Contacts of the helix formed by residues 12 - 27 (chain D) in PDB entry 5XAC
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 12 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ARG 5.9 0.2 - - - +
11D ARG* 1.3 78.5 - - - +
13D PHE* 1.3 64.3 + - - +
14D GLU* 3.5 9.2 + - - +
15D GLN* 2.9 41.1 + - - +
16D ARG* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 13 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D THR* 1.3 72.3 - - - +
14D GLU* 1.3 65.6 + - - +
16D ARG* 3.3 30.6 + - - +
17D VAL* 3.0 46.5 + - + +
104D ASP* 5.1 0.4 - - - -
105D GLU* 3.6 41.7 - - + -
106D ASP* 3.7 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 14 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D THR* 3.2 9.3 + - - +
13D PHE* 1.3 82.3 - - - +
15D GLN* 1.3 68.2 + - - +
17D VAL* 3.5 4.5 + - - +
18D GLU* 3.0 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 15 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ARG 4.3 2.6 - - - +
11D ARG* 3.4 20.7 - - + +
12D THR* 2.9 50.5 + - - +
14D GLU* 1.3 83.2 - - + +
16D ARG* 1.3 57.2 + - - +
18D GLU* 3.3 7.1 + - - +
19D ASP* 2.9 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 16 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D PHE* 4.1 17.3 - - + -
8D LYS* 3.4 39.0 + - - +
11D ARG* 3.0 40.8 + - + -
12D THR 3.0 14.9 + - - +
13D PHE* 3.4 28.1 - - - +
15D GLN* 1.3 71.9 - - - +
17D VAL* 1.3 66.0 + - - +
19D ASP* 3.2 9.5 + - - +
20D VAL* 3.0 27.2 + - - +
104D ASP* 4.6 0.4 + - - -
106D ASP* 2.8 56.0 + - + +
108D PHE* 3.6 5.6 - - + -
110D TYR* 3.6 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 17 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D PHE* 3.0 53.1 + - + +
14D GLU* 3.9 4.3 - - - +
16D ARG* 1.3 75.7 - - - +
18D GLU* 1.3 65.3 + - + +
20D VAL* 3.3 3.9 + - + +
21D ARG* 3.0 22.5 + - + +
105D GLU 4.9 0.9 - - - +
106D ASP* 3.8 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 18 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D GLU* 3.0 30.2 + - + +
15D GLN* 3.5 7.4 - - - +
17D VAL* 1.3 79.2 - - + +
19D ASP* 1.3 64.5 + - - +
21D ARG* 2.8 49.0 + - - +
22D LEU* 3.0 34.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 19 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D PHE* 4.5 1.4 - - - -
11D ARG* 3.9 22.2 + - - -
15D GLN* 2.9 22.8 + - - +
16D ARG* 3.2 14.4 + - - +
18D GLU* 1.3 77.8 - - - +
20D VAL* 1.3 57.4 - - - +
22D LEU* 3.3 11.6 + - - +
23D ILE* 2.9 39.8 + - + +
108D PHE* 3.7 17.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ARG 3.0 12.5 + - - +
17D VAL 3.7 7.4 - - - +
19D ASP* 1.3 74.8 - - - +
21D ARG* 1.3 58.7 + - - +
23D ILE* 3.3 8.5 + - - +
24D ARG* 2.8 35.8 + - + +
32D PRO* 4.6 6.3 - - + -
99D TYR* 4.1 8.1 - - - +
106D ASP 3.4 21.8 - - - +
107D GLY* 3.6 32.1 - - - +
108D PHE* 3.7 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 21 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D VAL* 3.0 14.5 + - + +
18D GLU* 2.8 47.8 + - - +
20D VAL* 1.3 78.0 - - - +
22D LEU* 1.3 78.9 + - - +
24D ARG* 3.2 7.5 + - - +
25D GLU* 2.8 59.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D GLU* 3.0 29.7 + - + +
19D ASP* 3.8 10.8 - - - +
21D ARG* 1.3 105.9 - - - +
23D ILE* 1.3 58.3 + - + +
25D GLU* 3.1 14.8 + - - +
26D GLN* 2.9 51.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ASP* 2.9 30.1 + - + +
20D VAL* 3.7 4.5 - - - +
22D LEU* 1.3 75.9 - - + +
24D ARG* 1.3 56.5 + - - +
26D GLN* 5.6 0.4 - - - -
27D HIS* 2.7 50.4 + - + +
30D LYS 5.0 3.1 - - - +
32D PRO* 4.2 21.8 - - + -
53D LEU* 3.6 32.1 - - + -
108D PHE* 4.0 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D VAL* 2.8 26.9 + - + +
21D ARG* 3.5 7.2 - - + +
23D ILE* 1.3 75.7 - - - +
25D GLU* 1.3 62.8 + - - +
27D HIS 4.3 2.0 - - - -
28D PRO* 3.1 50.4 + - + +
30D LYS 3.1 26.0 + - - +
31D ILE* 4.2 9.1 - - - +
32D PRO* 5.5 2.7 - - - -
56D ASP* 4.3 4.0 + - - -
99D TYR* 3.8 29.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ARG* 2.8 45.1 + - + +
22D LEU* 3.1 19.9 + - - +
24D ARG* 1.3 79.7 - - + +
26D GLN* 1.3 65.0 + - + +
28D PRO* 4.0 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D LEU* 2.9 42.0 + - - +
23D ILE* 5.6 0.4 - - - -
25D GLU* 1.3 80.4 + - + +
27D HIS* 1.3 85.4 + - + +
28D PRO* 3.6 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ILE* 2.7 31.3 + - + +
24D ARG* 4.2 2.6 + - - +
26D GLN* 1.3 100.1 + - + +
28D PRO* 1.3 67.1 - - - +
29D THR* 3.1 5.2 + - - -
30D LYS* 3.2 44.9 + - + +
53D LEU* 3.7 28.7 - - + +
----------------------------------------------------------
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