Contacts of the helix formed by residues 8 - 24 (chain C) in PDB entry 5XBY
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 8 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C PRO* 1.3 72.1 - - - +
9C LEU* 1.3 63.0 + - - +
10C THR* 3.3 3.6 - - - +
11C GLU* 3.5 22.2 + - - +
12C LEU* 3.0 26.3 + - - +
28D LEU* 4.0 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 9 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B TRP* 6.3 0.2 - - + -
5C ILE* 3.5 22.2 - - + -
6C PRO* 3.1 33.5 + - + +
7C PRO 3.3 1.4 + - - -
8C GLY* 1.3 77.7 - - - +
10C THR* 1.3 64.1 + - - +
12C LEU* 3.8 3.2 - - + +
13C LEU* 3.2 26.3 + - + +
16D TYR* 3.3 40.8 - - + +
17D THR* 3.4 35.0 - - + +
20D VAL* 4.5 10.3 - - + -
21D LEU* 5.5 0.2 - - + -
28D LEU* 3.8 11.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 10 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ARG* 5.4 4.2 + - - +
3B TRP* 4.1 16.3 - - - -
5C ILE* 5.0 12.6 - - + -
6C PRO 5.6 0.2 - - - +
7C PRO* 6.2 0.2 - - + -
8C GLY 5.1 1.6 - - - +
9C LEU* 1.3 80.0 - - - +
11C GLU* 1.3 88.4 + - - +
13C LEU* 3.3 3.5 + - - +
14C GLN* 2.8 40.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 11 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLY* 3.5 23.5 + - - +
10C THR* 1.3 93.4 - - - +
12C LEU* 1.3 63.4 + - - +
14C GLN* 3.4 21.9 + - - +
15C GLY* 3.4 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 12 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLY 3.0 19.0 + - - +
9C LEU* 3.8 4.0 - - - +
11C GLU* 1.3 79.2 - - - +
13C LEU* 1.3 61.0 + - - +
15C GLY* 3.5 1.7 + - - -
16C TYR* 3.5 16.8 + - - +
35C TYR* 4.9 1.4 + - - -
36C PHE* 3.9 18.3 - - + -
39C LEU* 3.7 30.7 - - + -
43C ARG* 4.2 9.2 - - - +
16D TYR* 3.7 28.0 - - + +
28D LEU* 3.8 28.3 - - + +
29D VAL* 3.9 15.3 - - + +
32D ALA* 4.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 13 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B TRP* 3.4 36.8 - - + -
9C LEU* 3.2 20.2 + - + +
12C LEU* 1.3 75.3 - - + +
14C GLN* 1.3 59.9 + - - +
16C TYR* 3.4 6.5 + - - +
17C THR* 2.8 32.3 + - - -
36C PHE* 4.5 15.7 - - + -
13D LEU* 3.4 34.3 - - + +
16D TYR* 3.6 29.4 - - + -
17D THR* 3.5 22.7 - - - +
36D PHE* 5.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 14 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 4.8 1.0 - - - +
22A ARG* 2.4 75.6 + - + +
3B TRP* 4.3 7.2 - - + -
10C THR* 2.8 49.5 + - - +
11C GLU* 3.5 24.3 + - - +
12C LEU 3.2 0.2 - - - -
13C LEU* 1.3 77.8 - - - +
15C GLY* 1.3 57.3 + - - +
17C THR* 2.9 10.1 + - - -
18C VAL* 2.8 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 15 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ARG* 4.8 1.3 - - - +
11C GLU 3.4 9.5 + - - -
12C LEU 3.5 2.8 + - - -
13C LEU 3.3 0.4 - - - -
14C GLN* 1.3 75.6 - - - +
16C TYR* 1.3 66.3 + - - +
18C VAL* 3.5 9.0 + - - +
19C GLU* 3.3 26.9 + - - +
35C TYR* 3.7 15.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 16 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU 3.5 6.1 + - - +
