Contacts of the helix formed by residues 57 - 72 (chain D) in PDB entry 1L9W
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 SER 57 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D ASP* 3.5 7.6 + - - +
55D ILE 3.3 2.4 - - - -
56D ALA* 1.3 80.9 - - - +
58D THR* 1.3 60.6 + - - +
59D GLN* 3.7 7.3 + - - +
60D SER* 3.0 37.1 + - - -
61D VAL* 3.5 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D ALA 4.0 2.0 + - - -
57D SER* 1.3 71.1 + - - +
59D GLN* 1.3 57.5 + - - +
61D VAL* 3.3 8.7 + - + +
62D LEU* 3.0 34.0 + - + +
96D HIS* 4.9 4.2 - - - -
99D THR* 3.9 20.9 - - + +
100D LEU* 4.3 14.1 - - + +
103D ALA* 3.6 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D SER* 3.3 6.6 + - - +
58D THR* 1.3 81.0 - - - +
60D SER* 1.3 61.5 + - - +
62D LEU* 3.4 17.4 + - - +
63D THR* 3.0 40.5 + - - +
66D ARG* 3.8 20.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ILE* 3.7 11.7 - - - +
52D PHE* 3.5 14.2 - - - -
54D ASP* 3.9 25.1 - - - +
57D SER* 3.0 28.3 + - - -
59D GLN* 1.3 75.0 - - - +
61D VAL* 1.3 55.6 + - - +
63D THR* 3.3 7.5 + - - -
64D ALA 3.1 21.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D TRP* 3.4 21.0 - - + -
49D VAL* 4.1 7.4 - - + -
52D PHE* 4.0 22.9 - - + -
54D ASP 4.0 5.8 - - - +
55D ILE* 4.1 10.3 - - + -
57D SER 3.5 13.5 - - - +
58D THR* 3.3 10.0 + - + +
60D SER* 1.3 72.4 - - - +
62D LEU* 1.3 63.9 + - + +
64D ALA 3.3 1.9 + - - -
65D ALA* 2.9 23.9 + - - +
79D PHE* 4.0 25.4 - - + -
100D LEU* 4.0 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D THR* 3.0 33.7 + - + +
59D GLN* 3.4 23.3 + - - +
60D SER 3.4 0.2 - - - -
61D VAL* 1.3 83.3 - - + +
63D THR* 1.3 62.1 + - - +
65D ALA* 3.4 9.0 + - + +
66D ARG* 3.1 30.5 + - - +
79D PHE* 5.8 0.7 - - + -
100D LEU 5.7 0.2 - - - +
103D ALA* 3.9 21.5 - - + +
104D ALA* 4.1 12.8 - - + +
107D SER* 3.8 28.9 - - - +
109D LEU* 3.7 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ILE* 3.9 26.2 - - + -
59D GLN* 3.0 30.8 + - - +
60D SER* 3.6 7.0 - - - -
61D VAL 3.2 0.2 - - - -
62D LEU* 1.3 76.2 - - - +
64D ALA* 1.3 57.9 + - - +
66D ARG* 3.3 20.7 + - - +
67D VAL* 3.1 30.1 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
27D ILE* 4.0 9.6 - - + +
30D VAL* 4.0 9.4 - - + +
47D TRP* 3.6 25.6 - - + -
52D PHE* 3.7 22.4 - - + -
60D SER 3.1 16.9 + - - +
61D VAL 3.6 0.2 - - - +
62D LEU 3.3 0.2 - - - -
63D THR* 1.3 75.1 - - - +
65D ALA* 1.3 62.5 + - - +
67D VAL* 3.2 16.7 + - - +
68D ILE* 3.2 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D TRP* 3.8 20.8 - - + -
61D VAL 2.9 15.2 + - - +
62D LEU* 3.6 15.3 - - + +
