Contacts of the helix formed by residues 57 - 75 (chain D) in PDB entry 1O1L
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 ASN 57 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D PHE 2.9 29.9 + - - +
46D GLY* 4.2 3.6 - - - -
47D ASP 3.7 19.8 + - - +
48D LEU* 4.2 3.0 - - - +
53D ALA 2.9 16.5 + - - +
54D VAL* 3.2 12.1 + - - +
56D GLY* 1.3 77.5 - - - +
58D PRO* 1.3 73.2 - - - +
59D LYS* 2.9 28.1 + - - +
60D VAL* 3.3 19.4 + - + +
61D LYS* 3.1 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D GLY 3.3 8.3 - - - +
57D ASN* 1.3 96.8 - - - +
59D LYS* 1.3 74.2 + - + +
61D LYS* 3.7 10.0 - - + +
62D ALA* 3.1 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D SER 4.7 5.1 + - - +
45D PHE* 3.4 59.0 + - + +
46D GLY* 5.1 4.0 - - - +
57D ASN* 2.9 7.3 + - - +
58D PRO* 1.3 87.7 - - + +
60D VAL* 1.3 61.4 + - - +
62D ALA* 3.8 5.1 - - - +
63D HIS* 2.9 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D GLY* 4.3 7.0 - - - +
28D LEU* 3.5 13.4 - - + +
29D GLY* 4.0 27.6 - - - +
32D LEU* 3.8 22.9 - - + -
45D PHE* 4.1 16.2 - - + -
48D LEU* 4.2 8.5 - - + -
54D VAL* 3.8 16.4 - - + +
55D MET* 5.5 1.1 - - - +
57D ASN* 3.3 28.2 + - + +
59D LYS* 1.3 78.4 - - - +
61D LYS* 1.3 66.9 + - + +
63D HIS 3.4 0.3 + - - -
64D GLY* 2.9 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ASP 4.9 2.1 - - - +
25D GLY* 4.2 21.0 + - - +
55D MET 3.6 22.4 - - - +
56D GLY* 4.6 9.2 - - - +
57D ASN 3.1 13.8 + - - +
58D PRO* 3.7 13.2 - - + +
59D LYS 3.2 0.2 - - - -
60D VAL* 1.3 82.6 - - + +
62D ALA* 1.3 61.6 + - - +
64D GLY* 3.3 1.2 + - - -
65D LYS* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D PRO 3.1 16.8 + - - +
59D LYS* 3.8 5.8 - - - +
61D LYS* 1.3 74.9 - - - +
63D HIS* 1.3 66.1 + - - +
65D LYS* 3.1 19.6 + - - +
66D LYS* 3.2 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D LEU* 3.4 24.9 - - + -
42D PHE* 3.5 18.9 - + - -
45D PHE* 3.7 17.0 - + + -
59D LYS 2.9 18.1 + - - +
62D ALA* 1.3 75.4 - - - +
64D GLY* 1.3 62.8 + - - +
66D LYS* 3.1 28.1 + - + +
67D VAL* 2.9 41.5 + - + +
147D HEM 3.3 64.9 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D GLY* 3.5 34.0 - - - +
28D LEU* 3.6 12.3 - - - +
60D VAL 2.9 17.4 + - - -
61D LYS 3.7 2.2 - - - -
62D ALA 3.2 0.2 - - - -
63D HIS* 1.3 77.6 - - - +
65D LYS* 1.3 60.8 + - - +
67D VAL* 3.4 5.1 + - - +
68D LEU* 3.0 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D VAL* 4.1 13.9 - - + +
21D ASP* 2.8 45.7 + - - +
24D GLY 4.4 1.0 - - - -
61D LYS 3.1 11.9 + - - +
62D ALA* 3.1 13.2 + - - +
64D GLY* 1.3 76.6 - - - +
66D LYS* 1.3 57.8 + - + +
68D LEU 3.9 0.2 - - - -
69D GLY* 2.9 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D PHE* 5.9 1.2 - - - -
62D ALA* 3.2 17.4 + - - +
63D HIS* 3.1 35.9 + - + +
65D LYS* 1.3 77.6 - - + +
67D VAL* 1.3 65.1 + - + +
69D GLY* 3.3 1.8 + - - -
70D ALA* 3.1 23.6 + - - +
147D HEM 4.2 45.0 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