13C LEU 3.4 7.3 + - - +
14C GLN 3.3 0.2 - - - -
15C GLY* 1.3 75.0 - - - +
17C THR* 1.3 66.5 + - - +
19C GLU* 3.3 4.2 + - - +
20C VAL* 3.1 38.6 + - + +
28C LEU* 2.9 36.3 + - - +
31C PHE* 4.1 8.5 - + - -
32C ALA* 3.6 26.5 - - + -
35C TYR* 3.9 19.2 - + + -
36C PHE* 3.7 35.4 - + + -
9D LEU* 3.9 12.8 - - + -
12D LEU* 3.6 28.5 - - + +
13D LEU* 3.7 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 17 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 4.7 12.1 - - + -
21A LEU* 3.9 20.6 - - + -
3B TRP* 4.4 6.4 - - + +
13C LEU 2.8 17.9 + - - -
14C GLN* 2.9 13.3 + - - -
16C TYR* 1.3 81.4 - - - +
18C VAL* 1.3 62.1 + - - +
20C VAL* 3.3 5.8 + - - +
21C LEU* 3.3 25.1 + - + +
9D LEU* 3.8 24.9 - - + +
13D LEU* 3.4 21.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLN* 4.6 0.5 - - - +
18A VAL* 3.8 33.7 - - + -
22A ARG* 4.0 11.2 - - - +
14C GLN 2.8 22.2 + - - +
15C GLY* 3.8 9.6 - - - +
17C THR* 1.3 74.3 - - - +
19C GLU* 1.3 65.6 + - - +
21C LEU* 3.4 4.7 + - - +
22C ARG* 3.2 55.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C GLY 3.3 15.0 + - - +
16C TYR 3.3 5.4 + - - +
17C THR 3.3 0.4 - - - -
18C VAL* 1.3 78.3 - - + +
20C VAL* 1.3 66.1 + - - +
22C ARG* 3.0 37.4 + - - +
23C GLN* 2.8 56.7 + - - +
31C PHE* 4.0 12.6 - - + -
35C TYR* 4.1 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TYR* 3.1 49.7 + - + +
17C THR* 3.8 9.0 - - + +
18C VAL 3.3 0.4 - - - -
19C GLU* 1.3 77.2 - - - +
21C LEU* 1.3 60.2 + - + +
24C GLN* 2.9 29.8 + - - -
25C PRO* 4.0 13.2 - - + -
28C LEU* 3.7 17.0 - - + -
31C PHE* 4.1 12.3 - - + -
6D PRO* 3.7 28.9 - - + -
9D LEU* 5.1 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLN* 3.9 34.4 + - + +
17A THR* 4.4 11.0 - - + -
18A VAL* 3.4 33.0 - - + -
21A LEU* 5.4 2.5 - - + -
17C THR* 3.3 17.0 + - + +
18C VAL 3.7 6.5 - - - +
19C GLU 3.2 0.4 - - - -
20C VAL* 1.3 80.4 - - + +
22C ARG* 1.3 61.5 + - - +
24C GLN* 3.0 21.9 + - - +
3D TRP* 4.1 12.5 + - + -
4D GLN 4.6 0.9 - - - +
5D ILE* 2.3 45.3 - - + -
6D PRO* 4.5 5.6 - - + -
9D LEU* 5.6 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU* 6.0 7.4 - - - +
14A GLN* 3.5 19.6 + - - +
18C VAL* 3.2 32.5 + - - +
19C GLU* 3.0 41.2 + - - +
21C LEU* 1.3 79.2 - - - +
23C GLN* 1.3 63.3 + - + +
24C GLN* 4.0 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C GLU* 2.8 37.6 + - - +
22C ARG* 1.3 79.5 - - + +
24C GLN* 1.3 72.7 + - - +
25C PRO* 3.3 9.1 - - + +
31C PHE* 3.1 36.9 - - + -
35C TYR* 6.0 0.2 - - - -
38C ARG* 5.6 8.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C VAL* 2.9 19.2 + - - -
21C LEU* 3.0 28.5 + - - +
22C ARG 4.7 2.5 - - - +
23C GLN* 1.3 79.2 - - - +
25C PRO* 1.3 70.2 - - - +
26C PRO* 3.6 4.5 - - - +
3D TRP* 4.3 19.6 - - + +
4D GLN* 3.5 33.6 + - - +
6D PRO* 4.7 11.5 - - - +
----------------------------------------------------------
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