Contacts of the helix formed by residues 10 - 32 (chain B) in PDB entry 5FUR
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 VAL 10 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B THR* 1.3 89.8 - - + +
11B PRO* 1.3 74.9 - - + +
12B LYS 3.0 1.6 - - - -
13B LEU* 3.1 13.1 + - - +
14B TYR* 3.1 47.1 + - + +
364C ASP* 4.4 21.3 - - + +
365C TYR* 4.8 1.3 - - - -
366C ILE* 4.5 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 11 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B THR 4.0 7.4 - - - +
10B VAL* 1.3 95.0 - - + +
12B LYS* 1.3 66.8 + - + +
14B TYR* 3.2 10.5 + - + +
15B ARG* 2.9 50.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 12 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B THR* 4.0 27.3 - - - +
11B PRO* 1.3 87.4 - - + +
13B LEU* 1.3 58.0 + - - +
15B ARG* 3.3 8.4 + - + +
16B SER* 2.8 29.7 + - - -
51D ARG* 4.6 14.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B THR 3.8 10.4 + - - +
10B VAL 3.1 8.9 + - - +
12B LYS* 1.3 77.5 - - - +
14B TYR* 1.3 65.3 + - + +
16B SER* 3.1 8.4 + - - -
17B VAL* 2.7 44.8 + - + +
366C ILE* 3.4 28.7 - - + -
44D ILE* 4.3 21.3 - - + -
47D ALA* 3.8 16.2 - - + +
48D LEU* 4.8 1.6 - - + -
51D ARG* 3.8 30.0 - - + +
52D VAL* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 3.1 31.2 + - + +
11B PRO* 3.5 10.5 - - + +
13B LEU* 1.3 93.9 - - + +
15B ARG* 1.3 63.5 + - - +
17B VAL* 3.2 4.5 + - - +
18B ILE* 2.8 38.4 + - - +
50B LEU* 3.9 41.5 - - + -
357C ILE* 4.2 14.7 - - + +
364C ASP* 2.5 38.6 + - + +
366C ILE* 4.2 8.8 - - + +
11D LEU* 4.0 29.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PRO* 2.9 35.9 + - - +
12B LYS* 3.6 9.4 - - + +
14B TYR* 1.3 75.7 - - - +
16B SER* 1.3 55.3 + - - +
18B ILE* 3.7 17.2 - - - +
19B GLU* 2.8 48.4 + - + +
47B GLU* 4.6 21.7 + - - +
50B LEU* 4.0 26.0 - - - +
51B MET* 5.4 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LYS 2.8 13.8 + - - -
13B LEU* 3.1 11.9 - - - -
15B ARG* 1.3 77.9 - - - +
17B VAL* 1.3 58.9 + - - +
19B GLU* 3.7 5.1 - - - +
20B ASP* 3.0 43.9 + - - +
47D ALA* 5.8 2.8 - - - +
51D ARG* 3.2 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 2.7 34.2 + - + +
14B TYR 3.8 3.1 - - - +
16B SER* 1.3 70.3 - - - +
18B ILE* 1.3 61.5 - - - +
20B ASP* 3.4 5.8 + - - +
21B VAL* 2.8 49.9 + - + +
46B TRP* 4.6 2.0 - - + -
11D LEU* 4.1 20.6 - - + -
40D PHE* 4.4 11.4 - - + -
43D ALA* 4.2 14.6 - - + +
44D ILE* 4.4 9.4 - - + +
47D ALA* 3.9 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B TYR 2.8 23.5 + - - +
15B ARG* 3.7 12.3 - - - +
17B VAL* 1.3 72.0 - - - +
19B GLU* 1.3 58.2 + - + +
21B VAL* 3.8 0.3 - - - +
22B ILE* 2.8 44.2 + - + +
43B LYS* 3.9 29.8 - - + -
46B TRP* 3.9 41.5 - - + -
47B GLU* 3.9 22.9 - - + +
50B LEU* 3.8 28.7 - - + -
11D LEU* 4.5 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ARG* 2.8 34.2 + - + +
16B SER* 3.7 6.3 - - - +
18B ILE* 1.3 73.9 - - - +
20B ASP* 1.3 62.3 + - - +
22B ILE* 3.7 4.0 - - - +
23B ASN* 2.8 47.9 + - - +
43B LYS* 2.7 36.3 + - - -
47B GLU* 4.7 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B SER* 3.0 29.1 + - - +
