - - - +
42A GLU* 3.2 27.8 + - - +
50A ILE* 5.0 19.0 - - + +
51A ASP 5.0 5.6 - - - +
52A SER* 4.3 18.8 - - - +
55A PHE* 3.8 31.9 - - + -
81A LEU* 3.7 31.9 - - + -
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Residues in contact with LYS 39 (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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35A ALA 3.0 16.6 + - - +
36A GLN* 3.9 31.4 - - - +
38A LEU* 1.3 77.2 - - - +
40A TRP* 1.3 59.9 + - - +
42A GLU* 3.8 9.7 - - - +
43A ASN* 3.0 41.2 + - - +
52A SER* 6.6 0.2 - - - -
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Residues in contact with TRP 40 (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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16A ILE* 4.6 9.6 - - + -
17A ALA 3.8 20.1 + - - -
18A LEU* 3.7 26.9 - - + -
19A PRO* 3.4 33.5 - - + +
21A HIS* 5.4 3.1 - + + +
22A LEU* 4.8 0.7 - - + -
36A GLN 3.2 18.4 + - - +
37A TRP* 3.8 16.8 - + - +
38A LEU 3.2 0.2 - - - -
39A LYS* 1.3 74.0 - - - +
41A ALA* 1.3 67.4 + - - +
42A GLU 3.2 1.6 - - - -
43A ASN* 3.2 5.9 + - + +
44A GLU* 2.7 69.4 + - + +
45A PHE* 3.8 26.7 - + - -
84A LEU* 3.9 17.3 - - + -
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Residues in contact with ALA 41 (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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37A TRP* 2.9 22.6 + - + +
38A LEU 4.0 1.8 - - - +
40A TRP* 1.3 77.6 - - + +
42A GLU* 1.3 53.9 + - - +
45A PHE* 2.7 49.0 + - + +
47A LEU* 4.1 3.2 - - + +
81A LEU* 3.8 21.8 - - + -
84A LEU* 3.6 28.0 - - + -
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Residues in contact with GLU 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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38A LEU 3.2 17.6 + - - +
39A LYS* 3.8 10.3 - - - +
40A TRP 3.2 0.4 - - - -
41A ALA* 1.3 77.7 - - - +
43A ASN* 1.3 61.9 + - - +
46A SER* 3.0 22.5 + - - -
47A LEU* 3.0 26.2 + - + +
48A ARG 3.4 22.0 - - - +
49A PRO* 3.1 23.4 - - - +
50A ILE* 3.5 25.7 + - + +
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Residues in contact with ASN 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 LYS* 3.0 35.0 + - - +
40A TRP* 3.2 8.0 + - + +
42A GLU* 1.3 81.2 - - - +
44A GLU* 1.3 65.6 + - - +
45A PHE 3.4 0.5 + - - -
46A SER* 3.6 9.9 + - - -
58B ASN* 5.0 0.2 + - - -
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Residues in contact with GLU 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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16A ILE* 5.7 1.8 - - + +
17A ALA 5.9 0.2 - - - -
40A TRP* 2.7 61.1 + - + +
43A ASN* 1.3 74.9 - - - +
45A PHE* 1.3 79.9 + - + +
58B ASN* 2.9 17.0 + - - -
60B LYS* 2.7 41.7 + - - +
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Residues in contact with PHE 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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16A ILE* 4.2 15.7 - - + -
40A TRP* 3.8 13.7 - + - -
41A ALA* 2.7 39.2 + - + +
44A GLU* 1.3 92.4 - - + +
46A SER* 1.3 62.8 + - - +
47A LEU* 3.4 13.0 + - + -
80A VAL* 5.1 3.6 - - + -
84A LEU* 3.5 40.4 - - + -
57B MET* 3.5 5.4 - - - +
58B ASN* 3.0 31.2 + - - +
60B LYS* 4.0 18.6 - - + -
61B ALA* 3.6 30.5 - - + -
64B LEU* 4.1 15.9 - - + -
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Residues in contact with SER 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 GLU 3.0 10.9 + - - -
43A ASN* 3.6 7.8 + - - +
44A GLU 3.6 1.4 - - - -
45A PHE* 1.3 79.6 - - - +
47A LEU* 1.3 62.2 + - - +
30B SER* 5.6 0.5 - - - -
31B ARG* 3.3 49.8 + - - +
56B GLU 3.7 7.1 - - - +
57B MET* 4.0 0.3 - - - -
58B ASN* 3.5 18.3 + - - +
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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