28D LEU* 5.4 4.5 - - + -
63D HIS* 2.9 50.4 + - + +
64D GLY* 3.7 6.3 - - - +
66D LYS* 1.3 76.9 - - - +
68D LEU* 1.3 64.3 + - + +
70D ALA* 3.3 4.9 + - - +
71D PHE* 2.9 23.4 + - - +
106D LEU* 4.0 17.7 - - + -
147D HEM 3.7 54.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D TRP* 3.9 21.9 - - + -
18D VAL* 5.0 0.2 - - + -
20D VAL* 3.4 20.1 - - + +
23D VAL* 3.4 33.9 - - + -
24D GLY* 3.7 17.9 - - - +
27D ALA* 5.2 5.8 - - + -
64D GLY 3.0 16.5 + - - +
67D VAL* 1.3 83.0 - - + +
69D GLY* 1.3 62.1 + - - +
71D PHE* 3.3 13.2 - - + +
72D SER* 2.7 29.1 + - - -
106D LEU* 5.8 5.4 - - + -
110D LEU* 3.8 27.4 - - + -
147D HEM 6.0 0.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
20D VAL* 3.5 10.0 - - - +
65D LYS 2.9 19.1 + - - -
66D LYS* 3.8 1.8 - - - -
67D VAL 3.2 0.2 - - - -
68D LEU* 1.3 77.6 - - - +
70D ALA* 1.3 60.7 + - - +
72D SER* 3.1 5.9 + - - -
73D ASP* 3.1 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D LYS 3.1 12.7 + - - +
67D VAL 3.6 7.6 - - - +
69D GLY* 1.3 72.1 - - - +
71D PHE* 1.3 67.3 + - - +
73D ASP* 3.2 12.9 + - - +
74D GLY 3.2 15.6 + - - -
85D PHE* 3.8 11.7 - - + -
88D LEU* 4.3 11.0 - - + -
147D HEM 3.8 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D TRP* 3.5 39.9 - + - -
67D VAL 2.9 13.8 + - - +
68D LEU* 3.3 20.6 - - + +
70D ALA* 1.3 78.4 - - - +
72D SER* 1.3 56.0 + - - +
74D GLY* 2.9 18.2 + - - -
75D LEU* 3.4 33.7 + - + +
85D PHE* 4.5 7.2 - - - -
110D LEU* 3.9 20.4 - - + -
130D TYR* 5.2 5.4 - + - -
133D VAL* 4.2 11.7 - - + -
134D VAL* 4.4 15.0 - - + -
137D VAL* 4.1 26.4 - - + +
147D HEM 4.1 24.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D TRP* 2.7 36.6 + - - +
20D VAL* 4.1 10.8 - - - +
68D LEU 2.7 17.1 + - - -
69D GLY* 3.2 14.1 - - - -
71D PHE* 1.3 74.8 - - - +
73D ASP* 1.3 65.1 + - - +
75D LEU* 3.1 19.4 + - - +
76D ALA* 3.8 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D GLY 3.1 16.8 + - - +
70D ALA* 3.7 12.7 - - - +
71D PHE 3.2 0.2 - - - -
72D SER* 1.3 78.9 - - - +
74D GLY* 1.3 61.9 + - - +
76D ALA* 3.2 16.5 + - - +
77D HIS* 3.4 19.7 + - + +
84D THR* 4.7 4.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D ALA 3.2 5.7 + - - -
71D PHE 2.9 11.0 + - - -
73D ASP* 1.3 79.5 - - - +
75D LEU* 1.3 58.9 + - - +
76D ALA 3.1 0.4 - - - -
77D HIS* 3.0 27.0 + - - +
78D LEU* 3.6 1.4 + - - -
81D LEU* 3.7 11.1 - - - +
84D THR* 4.3 8.3 - - - +
85D PHE* 3.7 26.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D VAL* 3.7 27.4 - - + -
12D THR* 5.1 11.1 - - + +
15D TRP* 3.9 35.9 - - + -
71D PHE* 3.7 37.7 - - + +
72D SER* 3.1 13.7 + - - +
74D GLY* 1.3 78.6 - - - +
76D ALA* 1.3 59.2 + - - +
77D HIS 3.2 0.6 + - - -
78D LEU* 3.7 27.9 + - + +
130D TYR* 4.9 1.8 - - + -
133D VAL* 4.0 19.5 - - + -
137D VAL* 5.1 3.8 - - + -
----------------------------------------------------------
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