Contacts of the helix formed by residues 18 - 35 (chain x) in PDB entry 6QXT
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 THR 18 (chain x).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16x THR 3.3 4.8 - - - +
17x ASP* 1.3 82.4 - - - +
19x ALA* 1.3 59.7 + - - +
20x GLU* 3.3 6.5 - - - -
21x GLU* 3.3 17.2 + - - +
22x ARG* 3.0 23.6 + - - +
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Residues in contact with ALA 19 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271 T 3.7 34.0 - - + +
17x ASP 3.8 0.8 + - - -
18x THR* 1.3 71.0 - - - +
20x GLU* 1.3 60.4 + - - +
22x ARG* 3.2 7.7 + - - +
23x LYS* 2.9 28.8 + - - +
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Residues in contact with GLU 20 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271 T 5.8 0.7 - - - -
18x THR* 3.3 6.3 - - - -
19x ALA* 1.3 77.6 - - - +
21x GLU* 1.3 58.3 + - - +
23x LYS* 3.4 6.6 + - - +
24x ALA* 2.9 29.3 + - - +
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Residues in contact with GLU 21 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14x MET* 6.2 0.3 - - - +
15x PRO 3.1 28.5 - - - +
16x THR* 4.3 2.4 - - - -
17x ASP 4.6 0.2 - - - +
18x THR* 3.3 24.6 + - - +
19x ALA 3.2 0.6 - - - -
20x GLU* 1.3 76.9 - - - +
22x ARG* 1.3 58.4 + - - +
24x ALA* 3.4 7.3 + - - +
25x TYR* 2.9 28.1 + - - +
68x LYS 6.2 0.2 - - - +
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Residues in contact with ARG 22 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271 T 5.3 5.2 - - - +
382 A 6.2 2.2 - - - +
16x THR* 4.3 13.9 + - - +
18x THR 3.0 13.6 + - - +
19x ALA* 3.2 9.6 + - - +
21x GLU* 1.3 74.3 - - - +
23x LYS* 1.3 59.2 + - - +
25x TYR* 3.1 7.3 + - - +
26x ARG* 2.9 29.1 + - - +
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Residues in contact with LYS 23 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261 T 4.0 26.4 - - + +
271 T 5.0 9.5 + - + +
382 A 6.0 1.6 - - - +
19x ALA 2.9 16.9 + - - +
20x GLU* 3.7 7.6 - - - +
22x ARG* 1.3 76.1 - - - +
24x ALA* 1.3 58.0 + - - +
26x ARG* 3.3 7.2 + - - +
27x LYS* 2.9 29.0 + - - +
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Residues in contact with ALA 24 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20x GLU 2.9 17.4 + - - +
21x GLU* 3.7 7.6 - - - +
23x LYS* 1.3 76.5 - - - +
25x TYR* 1.3 57.3 + - - +
27x LYS* 3.4 6.7 + - - +
28x PHE* 2.9 30.1 + - - +
67x PRO* 4.0 25.6 - - + +
68x LYS 5.7 1.3 - - - +
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Residues in contact with TYR 25 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14x MET* 6.0 6.1 - - + -
16x THR* 6.0 5.6 - - - -
21x GLU 2.9 17.3 + - - +
22x ARG* 3.1 9.4 + - - +
24x ALA* 1.3 74.8 - - - +
26x ARG* 1.3 59.3 + - - +
28x PHE* 3.4 5.0 + - - +
29x ARG* 2.9 30.4 + - - +
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Residues in contact with ARG 26 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261 T 6.2 2.7 - - + -
382 A 5.9 6.1 - - - +
22x ARG 2.9 15.1 + - - +
23x LYS* 3.7 7.6 - - - +
25x TYR* 1.3 76.0 - - - +
27x LYS* 1.3 58.3 + - - +
29x ARG* 3.4 6.2 + - - +
30x LYS* 2.9 30.5 + - - +
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Residues in contact with LYS 27 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23x LYS 2.9 16.4 + - - +
24x ALA* 3.7 7.9 - - - +
25x TYR 3.3 0.2 - - - -
26x ARG* 1.3 78.0 - - - +
28x PHE* 1.3 57.2 + - - +
30x LYS* 3.4 5.8 + - - +
31x PHE* 2.9 29.4 + - - +
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Residues in contact with PHE 28 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24x ALA 2.9 18.0 + - - +
25x TYR* 3.9 5.2 - - - +
27x LYS* 1.3 76.3 - - - +
29x ARG* 1.3 57.5 + - - +
31x PHE* 3.2 7.4 + - - +
32x LEU* 2.9 27.9 + - - +
65x ASN* 4.7 15.5 - - - +
66x ASN* 6.0 0.4 - - - -
67x PRO* 5.1 9.9 - - + -
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Residues in contact with ARG 29 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25x TYR 2.9 18.5 + - - +
26x ARG* 3.8 6.5 - - - +
28x PHE* 1.3 77.5 - - - +
30x LYS* 1.3 56.8 + - - +
32x LEU* 3.1 8.9 + - - +
33x LEU* 2.9 27.9 + - - +
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Residues in contact with LYS 30 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26x ARG 2.9 18.3 + - - +
27x LYS* 3.7 6.3 - - - +
28x PHE 3.3 0.2 - - - -
29x ARG* 1.3 76.5 - - - +
31x PHE* 1.3 58.4 + - - +
33x LEU* 3.4 7.5 + - - +
34x SER* 2.9 29.3 + - - -
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Residues in contact with PHE 31 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27x LYS 2.9 17.2 + - - +
28x PHE* 3.5 9.6 - - - +
30x LYS* 1.3 77.7 - - - +
32x LEU* 1.3 61.1 + - - +
34x SER* 3.3 6.7 + - - -
35x GLU* 3.1 23.6 + - - +
65x ASN* 5.2 13.9 - - + -
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Residues in contact with LEU 32 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28x PHE 2.9 12.9 + - - +
29x ARG* 3.1 11.4 + - - +
31x PHE* 1.3 77.3 - - - +
33x LEU* 1.3 60.4 + - - +
35x GLU* 3.3 10.3 + - - +
36x GLY 3.5 0.2 + - - -
37x PHE* 3.0 40.2 + - + +
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Residues in contact with LEU 33 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29x ARG 2.9 15.4 + - - +
30x LYS* 3.8 7.9 - - - +
31x PHE 3.3 0.2 - - - -
32x LEU* 1.3 77.4 - - - +
34x SER* 1.3 61.2 + - - +
36x GLY* 3.3 12.3 + - - -
37x PHE 3.7 13.9 + - - +
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Residues in contact with SER 34 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30x LYS 2.9 17.4 + - - -
31x PHE* 3.8 8.3 - - - -
32x LEU 3.3 0.2 - - - -
33x LEU* 1.3 77.0 - - - +
35x GLU* 1.3 59.3 + - - +
36x GLY 3.5 0.5 + - - -
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Residues in contact with GLU 35 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31x PHE 3.1 15.4 + - - +
32x LEU* 3.8 8.3 - - - +
33x LEU 3.2 0.8 - - - -
34x SER* 1.3 75.8 - - - +
36x GLY* 1.3 57.8 + - - +
37x PHE* 3.6 2.2 - - + +
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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