Contacts of the helix formed by residues 28 - 45 (chain D) in PDB entry 2H8C
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 28 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ARG 2.8 19.5 + - - -
17D TYR 2.7 24.6 + - - -
18D TYR 4.2 5.2 - - - -
19D ARG* 4.4 2.9 - - - -
27D VAL* 1.3 80.9 - - - +
29D ALA* 1.3 57.5 + - - +
30D GLU* 3.4 11.4 + - - +
31D GLY 2.8 5.0 + - - -
32D GLN* 2.5 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D SER* 1.3 70.0 - - - +
30D GLU* 1.3 65.4 + - - +
32D GLN* 4.3 5.1 - - - +
33D ALA* 2.9 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D PRO* 3.4 28.2 - - + +
16D ARG* 3.5 30.2 - - - +
28D SER* 3.3 9.2 + - - +
29D ALA* 1.3 80.7 - - + +
31D GLY* 1.3 60.3 + - - +
33D ALA* 3.7 6.6 + - - +
34D TYR* 3.4 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D PRO* 3.7 14.3 - - - +
17D TYR* 3.7 37.2 + - - +
27D VAL* 4.3 2.7 - - - -
28D SER* 2.8 12.5 + - - -
30D GLU* 1.3 74.7 - - - +
32D GLN* 1.3 61.6 + - - +
34D TYR* 3.0 18.2 + - - +
35D ARG* 3.2 9.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D VAL* 4.2 8.4 - - + +
28D SER 2.5 25.1 + - - +
29D ALA* 3.6 5.6 - - - +
31D GLY* 1.3 67.2 - - - +
33D ALA* 1.3 51.3 + - - +
34D TYR 2.5 15.4 + - - -
35D ARG* 3.2 41.4 + - - +
36D ASP* 2.7 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D ALA 2.9 20.9 + - - +
30D GLU* 3.8 6.3 - - - +
32D GLN* 1.3 72.2 - - - +
34D TYR* 1.3 57.9 + - - +
36D ASP* 3.6 13.0 + - - +
37D ASN* 2.8 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 34 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LEU* 4.9 1.9 - - + -
9D PRO* 3.6 33.4 - - + -
10D TRP 3.8 6.7 - - - -
11D PRO* 3.4 44.7 - - + -
12D PRO* 3.5 12.3 - - + -
17D TYR* 3.6 26.7 - + - -
30D GLU 3.4 11.5 + - - +
31D GLY 3.0 11.4 + - - +
32D GLN 2.5 6.7 + - - -
33D ALA* 1.3 72.1 - - - +
35D ARG* 1.3 68.7 + - - +
36D ASP 3.1 1.1 - - - -
37D ASN* 2.8 22.7 + - + +
38D VAL* 3.2 17.4 + - + +
77D ALA* 4.7 6.3 - - + -
78D ALA* 5.7 1.4 - - - -
81D ALA* 4.5 15.0 - - + -
110D LEU* 3.8 13.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 35 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D TYR* 3.8 9.8 + - - +
18D TYR* 5.3 2.8 - - - -
27D VAL* 3.2 46.2 - - - +
31D GLY 3.2 1.5 + - - +
32D GLN* 3.2 30.5 + - - +
34D TYR* 1.3 76.8 - - - +
36D ASP* 1.3 64.1 + - - +
38D VAL* 2.9 6.5 + - - +
39D ALA* 2.9 24.8 + - - +
80D ASP* 2.7 39.9 + - - +
81D ALA* 4.2 17.0 - - - +
84D LYS* 3.4 47.2 - - + +
85D ALA* 5.2 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 36 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D GLN* 2.7 37.4 + - - +
33D ALA* 3.6 15.6 - - - +
35D ARG* 1.3 74.5 - - - +
37D ASN* 1.3 56.9 + - - +
38D VAL 3.1 0.2 + - - -
39D ALA* 3.2 5.9 + - - +
40D ARG* 2.6 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 37 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D PRO* 5.2 10.7 - - + +
33D ALA* 2.8 25.1 + - - +
34D TYR* 2.8 15.5 + - + +
36D ASP* 1.3 75.9 - - - +
38D VAL* 1.3 57.9 + - - +
40D ARG* 3.4 16.3 - - - +
41D ILE* 2.8 27.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LEU* 4.3 36.1 - - + -
9D PRO* 4.5 5.2 - - + -
34D TYR* 3.2 25.9 + - + +
35D ARG 2.9 8.7 + - - +
37D ASN* 1.3 73.9 - - - +
39D ALA* 1.3 58.8 + - - +
40D ARG 2.9 1.1 - - - -
41D ILE* 2.5 33.6 + - - +
42D ILE* 2.8 12.0 + - + -
81D ALA* 3.9 29.2 - - + +
82D LEU* 4.8 5.8 - - + +
85D ALA* 4.0 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D ARG 2.9 13.8 + - - +
36D ASP* 3.7 9.4 - - - +
38D VAL* 1.3 74.0 - - - +
40D ARG* 1.3 62.3 + - - +
42D ILE* 3.7 2.8 - - - +
43D LYS* 2.9 32.9 + - + +
84D LYS* 5.3 1.1 - - + +
85D ALA* 3.5 32.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D ASP* 2.6 29.2 + - + +
37D ASN* 3.4 22.2 - - - +
38D VAL 2.8 0.2 + - - -
39D ALA* 1.3 75.8 - - - +
41D ILE* 1.3 59.2 + - + +
43D LYS* 3.2 5.3 + - - +
44D ASN* 2.9 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 41 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ILE* 5.2 5.0 - - + +
7D THR 4.3 8.5 - - - +
8D LEU* 4.2 16.8 - - + -
9D PRO* 4.0 24.7 - - + -
37D ASN 2.8 22.7 - - - +
38D VAL* 2.5 22.1 + - - +
40D ARG* 1.3 72.3 - - + +
42D ILE* 1.3 58.3 + - - +
43D LYS 3.2 0.4 - - - -
44D ASN* 3.8 11.7 - - + +
45D ALA* 3.0 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 42 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ILE* 5.5 4.7 - - + -
8D LEU* 6.3 0.2 - - - +
38D VAL* 2.8 15.0 + - + +
39D ALA* 3.7 11.2 - - - +
41D ILE* 1.3 76.4 - - - +
43D LYS* 1.3 59.4 + - + +
46D MET* 3.1 0.6 - - - +
47D LEU* 2.2 53.9 + - + +
48D ASP 2.9 6.9 + - - +
82D LEU* 6.1 1.6 - - + -
85D ALA* 4.1 21.8 - - + +
87D PHE* 5.2 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D ALA* 2.9 22.8 + - + +
40D ARG* 3.6 5.6 - - - +
42D ILE* 1.3 78.5 - - + +
44D ASN* 1.3 66.6 + - - +
46D MET* 3.4 13.4 - - - +
48D ASP* 3.0 29.2 - - + +
85D ALA 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D ARG* 2.9 27.6 + - - +
41D ILE* 3.6 11.7 + - + +
43D LYS* 1.3 80.2 - - - +
45D ALA* 1.3 60.1 + - - +
46D MET* 2.8 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ILE* 4.7 8.5 - - + -
41D ILE* 3.0 23.3 + - + +
44D ASN* 1.3 72.8 - - - +
46D MET* 1.3 72.9 + - - +
47D LEU* 3.4 17.8 - - + +
----------------------------------------------------------
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