Contacts of the helix formed by residues 18 - 35 (chain n) 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 n).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250Y SER* 5.3 15.7 - - - -
16n THR 3.2 7.5 - - - +
17n ASP* 1.3 80.6 - - - +
19n ALA* 1.3 60.1 + - - +
20n GLU* 4.2 5.6 - - - -
21n GLU* 3.3 18.0 + - - +
22n ARG* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 19 (chain n).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17n ASP 3.8 0.8 + - - -
18n THR* 1.3 70.6 - - - +
20n GLU* 1.3 61.7 + - - +
22n ARG* 3.2 7.8 + - - +
23n LYS* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 20 (chain n).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18n THR* 3.3 5.7 - - - -
19n ALA* 1.3 78.5 - - - +
21n GLU* 1.3 58.6 + - - +
23n LYS* 3.4 7.5 + - - +
24n ALA* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 21 (chain n).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14n MET* 6.1 1.0 - - - +
15n PRO 3.1 28.5 - - - +
16n THR* 4.3 2.4 - - - -
18n THR* 3.3 24.7 + - - +
19n ALA 3.2 0.2 - - - -
20n GLU* 1.3 77.6 - - - +
22n ARG* 1.3 60.0 + - - +
24n ALA* 3.4 6.9 + - - +
25n TYR* 2.9 27.8 + - - +
68n LYS 6.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 22 (chain n).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16n THR* 4.3 13.9 + - - +
18n THR 3.0 12.7 + - - +
19n ALA* 3.2 10.3 + - - +
21n GLU* 1.3 74.5 - - - +
23n LYS* 1.3 60.9 + - - +
25n TYR* 3.1 8.5 + - - +
26n ARG* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain n).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19n ALA 2.9 16.7 + - - +
20n GLU* 3.7 7.4 - - - +
22n ARG* 1.3 75.0 - - - +
24n ALA* 1.3 58.7 + - - +
26n ARG* 3.3 6.9 + - - +
27n LYS* 2.9 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain n).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20n GLU 2.9 17.4 + - - +
21n GLU* 3.7 8.1 - - - +
23n LYS* 1.3 76.4 - - - +
25n TYR* 1.3 57.9 + - - +
27n LYS* 3.4 7.4 + - - +
28n PHE* 2.9 31.2 + - - +
67n PRO* 3.9 25.6 - - + +
68n LYS 5.6 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 25 (chain n).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14n MET* 5.9 7.2 - - + -
16n THR* 6.0 5.2 - - - -
21n GLU 2.9 17.6 + - - +
22n ARG* 3.1 8.3 + - - +
24n ALA* 1.3 74.8 - - - +
26n ARG* 1.3 59.1 + - - +
28n PHE* 3.4 4.6 + - - +
29n ARG* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 26 (chain n).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22n ARG 2.9 15.3 + - - +
23n LYS* 3.7 7.6 - - - +
25n TYR* 1.3 76.5 - - - +
27n LYS* 1.3 57.9 + - - +
29n ARG* 3.4 5.7 + - - +
30n LYS* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 27 (chain n).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23n LYS 2.9 17.4 + - - +
24n ALA* 3.7 7.2 - - - +
26n ARG* 1.3 77.2 - - - +
28n PHE* 1.3 57.7 + - - +
30n LYS* 3.4 6.5 + - - +
31n PHE* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 28 (chain n).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24n ALA 2.9 19.3 + - - +
25n TYR* 3.9 5.4 - - - +
27n LYS* 1.3 75.3 - - - +
29n ARG* 1.3 58.4 + - - +
31n PHE* 3.2 8.3 + - - +
32n LEU* 2.9 27.4 + - - +
65n ASN 4.7 14.8 - - - +
66n ASN* 6.0 0.4 - - - -
67n PRO* 5.0 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 29 (chain n).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25n TYR 2.9 17.9 + - - +
26n ARG* 3.8 6.7 - - - +
28n PHE* 1.3 76.6 - - - +
30n LYS* 1.3 56.6 + - - +
32n LEU* 3.1 9.1 + - - +
33n LEU* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 30 (chain n).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26n ARG 2.9 17.4 + - - +
27n LYS* 3.7 6.3 - - - +
29n ARG* 1.3 76.2 - - - +
31n PHE* 1.3 58.1 + - - +
33n LEU* 3.4 6.9 + - - +
34n SER* 2.9 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 31 (chain n).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27n LYS 2.9 18.3 + - - +
28n PHE* 3.5 9.2 - - - +
29n ARG 3.2 0.2 - - - -
30n LYS* 1.3 77.5 - - - +
32n LEU* 1.3 61.6 + - - +
34n SER* 3.3 7.3 + - - -
35n GLU* 3.1 23.7 + - - +
65n ASN* 5.2 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain n).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28n PHE 2.9 13.1 + - - +
29n ARG* 3.1 11.4 + - - +
31n PHE* 1.3 77.4 - - - +
33n LEU* 1.3 59.9 + - - +
35n GLU* 3.3 10.7 + - - +
36n GLY 3.5 0.2 + - - -
37n PHE* 3.0 39.9 + - + +
45n TYR* 5.8 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain n).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29n ARG 2.9 15.4 + - - +
30n LYS* 3.8 7.9 - - - +
32n LEU* 1.3 76.1 - - - +
34n SER* 1.3 62.1 + - - +
36n GLY* 3.3 12.3 + - - -
37n PHE 3.7 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 34 (chain n).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30n LYS 2.9 17.4 + - - -
31n PHE* 3.8 8.3 - - - -
32n LEU 3.3 0.2 - - - -
33n LEU* 1.3 77.5 - - - +
35n GLU* 1.3 59.7 + - - +
36n GLY 3.3 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 35 (chain n).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31n PHE 3.1 15.5 + - - +
32n LEU* 3.3 7.8 + - - +
33n LEU 3.2 0.6 - - - -
34n SER* 1.3 77.1 - - - +
36n GLY* 1.3 58.3 + - - +
37n PHE* 3.6 2.5 - - + +
47n LYS* 5.5 2.3 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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