Contacts of the helix formed by residues 54 - 69 (chain D) in PDB entry 1R6O
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 ASP 54 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A YBT 3.7 34.2 + - - +
48D GLN* 3.2 3.8 - - - -
52D SER 3.9 1.8 + - - -
53D TYR* 1.3 75.3 - - - +
55D VAL* 1.3 65.9 + - - +
56D GLU* 3.2 17.6 - - - +
57D ARG* 3.0 28.2 + - - +
58D ALA* 2.9 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLN* 3.6 23.6 - - - +
7A GLU* 4.0 16.2 - - + +
8A LEU* 3.9 26.9 - - + +
11A ASN* 3.8 30.3 - - + +
413A YBT 4.7 2.4 + - - +
44D ILE* 4.5 2.7 - - + -
48D GLN* 3.0 26.7 + - - +
54D ASP* 1.3 74.9 - - - +
56D GLU* 1.3 60.1 + - - +
58D ALA* 3.4 2.4 + - - +
59D THR* 2.8 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLU* 3.3 10.8 - - - +
11A ASN* 3.8 22.3 + - - +
413A YBT 2.4 54.6 + - - +
7C TRP* 4.0 20.9 + - + +
8C LEU 5.0 4.7 - - - +
9C ASP* 5.5 2.7 - - - +
10C PHE* 5.7 3.8 - - + +
54D ASP* 3.2 16.1 - - - +
55D VAL* 1.3 77.2 + - - +
57D ARG* 1.3 62.0 + - - +
59D THR* 3.3 4.2 + - - -
60D GLN* 3.1 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D TYR* 3.5 33.3 + - + -
54D ASP* 3.0 19.9 + - - +
56D GLU* 1.3 74.6 - - - +
58D ALA* 1.3 65.6 + - - +
60D GLN* 3.4 41.2 + - - +
61D LEU* 3.0 52.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ILE* 3.9 12.3 - - + -
47D LEU* 3.3 33.8 - - + +
48D GLN* 3.8 23.8 - - + -
53D TYR* 4.1 6.2 - - + +
54D ASP 2.9 17.6 + - - +
55D VAL 3.6 4.0 - - - +
57D ARG* 1.3 75.7 - - - +
59D THR* 1.3 58.2 + - - +
61D LEU* 3.4 1.0 + - - -
62D MET* 2.9 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASN* 3.4 38.5 - - + +
15A ALA* 3.9 13.7 - - + -
7C TRP* 3.5 23.1 - - + -
44D ILE* 3.5 17.1 - - + +
55D VAL* 2.8 24.1 + - - +
56D GLU 3.6 4.7 - - - -
58D ALA* 1.3 77.2 - - - +
60D GLN* 1.3 61.2 + - - +
62D MET* 3.4 12.2 + - + +
63D LEU* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C TRP* 3.8 45.5 - - + +
56D GLU* 3.1 22.5 + - - +
57D ARG* 3.6 41.0 - - - +
59D THR* 1.3 73.3 - - - +
61D LEU* 1.3 59.7 + - - +
63D LEU* 3.2 9.4 + - - +
64D ALA* 2.9 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D LEU* 3.8 17.0 - - + -
53D TYR* 3.4 47.6 - - + +
57D ARG* 3.0 47.7 + - - +
58D ALA 3.8 3.6 - - - +
60D GLN* 1.3 73.3 - - - +
62D MET* 1.3 60.8 + - - +
64D ALA* 3.0 9.0 + - + +
65D VAL* 2.8 34.6 + - + +
71D ALA* 4.1 14.2 - - + +
72D ILE 3.8 21.1 - - - +
73D CYS* 5.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA* 3.7 24.9 - - + -
19A GLU* 4.1 16.2 - - - +
40D MET* 3.6 36.3 - - + +
43D VAL* 3.7 40.4 - - + -
44D ILE* 4.2 7.4 - - + -
47D LEU* 3.9 0.8 - - - +
58D ALA 2.9 17.5 + - - +
59D THR* 3.4 23.3 - - + +
60D GLN 3.2 0.2 - - - -
61D LEU* 1.3 76.5 - - - +
63D LEU* 1.3 58.6 + - + +
65D VAL* 3.3 6.9 + - - +
66D HIS* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA* 4.0 17.7 - - + +
18A ARG* 3.9 26.0 - - + +
19A GLU* 3.5 36.8 - - + +
7C TRP* 3.6 35.0 - - + -
59D THR 3.0 12.7 + - - +
60D GLN* 3.2 9.2 + - - +
62D MET* 1.3 81.2 - - + +
64D ALA* 1.3 59.0 + - - +
66D HIS* 3.2 5.2 + - + +
67D TYR* 2.9 49.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D GLN 2.9 13.4 + - - +
61D LEU* 3.0 15.7 + - + +
63D LEU* 1.3 74.1 - - - +
65D VAL* 1.3 59.2 + - - +
67D TYR* 5.0 1.3 - - - -
68D GLN* 2.7 58.8 + - - +
70D LYS 3.7 2.6 - - - +
71D ALA* 4.1 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D LEU* 3.9 35.4 - - + +
33D VAL 3.9 5.4 - - - +
34D ASN* 3.3 38.5 - - + +
43D VAL* 5.1 4.5 - - + -
47D LEU* 5.7 0.9 - - + -
61D LEU* 2.8 21.8 + - + +
62D MET* 3.4 11.9 - - - +
64D ALA* 1.3 74.9 - - - +
66D HIS* 1.3 58.6 + - - +
69D GLY* 2.9 27.5 + - - -
70D LYS* 4.0 8.3 - - - -
71D ALA* 3.6 17.2 - - + +
99D LEU* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU* 3.6 38.4 + - + +
34D ASN* 3.8 22.0 + - - -
62D MET* 3.0 15.3 + - - +
63D LEU* 3.3 8.7 - - - +
65D VAL* 1.3 79.5 - - - +
67D TYR* 1.3 97.5 + + - +
69D GLY* 4.3 1.6 + - - -
413D Y1 2.2 31.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 3.2 28.6 + - + +
19A GLU* 3.6 11.6 + - - -
21A ARG* 4.5 9.6 + - - +
63D LEU* 2.9 45.9 + - + +
64D ALA* 4.4 2.0 - - - +
66D HIS* 1.3 99.4 - + - +
68D GLN* 1.3 68.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D ALA* 2.7 39.2 + - - +
67D TYR* 1.3 80.2 - - + +
69D GLY* 1.3 54.7 + - - +
70D LYS* 3.2 23.4 + - + +
71D ALA* 5.4 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D VAL* 3.9 6.4 - - - +
34D ASN* 3.0 31.8 + - - +
65D VAL 2.9 17.0 + - - -
66D HIS 4.3 1.3 + - - -
67D TYR 3.5 2.6 + - - -
68D GLN* 1.3 77.1 - - - +
70D LYS* 1.3 62.1 + - - +
----------------------------------------------------------
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