Contacts of the helix formed by residues 20 - 40 (chain D) in PDB entry 4XHW
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 20 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D LEU* 3.4 40.0 + - + +
16D HIS 4.0 0.6 + - - -
18D GLU* 3.8 30.3 - - + -
19D GLY* 1.3 79.5 - - - +
21D SER* 1.3 64.1 + - - +
22D ILE 3.3 2.9 - - - -
23D PRO* 3.1 18.2 - - + +
24D LEU* 3.1 21.9 + - + +
55D GLU* 5.2 5.4 - - + -
58D GLU* 4.7 15.9 - - + -
59D ALA* 3.9 39.3 - - + -
62D ASN* 3.7 27.6 - - + -
64D GLN* 5.7 0.4 - - - -
65D PHE* 4.6 6.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 21 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASP* 5.9 1.1 - - - -
16D HIS* 3.6 37.2 + - - -
19D GLY 3.5 5.3 + - - -
20D PHE* 1.3 76.2 - - - +
22D ILE* 1.3 64.9 + - - +
24D LEU* 3.1 4.2 + - - +
25D LEU* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 4.1 17.5 - - + +
53B THR* 4.3 24.2 - - + -
54B GLU 5.9 0.9 - - - +
21D SER* 1.3 84.8 + - - +
23D PRO* 1.4 74.3 - - + +
25D LEU* 3.0 13.5 + - + +
26D TRP* 3.0 21.0 + - + +
55D GLU* 3.8 20.8 + - + +
56D ASN* 4.1 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D PHE* 3.1 26.7 - - + +
22D ILE* 1.4 90.2 - - + +
24D LEU* 1.3 55.3 + - - +
26D TRP* 3.3 10.3 + - + +
27D LEU* 2.9 29.5 + - - +
55D GLU* 3.5 23.1 - - + +
56D ASN* 3.9 21.5 - - - +
59D ALA* 3.6 32.1 - - + -
65D PHE* 3.9 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ASN* 4.3 5.4 - - - +
15D LEU* 4.3 7.6 - - + -
16D HIS* 3.6 57.0 - - + +
20D PHE* 3.1 20.3 + - + +
21D SER* 3.2 8.5 - - - +
22D ILE 3.1 0.6 - - - -
23D PRO* 1.3 74.9 - - - +
25D LEU* 1.3 59.1 + - - +
27D LEU* 3.2 8.0 + - + +
28D GLN* 2.8 31.4 + - - +
65D PHE* 4.3 14.8 - - + -
68D LEU* 4.0 26.7 - - + -
103D LEU* 3.8 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PRO* 5.8 2.9 - - + -
50A VAL* 4.0 32.5 - - + -
52A LEU* 4.4 13.5 - - + -
52B LEU* 4.1 34.8 - - + +
21D SER 2.9 12.0 + - - +
22D ILE* 3.0 15.7 + - + +
24D LEU* 1.3 76.0 - - - +
26D TRP* 1.3 62.5 + - - +
28D GLN* 3.2 23.9 + - - +
29D ASN* 3.0 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 3.8 25.9 - - + +
22D ILE* 3.0 12.0 + - + +
23D PRO* 3.4 20.0 - - + +
25D LEU* 1.3 75.8 - - - +
27D LEU* 1.3 70.7 + - + +
29D ASN* 3.1 6.0 + - - +
30D CYS* 3.0 39.5 + - - -
49D LEU* 3.9 27.1 - - + -
50D VAL 3.2 35.4 + - - -
51D PRO* 4.0 12.6 - - + -
52D LEU* 5.6 4.8 - - + +
56D ASN* 3.2 36.9 - - + +
60D MSE 4.0 26.5 - - + -
65D PHE* 5.1 5.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D PRO 2.9 16.7 + - - +
24D LEU* 3.5 7.4 - - + +
26D TRP* 1.3 83.3 - - + +
28D GLN* 1.3 65.6 + - - +
30D CYS* 2.8 17.0 + - - +
31D LEU* 3.0 38.1 + - + +
49D LEU* 4.1 21.8 - - + -
65D PHE* 4.5 13.2 - - + -
68D LEU* 4.6 6.7 - - + -
69D LEU* 3.8 32.1 - - + -
72D LEU* 4.1 18.2 - - + -
74D VAL* 5.0 3.6 - - + -
87D ILE* 5.9 0.2 - - + -
103D LEU* 4.4 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ARG* 4.9 12.3 + - - +
52A LEU* 4.1 15.3 - - + +
24D LEU 2.8 15.9 + - - +
25D LEU* 3.3 29.3 - - - +
27D LEU* 1.3 74.4 - - - +
29D ASN* 1.3 62.8 + - - +
31D LEU* 3.3 4.5 + - - +
32D ILE* 3.0 27.0 + - + +
100D ALA* 2.9 41.3 + - + +
101D ALA* 4.7 2.8 - - - +
103D LEU* 3.7 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.6 25.1 - - + +
50B VAL* 3.9 12.4 + - - +
52B LEU* 3.7 27.3 - - + +
25D LEU 3.0 9.8 + - - +
26D TRP* 3.1 7.5 + - - +
28D GLN* 1.3 77.4 - - - +
30D CYS* 1.3 65.5 + - - +
32D ILE* 4.4 2.2 - - - +
33D ARG* 2.8 73.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D TRP* 3.0 42.2 + - - -
27D LEU* 2.8 10.0 + - + +
29D ASN* 1.3 80.3 - - - +
31D LEU* 1.3 65.2 + - - +
33D ARG* 4.0 3.7 - - - +
