Contacts of the helix formed by residues 50 - 60 (chain D) in PDB entry 1WOI
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 PHE 50 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B TYR* 3.9 26.0 - - + -
44C PHE* 4.0 11.7 - + - -
45C ARG* 4.1 17.5 - - + -
46C PRO* 3.7 31.9 - - + -
47D GLY* 2.9 28.3 + - - +
49D ARG* 1.3 88.8 - - + +
51D ALA* 1.3 61.5 + - - +
52D PRO* 3.4 2.5 - - - -
53D ARG* 3.4 12.8 + - + +
54D ALA* 3.1 21.0 + - - +
277D PRO* 3.9 11.4 - - + -
278D ASN* 4.5 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D ALA 3.0 5.6 + - - +
50D PHE* 1.3 75.3 - - - +
52D PRO* 1.3 56.4 - - - +
54D ALA* 3.6 0.4 - - - +
55D LEU* 2.7 42.7 + - + +
118D GLY 3.2 22.4 - - - +
275D LEU* 3.3 42.6 - - + +
277D PRO* 3.8 12.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D GLY* 4.3 4.9 - - - -
36D VAL 4.1 0.4 - - - +
37D PRO* 4.0 18.8 - - + -
48D ALA 3.6 6.5 - - - +
49D ARG 3.6 8.5 - - - +
50D PHE 3.5 4.3 - - - -
51D ALA* 1.3 90.3 - - + +
53D ARG* 1.3 56.3 + - - +
55D LEU* 3.6 1.6 - - - +
56D ARG* 2.9 52.5 + - - +
85D ASP* 4.3 6.7 - - - +
117D LEU* 3.5 32.4 - - + +
118D GLY 3.4 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PRO 3.4 16.8 + - - -
9B TYR* 3.2 36.9 + - - +
10B GLY 3.4 6.9 + - - -
11B GLY 2.9 28.0 + - - -
13B PRO* 4.0 15.0 - - + +
57B GLU* 3.8 34.5 + - - +
60B LEU* 3.5 14.6 - - - +
44C PHE* 6.1 1.2 - - - -
13D PRO* 5.7 0.7 - - + -
50D PHE* 3.4 14.9 + - - +
51D ALA 3.3 0.2 - - - -
52D PRO* 1.3 79.8 - - - +
54D ALA* 1.3 62.3 + - - +
56D ARG* 3.3 12.2 + - - +
57D GLU* 3.1 43.3 + - + +
85D ASP* 5.4 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D PHE 3.1 9.4 + - - +
51D ALA* 3.2 3.1 + - - +
53D ARG* 1.3 76.2 - - - +
55D LEU* 1.3 57.7 + - - +
57D GLU* 3.4 12.8 + - - +
58D ALA* 2.9 29.6 + - - +
275D LEU* 4.6 0.4 - - + -
277D PRO* 3.4 39.0 - - + -
286D GLU* 4.0 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D PHE* 4.2 5.1 - - + -
51D ALA* 2.7 31.8 + - + +
52D PRO 3.6 3.4 - - - +
54D ALA* 1.3 69.5 - - - +
56D ARG* 1.3 60.4 + - - +
58D ALA* 3.7 3.5 - - - +
59D SER* 2.8 31.9 + - - -
117D LEU* 4.1 34.5 - - + -
118D GLY 4.7 1.8 - - - +
272D LEU* 3.8 24.2 - - + -
275D LEU* 3.7 22.2 - - + -
286D GLU 3.9 5.2 - - - +
289D MET* 4.1 10.3 - - + +
290D ALA* 3.8 32.7 - - - +
293D VAL* 5.6 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLY 5.2 2.2 + - - -
12B ILE* 3.1 17.6 - - - +
13B PRO* 5.7 2.7 - - - -
13D PRO* 3.5 28.7 - - + +
14D THR 3.9 2.4 - - - +
15D PHE* 3.9 13.4 - - - +
33D ALA* 4.9 1.2 + - - +
34D LEU 4.7 1.0 - - - -
35D GLY 3.8 6.3 - - - +
52D PRO* 2.9 40.1 + - - +
53D ARG* 3.6 10.2 - - - +
55D LEU* 1.3 77.2 - - - +
57D GLU* 1.3 61.8 + - - +
59D SER* 2.6 25.1 + - - -
60D LEU* 3.6 9.0 + - - +
82D ASP* 2.8 31.9 + - - +
84D GLY* 2.8 21.2 + - - -
85D ASP* 2.8 36.7 + - - -
117D LEU* 4.5 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ARG* 3.6 25.9 + - - +
57B GLU* 2.4 30.9 - - - +
8D PRO* 4.8 2.8 - - - +
13D PRO* 3.6 26.2 - - + +
53D ARG* 3.1 25.0 + - - +
54D ALA* 3.7 10.5 - - - +
56D ARG* 1.3 78.0 - - - +
58D ALA* 1.3 61.7 + - - +
60D LEU* 3.3 23.4 + - - +
61D ARG* 4.5 1.9 + - - +
44E PHE* 5.8 2.9 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
54D ALA 2.9 18.4 + - - +
55D LEU 3.8 0.9 - - - +
57D GLU* 1.3 72.2 - - - +
59D SER* 1.3 61.8 + - - +
60D LEU 3.1 5.4 - - - -
61D ARG* 3.1 22.9 + - - +
62D SER* 4.2 1.7 + - - -
286D GLU* 3.3 38.4 - - + +
287D LEU* 3.8 21.2 - - + +
290D ALA* 3.7 10.0 - - + +
44E PHE* 6.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D THR 3.6 1.0 + - - -
15D PHE* 3.5 21.7 - - - -
16D ALA* 2.8 29.9 + - - -
55D LEU 2.8 14.6 + - - -
56D ARG 2.6 20.3 + - - -
58D ALA* 1.3 72.2 - - - +
60D LEU* 1.3 57.0 + - - +
61D ARG 2.9 6.3 - - - -
62D SER* 2.8 33.0 + - - +
63D VAL* 3.6 3.5 + - - +
290D ALA* 3.7 9.1 - - - +
294D MET* 5.2 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ARG* 3.7 21.3 - - - +
7D LEU 5.6 0.2 - - - -
8D PRO* 3.3 38.8 - - + +
10D GLY 4.3 2.0 - - - +
12D ILE 4.9 0.2 - - - +
13D PRO* 4.1 13.9 - - + -
14D THR 3.7 19.7 - - - +
17D ARG* 3.6 56.2 + - + +
56D ARG 3.7 5.4 - - - +
57D GLU 3.4 15.9 - - - +
58D ALA 3.1 0.8 - - - -
59D SER* 1.3 76.9 - - - +
61D ARG* 1.3 60.6 + - - +
62D SER 3.2 0.7 - - - -
63D VAL* 3.6 15.6 - - - +
----------------------------------------------------------
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