Contacts of the helix formed by residues 18 - 35 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16Q THR 3.3 4.6 - - - +
17Q ASP* 1.3 82.9 - - - +
19Q ALA* 1.3 61.5 + - - +
20Q GLU* 4.2 5.8 - - - -
21Q GLU* 3.3 18.0 + - - +
22Q ARG* 3.0 23.2 + - - +
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Residues in contact with ALA 19 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Q ASP 3.8 0.8 + - - -
18Q THR* 1.3 70.8 - - - +
20Q GLU* 1.3 61.1 + - - +
22Q ARG* 3.2 7.9 + - - +
23Q LYS* 2.9 28.8 + - - +
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Residues in contact with GLU 20 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18Q THR* 3.3 5.9 - - - -
19Q ALA* 1.3 79.1 - - - +
21Q GLU* 1.3 57.4 + - - +
23Q LYS* 3.4 6.4 + - - +
24Q ALA* 2.9 29.3 + - - +
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Residues in contact with GLU 21 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14Q MET* 5.9 1.8 - - + +
15Q PRO 3.1 29.2 - - - +
16Q THR* 4.3 2.0 - - - -
18Q THR* 3.3 23.7 + - - +
19Q ALA 3.2 0.6 - - - -
20Q GLU* 1.3 76.1 - - - +
22Q ARG* 1.3 60.5 - - - +
24Q ALA* 3.4 6.5 + - - +
25Q TYR* 2.9 28.6 + - - +
68Q LYS 6.1 1.1 - - - +
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Residues in contact with ARG 22 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16Q THR* 4.3 13.9 + - - +
18Q THR 3.0 14.2 + - - +
19Q ALA* 3.6 10.1 - - - +
21Q GLU* 1.3 74.4 - - - +
23Q LYS* 1.3 59.4 + - - +
25Q TYR* 3.1 8.1 + - - +
26Q ARG* 2.9 28.6 + - - +
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Residues in contact with LYS 23 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19Q ALA 2.9 16.9 + - - +
20Q GLU* 3.7 7.4 - - - +
22Q ARG* 1.3 76.0 - - - +
24Q ALA* 1.3 58.8 + - - +
26Q ARG* 3.3 7.1 + - - +
27Q LYS* 2.9 29.3 + - - +
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Residues in contact with ALA 24 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20Q GLU 2.9 18.3 + - - +
21Q GLU* 3.7 7.4 - - - +
22Q ARG 3.3 0.2 - - - -
23Q LYS* 1.3 76.5 - - - +
25Q TYR* 1.3 57.6 + - - +
27Q LYS* 3.4 6.8 + - - +
28Q PHE* 2.9 30.7 + - - +
67Q PRO* 3.8 25.7 - - + +
68Q LYS 5.5 2.0 - - - +
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Residues in contact with TYR 25 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Q MET* 5.9 7.0 - - + -
16Q THR* 6.0 5.2 - - - -
21Q GLU 2.9 17.8 + - - +
22Q ARG* 3.1 8.7 + - - +
24Q ALA* 1.3 74.5 - - - +
26Q ARG* 1.3 60.9 + - - +
28Q PHE* 3.4 5.3 + - - +
29Q ARG* 2.9 30.9 + - - +
67Q PRO* 5.3 1.3 - - - +
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Residues in contact with ARG 26 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22Q ARG 2.9 16.2 + - - +
23Q LYS* 3.3 7.2 + - - +
25Q TYR* 1.3 75.4 - - - +
27Q LYS* 1.3 57.7 + - - +
29Q ARG* 3.4 5.8 + - - +
30Q LYS* 2.9 30.1 + - - +
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Residues in contact with LYS 27 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23Q LYS 2.9 17.4 + - - +
24Q ALA* 3.7 7.6 - - - +
26Q ARG* 1.3 78.5 - - - +
28Q PHE* 1.3 57.2 + - - +
30Q LYS* 3.4 6.4 + - - +
31Q PHE* 2.9 28.7 + - - +
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Residues in contact with PHE 28 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24Q ALA 2.9 17.7 + - - +
25Q TYR* 3.9 5.6 - - - +
27Q LYS* 1.3 77.1 - - - +
29Q ARG* 1.3 57.3 + - - +
31Q PHE* 3.2 9.0 + - - +
32Q LEU* 2.9 27.4 + - - +
65Q ASN 4.7 15.0 - - - +
66Q ASN* 6.0 0.4 - - - -
67Q PRO* 4.9 10.8 - - + -
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Residues in contact with ARG 29 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25Q TYR 2.9 18.9 + - - +
26Q ARG* 3.8 6.5 - - - +
28Q PHE* 1.3 77.3 - - - +
30Q LYS* 1.3 56.4 + - - +
32Q LEU* 3.1 9.0 + - - +
33Q LEU* 2.9 28.1 + - - +
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Residues in contact with LYS 30 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26Q ARG 2.9 17.4 + - - +
27Q LYS* 3.7 6.5 - - - +
29Q ARG* 1.3 75.6 - - - +
31Q PHE* 1.3 58.0 + - - +
33Q LEU* 3.4 7.5 + - - +
34Q SER* 2.9 29.7 + - - -
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Residues in contact with PHE 31 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27Q LYS 2.9 17.0 + - - +
28Q PHE* 3.5 9.4 - - - +
29Q ARG 3.2 0.2 - - - -
30Q LYS* 1.3 78.3 - - - +
32Q LEU* 1.3 60.1 + - - +
34Q SER* 3.3 6.9 + - - -
35Q GLU* 3.1 24.1 + - - +
65Q ASN* 5.2 14.1 - - + -
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Residues in contact with LEU 32 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28Q PHE 2.9 13.1 + - - +
29Q ARG* 3.1 10.7 + - - +
31Q PHE* 1.3 78.6 - - - +
33Q LEU* 1.3 59.1 + - - +
35Q GLU* 3.3 10.7 + - - +
37Q PHE* 3.0 40.6 + - + +
45Q TYR* 5.8 4.5 - - + -
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Residues in contact with LEU 33 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Q ARG 2.9 15.1 + - - +
30Q LYS* 3.8 7.9 - - - +
32Q LEU* 1.3 77.1 - - - +
34Q SER* 1.3 62.2 + - - +
36Q GLY* 3.3 12.3 + - - -
37Q PHE 3.7 14.6 + - - +
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Residues in contact with SER 34 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30Q LYS 2.9 18.1 + - - -
31Q PHE* 3.8 8.1 - - - -
32Q LEU 3.3 0.4 - - - -
33Q LEU* 1.3 76.7 - - - +
35Q GLU* 1.3 59.2 + - - +
36Q GLY 3.5 0.9 + - - -
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Residues in contact with GLU 35 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31Q PHE 3.1 16.3 + - - +
32Q LEU* 3.3 8.0 + - - +
33Q LEU 3.2 0.8 - - - -
34Q SER* 1.3 75.8 - - - +
36Q GLY* 1.3 57.2 + - - +
37Q PHE* 3.6 2.5 - - + +
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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