34D ALA* 3.0 25.8 + - - +
47D VAL* 5.5 5.7 - - + +
48D PRO 5.5 1.8 - - - -
49D LEU* 3.5 35.7 - - + -
50D VAL 5.8 0.2 - - - -
87D ILE* 3.9 7.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LEU* 3.0 41.3 + - + +
28D GLN* 3.5 6.7 - - - +
30D CYS* 1.3 76.9 - - - +
32D ILE* 1.3 58.8 + - - +
34D ALA* 3.3 2.9 + - - +
35D ALA 3.0 22.7 + - - -
72D LEU* 4.4 10.3 - - + +
74D VAL* 4.9 9.9 - - + -
87D ILE* 4.5 16.2 - - + -
91D LEU* 6.2 0.4 - - + -
96D LEU* 3.5 39.1 - - + +
99D ALA* 4.0 15.3 - - + -
100D ALA* 3.6 36.3 - - + +
103D LEU* 4.7 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.6 55.6 - - + +
53A THR* 4.3 18.4 - - + -
28D GLN* 3.0 18.9 + - + +
29D ASN* 4.1 4.5 - - - +
31D LEU* 1.3 73.0 - - - +
33D ARG* 1.3 76.9 + - - +
35D ALA* 3.1 8.5 + - - +
36D ASP* 3.0 22.1 + - - +
97D ARG* 4.4 21.3 - - + +
100D ALA* 4.0 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 2.8 32.7 + - - +
53A THR* 4.4 4.8 - - - +
54A GLU 5.2 0.6 - - - +
47B VAL* 5.3 4.9 - - - -
48B PRO* 3.7 39.4 - - - +
50B VAL* 4.0 11.6 - - - +
84B PHE* 5.6 0.6 - - - -
29D ASN* 2.8 64.0 + - - +
30D CYS* 4.1 3.4 - - - +
32D ILE* 1.3 88.1 - - - +
34D ALA* 1.3 63.1 + - - +
36D ASP* 2.9 32.3 + - - +
37D ASP* 3.0 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 34 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D CYS 3.0 19.3 + - - +
31D LEU 3.6 5.4 - - - +
33D ARG* 1.3 77.8 - - - +
35D ALA* 1.3 61.8 + - - +
37D ASP* 3.4 5.8 + - - +
38D ARG* 3.0 39.2 + - - +
47D VAL* 4.5 17.5 - - + -
87D ILE* 4.4 14.4 - - + -
96D LEU* 3.8 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 35 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D LEU 3.0 14.1 + - - +
32D ILE 3.1 9.4 + - - +
34D ALA* 1.3 75.4 - - - +
36D ASP* 1.3 64.2 + - - +
38D ARG* 3.0 13.8 + - - +
39D GLU* 3.0 17.0 + - - +
93D PRO* 3.5 29.7 - - + +
96D LEU* 3.6 9.6 - - + +
97D ARG* 3.4 26.0 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
53A THR* 5.5 1.0 - - - -
54A GLU* 5.5 4.0 + - - +
45B GLN* 3.7 14.1 + - - +
32D ILE* 3.0 15.4 + - - +
33D ARG* 2.9 36.4 + - - +
35D ALA* 1.3 76.9 - - - +
37D ASP* 1.3 68.4 + - - +
39D GLU* 3.2 22.3 + - - +
97D ARG* 3.1 26.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 37 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASP* 2.6 32.3 - - + +
45B GLN* 3.6 30.7 - - + +
46B ALA 5.1 1.2 - - - +
47B VAL* 5.0 12.0 - - - +
33D ARG* 3.0 19.6 + - - +
34D ALA* 4.0 5.6 - - - +
36D ASP* 1.3 80.3 - - - +
38D ARG* 1.3 59.5 + - + +
39D GLU 3.1 4.4 + - - -
40D GLU* 3.7 5.9 + - - +
43D CYS* 3.2 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D ALA* 3.0 24.2 + - - +
35D ALA 3.0 5.5 + - - +
37D ASP* 1.3 76.0 - - + +
39D GLU* 1.3 63.7 + - - +
40D GLU 3.4 6.4 - - - +
41D ASP* 5.1 1.2 - - - -
43D CYS 3.4 17.4 - - - +
44D SER* 3.8 16.7 + - - +
45D GLN 2.9 27.8 + - - +
47D VAL* 4.3 5.5 - - - +
87D ILE* 3.2 20.9 + - - +
88D PRO 2.7 31.8 + - - -
89D ALA* 3.4 8.7 + - - +
91D LEU* 2.8 37.3 + - - +
93D PRO* 3.7 20.3 - - + +
96D LEU* 3.7 15.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLN* 5.4 2.2 - - - +
35D ALA 3.0 15.9 + - - +
36D ASP* 3.4 15.3 - - - +
37D ASP 3.1 1.2 - - - -
38D ARG* 1.3 76.9 - - - +
40D GLU* 1.3 65.8 + - - +
41D ASP* 3.3 4.9 + - - +
93D PRO* 3.8 16.1 - - - +
97D ARG* 2.2 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLY 4.8 9.6 - - - +
45B GLN* 4.2 23.0 - - - +
36D ASP 4.3 1.0 + - - -
37D ASP 3.7 4.0 + - - +
38D ARG 3.4 6.7 - - - +
39D GLU* 1.3 79.3 - - - +
41D ASP* 1.3 62.6 + - - +
43D CYS* 2.8 41.0 + - + +
----------------------------------------------------------
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