Contacts of the helix formed by residues 19 - 34 (chain A) in PDB entry 1QU2
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 GLY 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ARG* 3.6 10.7 - - - +
18A GLY* 1.3 76.1 - - - +
20A LEU* 1.3 65.5 + - - +
21A PRO* 3.4 6.3 - - - -
22A ASN* 3.0 16.4 + - - +
23A LYS* 2.9 20.2 + - - +
646A ARG* 5.7 0.4 - - - +
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Residues in contact with LEU 20 (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 GLY* 2.9 16.4 - - - +
19A GLY* 1.3 76.0 - - - +
21A PRO* 1.3 68.4 - - + +
22A ASN 2.8 6.8 + - - -
23A LYS* 4.3 5.8 - - + +
24A GLU* 2.9 59.0 + - + +
613A LYS 3.5 17.3 - - - +
614A GLY* 3.9 2.7 - - - -
616A ASP* 4.2 5.6 - - + +
617A ILE* 3.9 16.2 - - + -
645A TYR* 3.4 43.7 - - + +
646A ARG* 5.5 1.1 - - - +
649A ARG* 4.6 2.7 - - - +
762A HIS* 5.6 2.2 - - + -
763A THR* 4.4 5.4 - - - +
766A GLU* 5.2 3.4 - - - +
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Residues in contact with PRO 21 (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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19A GLY* 3.5 5.6 - - - -
20A LEU* 1.3 94.0 - - + +
22A ASN* 1.3 70.3 + - - +
25A PRO* 3.6 17.4 - - - +
141A ARG* 3.8 14.0 + - - +
610A VAL 3.8 8.7 - - - +
611A LYS* 3.1 30.7 - - - +
612A GLN 4.1 6.5 - - - +
613A LYS 3.8 13.5 - - - +
614A GLY* 4.6 0.2 - - - -
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Residues in contact with ASN 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLY* 3.0 15.0 + - - +
20A LEU 2.9 0.6 - - - -
21A PRO* 1.3 92.6 - - - +
23A LYS* 1.3 62.0 + - - +
24A GLU 3.8 0.2 - - - -
25A PRO* 3.8 5.0 - - - +
26A GLN* 3.3 22.0 - - - +
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Residues in contact with LYS 23 (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 GLY 4.3 6.3 - - - +
19A GLY 2.9 17.7 + - - +
20A LEU* 4.0 6.3 - - + +
22A ASN* 1.3 78.0 - - - +
24A GLU* 1.3 65.4 + - + +
25A PRO 3.3 1.6 - - - -
26A GLN* 3.2 31.7 + - + +
27A ILE* 3.2 32.2 + - + +
766A GLU* 3.8 38.1 + - - +
770A HIS* 5.6 4.9 + - - -
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Residues in contact with GLU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 2.9 40.3 + - + +
23A LYS* 1.3 77.6 - - + +
25A PRO* 1.3 65.6 - - + +
27A ILE* 3.4 4.5 + - + +
28A GLN* 2.9 28.6 + - - +
141A ARG* 3.0 24.4 + - - +
614A GLY* 3.6 1.9 - - - -
615A ALA* 2.7 28.1 + - - -
616A ASP* 2.9 29.1 + - - +
762A HIS* 3.3 31.8 + - + -
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Residues in contact with PRO 25 (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 PRO 3.6 24.5 - - - +
22A ASN* 3.8 6.3 - - - +
23A LYS 3.5 3.8 - - - -
24A GLU* 1.3 94.8 - - + +
26A GLN* 1.3 53.1 + - + +
28A GLN* 3.3 11.1 + - + +
29A GLU* 2.7 36.3 + - - +
141A ARG* 3.9 20.0 - - - +
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Residues in contact with GLN 26 (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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22A ASN 3.3 24.3 - - - +
23A LYS* 3.2 27.7 + - + +
25A PRO* 1.3 76.3 - - + +
27A ILE* 1.3 68.5 + - + +
29A GLU* 3.1 9.8 + - - +
30A LYS* 2.9 22.5 + - - +
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Residues in contact with ILE 27 (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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23A LYS* 3.2 44.8 + - + +
24A GLU* 3.8 5.6 - - - +
26A GLN* 1.3 76.3 - - + +
28A GLN* 1.3 63.9 + - - +
30A LYS* 3.2 9.0 + - - +
31A TRP* 3.0 58.7 + - + +
762A HIS* 3.8 33.2 - - + +
765A GLU* 4.2 13.2 - - + -
766A GLU* 4.7 8.5 - - + +
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Residues in contact with GLN 28 (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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24A GLU 2.9 17.2 + - - +
25A PRO* 3.5 6.4 - - + +
27A ILE* 1.3 73.5 - - - +
29A GLU* 1.3 67.7 + - - +
31A TRP* 3.0 28.8 + - + +
32A ASP* 2.9 24.3 + - - +
140A ARG* 3.2 24.4 + - - +
141A ARG* 3.3 46.0 + - - +
143A GLY* 3.8 2.4 - - - +
762A HIS* 2.9 31.8 + - - +
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Residues in contact with GLU 29 (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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25A PRO 2.7 18.6 + - - +
26A GLN* 3.2 13.9 - - - +
28A GLN* 1.3 73.3 - - - +
30A LYS* 1.3 61.4 + - - +
32A ASP* 3.4 11.5 + - - +
33A ALA* 3.0 28.5 + - + +
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Residues in contact with LYS 30 (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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26A GLN 2.9 12.9 + - - +
27A ILE* 3.6 10.1 - - + +
28A GLN 3.1 0.2 - - - -
29A GLU* 1.3 76.3 - - - +
31A TRP* 1.3 68.6 + - + +
33A ALA* 3.3 6.9 + - + +
34A GLU* 2.5 57.7 + - + +
765A GLU* 6.6 0.2 - - + -
777A GLU* 6.4 1.8 - - - -
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Residues in contact with TRP 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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27A ILE* 3.0 32.8 + - + +
28A GLN* 3.0 23.5 + - + +
30A LYS* 1.3 80.7 - - + +
32A ASP* 1.3 65.6 + - - +
34A GLU* 3.5 13.7 + - - +
35A ASP 3.4 1.7 + - - -
36A GLN* 3.1 50.3 + - + +
79A ARG* 4.4 16.8 - - - -
143A GLY 4.4 5.6 - - - -
761A VAL* 3.4 46.9 - - + -
762A HIS* 4.0 19.5 - + - -
765A GLU* 2.9 29.4 + - + +
780A HIS* 3.4 18.2 - + - -
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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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28A GLN* 2.9 24.5 + - - +
29A GLU* 3.7 12.6 - - - +
31A TRP* 1.3 80.6 - - - +
33A ALA* 1.3 55.3 + - - +
35A ASP* 2.7 28.7 + - - +
140A ARG* 3.7 29.1 + - - +
149A ASN* 6.3 1.1 - - - +
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Residues in contact with ALA 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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29A GLU* 3.0 21.6 + - + +
30A LYS* 3.6 8.7 - - + +
32A ASP* 1.3 80.4 - - - +
34A GLU* 1.3 56.7 + - - +
35A ASP* 3.2 5.0 + - - +
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Residues in contact with GLU 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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30A LYS* 2.5 61.2 + - + +
31A TRP* 3.5 14.2 - - - +
33A ALA* 1.3 74.8 - - - +
35A ASP* 1.3 67.6 + - - +
36A GLN* 2.9 21.8 + - + +
39A LYS* 3.4 19.2 - - - +
777A GLU* 5.4 5.8 - - - +
778A SER* 4.3 12.1 - - - -
781A LEU* 4.9 6.6 - - - +
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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