Contacts of the helix formed by residues 14 - 32 (chain R) in PDB entry 6QX2
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 ILE 14 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12R ARG 3.5 2.4 + - - -
13R ASN* 1.3 79.9 + - - +
15R THR* 1.3 65.8 + - - +
17R GLU* 3.4 6.2 + - - +
18R MET* 3.0 36.9 + - + +
521S LEU* 4.6 13.7 - - + -
525S TYR* 4.5 4.7 - - + -
532S ILE* 4.1 26.7 - - + -
606S VAL* 3.7 25.6 - - + -
607S LYS 3.2 17.0 + - - +
608S LEU* 4.2 23.8 - - + -
609S GLU 5.1 0.4 - - - +
614S ALA* 4.5 6.5 - - + -
618S PHE* 4.0 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 15 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13R ASN* 3.3 11.1 + - - +
14R ILE* 1.3 80.3 - - - +
16R SER* 1.3 60.3 + - - +
18R MET* 3.5 1.8 + - - +
19R ARG* 3.0 55.7 + - - +
610S ASP 5.0 0.7 + - - -
613S GLU* 3.6 34.5 + - - +
614S ALA* 3.9 23.2 + - - +
617S THR* 3.8 19.8 + - - +
618S PHE* 6.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 16 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12R ARG* 3.3 23.1 - - - -
13R ASN* 3.3 30.0 + - - +
15R THR* 1.3 77.8 - - - +
17R GLU* 1.3 57.3 + - - +
19R ARG* 3.5 4.7 + - - +
20R GLU* 3.0 42.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 17 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12R ARG* 3.0 38.2 + - + +
13R ASN 3.0 16.4 + - - +
14R ILE* 3.6 7.6 - - - +
15R THR 3.3 0.2 - - - -
16R SER* 1.3 73.4 - - - +
18R MET* 1.3 56.8 + - - +
20R GLU* 4.1 0.5 - - - +
21R SER* 2.8 49.1 + - - +
517S ARG* 2.5 36.0 + - + -
521S LEU* 3.8 23.8 - - + -
539S ILE* 3.9 17.9 - - + +
606S VAL* 6.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 18 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R ILE* 3.0 23.9 + - + +
15R THR* 3.6 4.9 - - - +
17R GLU* 1.3 75.6 - - - +
19R ARG* 1.3 56.5 + - - +
21R SER* 3.9 0.2 - - - -
22R PHE* 2.9 35.9 + - - +
518S THR* 3.8 40.3 - - - +
521S LEU* 4.0 12.3 - - + -
522S THR* 3.9 8.1 - - - +
617S THR* 4.0 8.7 - - + -
618S PHE* 3.6 47.1 - - + -
621S LEU* 3.6 20.0 - - + -
622S MET* 3.9 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 19 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15R THR* 3.0 36.5 + - - +
16R SER* 4.0 4.7 - - - +
17R GLU 3.4 0.2 - - - -
18R MET* 1.3 76.6 - - - +
20R GLU* 1.3 59.8 + - + +
23R LEU* 3.1 30.0 + - - +
613S GLU* 5.7 1.4 - - - +
616S GLN 5.3 0.4 - - - -
617S THR* 2.3 49.1 + - + +
620S MET* 3.1 31.0 - - - +
621S LEU* 4.0 4.7 - - + -
632S PHE* 3.5 35.7 - - + -
636S ASN* 5.7 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 20 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12R ARG* 3.6 33.1 + - - +
16R SER* 3.0 21.7 + - - +
19R ARG* 1.3 75.1 - - + +
21R SER* 1.3 60.4 + - - +
23R LEU* 3.6 9.2 + - + +
24R ASP* 3.1 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 21 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17R GLU* 2.8 44.7 + - - -
20R GLU* 1.3 74.9 - - - +
22R PHE* 1.3 63.8 + - - +
24R ASP* 3.3 3.6 + - - +
25R TYR* 3.2 18.4 + - - +
514S ALA* 3.3 25.9 - - - +
517S ARG* 2.9 17.1 + - - +
518S THR* 3.6 20.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 22 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18R MET 2.9 18.4 + - - +
19R ARG 4.3 0.9 - - - +
21R SER* 1.3 73.3 - - - +
23R LEU* 1.3 57.8 + - - +
25R TYR* 3.4 9.0 + + - +
26R ALA* 2.8 37.6 + - + +
177R VAL* 3.8 22.0 - - + -
515S HIS* 4.5 11.2 - + - -
518S THR* 3.7 15.1 - - + +
621S LEU* 3.5 37.9 - - + -
622S MET* 3.8 19.1 - - - -
629S ARG* 3.4 39.3 - - + -
632S PHE* 4.8 4.3 - + - -
633S ILE* 4.7 2.2 - - + -
2016W C 3.7 21.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19R ARG 3.1 22.6 + - - +