63D THR 3.3 0.4 - - - -
64D ALA* 1.3 74.6 - - - +
66D ARG* 1.4 57.2 + - - +
68D ILE* 3.4 7.0 + - - +
69D ARG* 3.1 28.1 + - - +
77D LEU* 4.3 5.8 - - + +
79D PHE* 5.3 2.5 - - + -
104D ALA* 6.6 0.2 - - + -
109D LEU* 4.0 20.1 - - + +
110D VAL* 5.1 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D GLN* 3.8 20.4 - - - +
62D LEU* 3.1 28.7 + - - +
63D THR* 3.5 20.9 + - - +
64D ALA 3.2 0.4 - - - -
65D ALA* 1.4 74.7 - - - +
67D VAL* 1.3 60.2 + - - +
68D ILE 3.2 0.2 - - - -
69D ARG* 4.4 0.9 - - + -
70D ASP* 2.8 49.2 + - - +
109D LEU* 4.1 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ILE* 4.4 21.1 - - + -
30D VAL* 4.4 5.8 - - + -
31D LYS* 3.7 44.9 - - + +
34D ALA* 4.6 4.0 - - + -
63D THR* 3.1 22.0 + - + +
64D ALA* 3.5 9.6 - - - +
66D ARG* 1.3 74.3 - - - +
68D ILE* 1.3 66.1 + - - +
70D ASP* 4.0 4.3 - - - +
71D ALA* 3.2 22.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D LEU* 4.1 14.1 - - + -
30D VAL* 3.6 24.9 - - + -
34D ALA* 4.5 8.7 - - + -
45D LEU* 3.6 29.8 - - + -
47D TRP* 3.6 44.4 - - + -
64D ALA 3.2 11.3 + - - +
65D ALA* 3.6 7.2 - - - +
66D ARG 3.2 1.0 - - - -
67D VAL* 1.3 76.4 - - - +
69D ARG* 1.3 64.9 + - - +
71D ALA* 3.3 4.5 + - - +
72D MET* 3.1 26.5 + - + +
77D LEU* 3.9 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D LYS* 3.8 7.9 - - - +
65D ALA 3.1 16.3 + - - +
66D ARG* 4.0 5.4 - - - +
67D VAL 3.3 0.2 - - - -
68D ILE* 1.3 81.6 - - - +
70D ASP* 1.3 69.6 + - - +
72D MET 3.3 20.5 + - - -
73D PRO* 3.2 42.5 + - + +
75D ILE 2.9 25.3 + - - -
77D LEU* 3.8 18.4 - - + +
108D GLY 5.3 2.4 + - - -
109D LEU* 3.3 47.0 + - + +
111D ASP* 3.1 30.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D ARG* 2.8 45.2 + - - +
67D VAL* 4.0 4.6 - - - +
69D ARG* 1.3 82.4 - - - +
71D ALA* 1.3 61.6 + - - +
72D MET 3.7 0.2 + - - -
73D PRO* 3.8 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D ALA* 4.0 25.6 - - + +
35D LEU* 5.1 8.3 - - + -
38D ARG* 3.6 24.2 + - - +
67D VAL* 3.2 17.2 + - + +
68D ILE 3.7 4.3 - - - +
70D ASP* 1.3 78.2 - - - +
72D MET* 1.3 65.3 + - + +
73D PRO* 3.5 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D LEU* 4.7 1.1 - - + -
34D ALA* 3.7 35.2 - - + +
37D TYR* 4.1 6.5 - - + +
38D ARG* 4.1 28.0 - - + -
42D PHE* 4.2 19.1 - - - -
45D LEU* 3.3 35.7 - - + -
68D ILE* 3.1 17.5 + - + +
69D ARG* 3.3 19.3 + - - +
71D ALA* 1.3 81.0 - - - +
73D PRO* 1.3 66.4 - - - +
74D ASP 3.3 3.6 + - - -
75D ILE* 3.6 24.5 + - + +
----------------------------------------------------------
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