Contacts of the helix formed by residues 53 - 65 (chain D) in PDB entry 2W8B
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 53 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D PRO* 4.7 5.5 - - - +
42D PHE 5.1 1.2 + - - -
50D ALA* 5.4 1.1 - - - -
52D GLU* 1.3 82.9 + - - +
54D ILE* 1.3 62.5 + - - +
55D GLY* 3.6 3.3 + - - -
56D GLY* 2.9 22.6 + - - -
57D ILE* 3.1 24.6 + - - +
73D ARG* 2.8 33.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D PHE* 3.4 36.2 - - + +
52D GLU* 3.6 19.5 + - + +
53D ASP* 1.3 71.2 + - - +
55D GLY* 1.3 63.0 + - - +
57D ILE* 3.0 8.7 + - + +
58D VAL* 3.0 25.1 + - + +
104D VAL* 3.8 24.1 - - + +
114D VAL* 3.8 26.7 - - + -
141D LEU* 3.4 31.0 - - + +
145D GLY* 4.0 17.7 - - - +
148D ALA* 5.4 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D VAL* 3.5 13.1 - - - +
40D VAL 4.0 9.6 - - - -
41D PRO* 4.5 1.1 - - - -
42D PHE* 3.6 30.2 - - - +
53D ASP* 3.4 4.6 + - - -
54D ILE* 1.3 76.4 - - - +
56D GLY* 1.3 55.3 + - - +
58D VAL* 3.2 1.3 + - - -
59D ALA* 3.0 28.0 + - - +
73D ARG* 3.8 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D ASP* 2.9 29.0 + - - -
55D GLY* 1.3 71.2 - - - +
57D ILE* 1.3 57.1 + - - +
59D ALA* 3.9 4.5 - - - +
60D ALA* 3.0 30.3 + - - +
73D ARG* 3.3 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D GLU* 3.8 27.6 - - + +
53D ASP 3.1 10.9 + - - +
54D ILE* 3.0 15.0 + - + +
56D GLY* 1.3 74.0 - - - +
58D VAL* 1.3 56.5 + - - +
60D ALA* 3.3 5.3 + - - +
61D ASP* 2.8 38.3 + - - +
142D ARG* 3.7 48.0 - - + +
145D GLY* 4.2 11.7 - - - -
146D HIS* 3.5 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D VAL* 4.0 15.5 - - + -
42D PHE* 4.3 13.2 - - + -
54D ILE* 3.0 22.1 + - + +
55D GLY 3.2 5.6 + - - +
57D ILE* 1.3 76.0 - - - +
59D ALA* 1.3 64.6 + - - +
61D ASP* 3.3 2.1 + - - +
62D LEU* 3.0 43.5 + - + +
100D VAL* 4.5 13.0 - - + -
145D GLY 3.9 11.7 - - - +
148D ALA* 4.2 14.8 - - + -
149D SER* 3.2 24.7 - - - +
152D VAL* 5.3 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D VAL* 3.9 25.7 - - + +
55D GLY 3.0 16.3 + - - +
56D GLY* 3.9 5.6 - - - +
58D VAL* 1.3 72.8 - - - +
60D ALA* 1.3 68.2 + - - +
62D LEU* 3.4 0.7 + - - -
63D ARG* 3.0 33.6 + - - +
70D PRO* 3.5 18.3 - - + +
73D ARG* 5.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D GLY 3.0 16.6 + - - +
57D ILE* 3.7 5.2 - - - +
59D ALA* 1.3 82.9 - - - +
61D ASP* 1.3 57.7 + - - +
63D ARG* 3.3 14.5 + - - +
64D ASN* 2.8 44.7 + - - +
142D ARG* 6.3 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D ILE* 2.8 24.3 + - - +
58D VAL 3.6 0.4 - - - +
60D ALA* 1.3 74.5 - - - +
62D LEU* 1.3 63.8 + - - +
64D ASN* 3.0 11.3 + - - -
65D SER 3.1 4.0 + - - -
146D HIS* 2.7 39.5 + - - -
149D SER* 2.7 31.7 + - - +
163D PHE* 3.0 34.3 - - + +
187D TYR* 2.6 27.9 + - - -
188D ASP* 4.2 2.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
37D ILE* 4.0 28.0 - - + -
39D VAL* 4.3 9.9 - - + -
58D VAL* 3.0 34.1 + - + +
59D ALA 4.0 2.5 - - - +
61D ASP* 1.3 74.3 - - - +
63D ARG* 1.3 60.6 + - - +
65D SER* 2.8 23.8 + - - -
68D PHE* 3.7 44.5 + - + +
70D PRO* 4.5 3.6 - - + -
100D VAL* 4.9 0.4 - - + -
149D SER* 4.2 8.3 - - - +
152D VAL* 4.1 10.1 - - + -
153D PHE* 4.1 23.3 - - + +
163D PHE* 4.2 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ILE* 3.6 23.6 - - + -
31D VAL* 3.8 30.2 - - + +
59D ALA* 3.0 22.9 + - - +
60D ALA* 3.7 21.5 - - - +
62D LEU* 1.3 73.6 - - - +
64D ASN* 1.3 61.5 + - - +
65D SER 3.0 6.3 + - - -
66D GLY* 3.3 10.2 + - - -
68D PHE 3.8 9.1 - - - +
69D ASN* 5.2 0.6 + - - -
70D PRO* 3.7 42.5 + - + +
71D LEU 4.8 4.4 + - - -
72D ASP* 5.4 4.2 - - - +
410D PHE* 3.3 11.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ILE* 3.5 35.2 - - + +
27D ILE* 3.6 17.5 - - - +
60D ALA* 2.8 36.9 + - - +
61D ASP* 3.0 5.5 + - - +
63D ARG* 1.3 74.6 - - - +
65D SER* 1.3 59.8 + - - +
66D GLY 3.2 0.4 - - - -
163D PHE* 5.2 0.9 - - + -
187D TYR* 3.0 33.1 + - + +
188D ASP* 4.5 5.7 + - - +
388D MET* 3.6 7.6 - - - +
403D LEU* 5.8 2.1 - - + +
410D PHE* 3.3 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D ASP 3.1 10.1 + - - -
62D LEU 2.8 17.2 + - - -
63D ARG 3.0 1.6 - - - -
64D ASN* 1.3 79.6 - - - +
66D GLY* 1.3 55.8 + - - +
67D LYS* 2.9 30.5 + - - +
68D PHE* 4.0 1.7 - - - -
153D PHE* 3.6 25.0 - - - -
163D PHE* 3.8 12.3 - - - -
387D THR* 5.0 5.7 + - - +
388D MET* 3.2 19.4 - - - +
405D SER* 5.2 1.0 - - - -
----------------------------------------------------------
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