20R GLU* 3.8 9.0 - - + +
22R PHE* 1.3 77.8 - - - +
24R ASP* 1.3 61.2 + - - +
26R ALA* 4.4 3.6 - - - -
27R MET* 2.8 57.8 + - + +
632S PHE* 4.5 7.6 - - + -
633S ILE* 3.9 34.1 - - + +
636S ASN* 4.0 35.4 - - + +
638S VAL* 6.0 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 24 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20R GLU* 3.1 22.2 + - - +
21R SER* 3.4 11.4 - - - +
22R PHE 3.3 0.2 - - - -
23R LEU* 1.3 83.6 - - - +
25R TYR* 1.3 61.8 + - - +
27R MET* 4.1 3.1 - - - +
28R SER* 3.3 24.4 + - - -
511S VAL* 4.1 12.8 - - + +
514S ALA* 4.6 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 25 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21R SER 3.2 8.5 + - - +
22R PHE* 3.5 16.6 - + - +
24R ASP* 1.3 74.8 - - - +
26R ALA* 1.3 67.8 + - - +
28R SER* 3.1 5.2 + - - -
29R VAL* 2.9 47.0 + - + +
33R ARG* 4.1 6.1 + - - -
177R VAL* 3.8 22.9 - - + +
460S LYS* 3.3 13.7 + - - -
511S VAL* 3.6 28.8 + - + +
512S ASP* 3.4 21.5 - - - -
515S HIS* 3.3 55.0 + + + +
2015W A 4.5 11.6 + - - -
2016W C 4.6 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22R PHE* 2.8 26.5 + - + +
23R LEU* 3.9 2.9 - - - +
25R TYR* 1.3 73.3 - - - +
27R MET* 1.3 63.0 + - - +
29R VAL* 3.4 2.4 + - - +
30R ILE* 3.1 30.1 + - - +
177R VAL* 3.7 24.9 - - + +
633S ILE* 3.7 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 27 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23R LEU* 2.8 42.6 + - + +
24R ASP* 4.1 4.3 - - - +
26R ALA* 1.3 72.6 - - - +
28R SER* 1.3 56.4 + - - +
30R ILE* 3.3 9.9 + - - +
31R VAL* 3.0 45.6 + - + +
501R JK8 3.6 40.4 - - + -
633S ILE* 4.4 4.5 - - + -
637S ALA* 3.9 22.0 - - - -
638S VAL 5.0 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 28 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24R ASP 3.3 17.8 + - - -
25R TYR 3.1 5.1 + - - -
27R MET* 1.3 76.8 - - - +
29R VAL* 1.3 58.4 + - - +
31R VAL* 4.6 5.6 - - - -
32R ALA* 3.0 41.4 + - - +
33R ARG* 4.9 3.8 + - - -
511S VAL* 3.5 32.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 29 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25R TYR* 2.9 54.7 + - + +
26R ALA 3.7 4.7 - - - +
28R SER* 1.3 75.9 - - - +
30R ILE* 1.3 58.5 + - - +
33R ARG* 3.5 27.6 - - + +
34R ALA* 3.1 33.5 + - + +
175R ILE 4.5 1.8 - - - +
176R ALA* 3.6 35.0 - - - -
177R VAL* 3.8 7.4 - - + +
511S VAL* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 30 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26R ALA 3.1 23.2 + - - +
27R MET* 3.6 6.3 - - - +
28R SER 3.2 0.2 - - - -
29R VAL* 1.3 78.5 - - - +
31R VAL* 1.3 71.4 + - + +
32R ALA 3.8 0.3 + - - -
35R LEU* 3.4 37.5 + - + +
176R ALA* 4.3 10.5 - - + -
177R VAL 3.3 28.0 - - - +
179R MET* 4.4 11.9 - - + -
338R LEU* 3.8 4.3 - - + +
343R PRO* 3.7 30.1 - - + -
501R JK8 4.5 6.1 - - + -
633S ILE* 4.1 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 31 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27R MET* 3.0 33.0 + - + +
28R SER* 4.4 2.0 - - - +
30R ILE* 1.3 87.2 - - + +
32R ALA* 1.3 66.7 + - + +
33R ARG 4.0 0.4 - - - -
35R LEU 5.5 0.2 - - - -
44R PRO* 4.9 3.4 - - - +
338R LEU* 3.8 22.7 - - + +
341R GLY* 3.6 24.7 - - - +
343R PRO* 5.1 0.4 - - + -
501R JK8 4.4 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 32 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28R SER* 3.0 21.9 + - - +
31R VAL* 1.3 87.5 - - + +
33R ARG* 1.3 67.2 + - - +
44R PRO* 3.6 22.8 - - + +
48R ARG* 5.7 3.7 + - - +
79R HIS* 6.1 0.2 - - - -
81R HIS* 5.8 1.6 + - - -
7V A 4.9 2.1 + - - -
----------------------------------------------------------
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