17B VAL* 3.8 6.2 - - - +
19B GLU* 1.3 78.3 - - - +
21B VAL* 1.3 57.9 + - - +
23B ASN* 3.7 7.7 + - - +
24B ASP* 2.8 44.3 + - - +
43D ALA* 4.9 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 2.8 34.3 + - + +
18B ILE 3.8 2.5 - - - +
20B ASP* 1.3 72.7 - - - +
22B ILE* 1.3 67.6 + - + +
24B ASP* 3.2 1.6 + - - -
25B VAL* 3.0 37.9 + - + +
42B LEU* 6.3 0.2 - - + -
46B TRP* 4.0 22.9 - - + -
15D LEU* 5.3 0.2 - - + -
36D VAL* 4.2 20.4 - - + +
39D GLN* 4.4 13.0 - - + +
40D PHE* 4.1 12.6 - - + +
43D ALA* 3.7 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ILE* 2.8 41.9 + - + +
19B GLU* 3.7 6.3 - - - +
21B VAL* 1.3 75.4 - - + +
23B ASN* 1.3 66.0 + - - +
25B VAL* 3.3 12.5 + - + +
26B ARG* 3.3 22.3 + - - +
39B LEU* 3.9 30.3 - - + +
40B MET* 5.2 2.9 - - + -
42B LEU* 4.3 19.3 - - + -
43B LYS* 3.9 42.8 - - + +
46B TRP* 4.4 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLU* 2.8 39.0 + - - +
20B ASP* 3.8 8.2 + - - +
22B ILE* 1.3 76.1 - - - +
24B ASP* 1.3 63.9 + - - +
25B VAL 3.3 1.6 + - - -
26B ARG* 3.1 38.3 + - - +
27B ASP* 4.8 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ASP* 2.8 36.1 + - - +
23B ASN* 1.3 76.0 - - - +
25B VAL* 1.3 59.3 + - - +
26B ARG 3.5 0.2 - - - -
27B ASP* 5.0 3.8 + - - +
28B ILE* 4.3 11.4 - - - +
39D GLN* 3.6 38.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B VAL* 3.0 25.5 + - + +
22B ILE* 3.4 13.9 - - + +
24B ASP* 1.3 78.1 - - - +
26B ARG* 1.3 66.7 + - - +
27B ASP 3.3 2.7 - - - -
28B ILE* 2.9 27.3 + - + +
29B PHE* 2.9 28.3 + - + -
39B LEU* 3.5 22.4 - - + -
42B LEU* 5.1 0.9 - - + -
36D VAL* 4.2 20.9 - - + -
39D GLN* 3.9 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE* 3.3 12.3 + - - +
23B ASN* 3.1 52.5 + - - +
25B VAL* 1.3 76.3 - - - +
27B ASP* 1.3 67.1 + - - +
29B PHE* 3.1 5.5 + - + +
30B LEU* 2.9 43.2 + - + +
36B GLU* 2.5 32.4 + - - +
39B LEU* 3.5 33.6 - - + +
40B MET* 3.9 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ASN 4.8 2.4 + - - -
24B ASP 5.0 3.9 + - - +
25B VAL 3.3 0.6 - - - -
26B ARG* 1.3 80.0 - - - +
28B ILE* 1.3 54.3 + - + +
30B LEU* 3.3 15.9 + - - +
31B ASP* 2.7 51.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ASP 4.3 7.4 - - - +
25B VAL* 2.9 30.0 + - + +
27B ASP* 1.3 74.6 - - + +
29B PHE* 1.3 67.1 + - + +
31B ASP* 3.3 8.7 + - + +
32B ASP* 3.0 28.8 + - - +
32D LEU* 3.3 24.9 - - + -
35D GLN* 4.4 33.4 - - + +
36D VAL* 6.4 0.2 - - + -
39D GLN* 5.3 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL* 2.9 29.8 + - + +
26B ARG* 3.4 10.1 - - - +
28B ILE* 1.3 75.9 - - - +
30B LEU* 1.3 63.0 + - + +
32B ASP* 3.1 5.9 + - - +
33B GLY 3.0 4.7 + - - -
34B VAL* 2.9 59.8 + - + +
35B ASP 4.7 1.8 - - - +
36B GLU* 6.0 1.6 - - - -
38B VAL* 4.2 9.9 - - + -
39B LEU* 3.7 43.1 - - + -
42B LEU* 3.9 17.5 - - + -
28D ILE* 4.3 9.0 - - + -
32D LEU* 3.8 30.7 - - + -
36D VAL* 4.0 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ARG* 2.9 35.8 + - + +
27B ASP* 3.5 19.1 - - - +
29B PHE* 1.3 76.8 - - + +
31B ASP* 1.3 60.5 + - - +
33B GLY* 2.9 20.0 + - - +
34B VAL 4.3 12.8 - - - +
35B ASP* 5.9 0.2 - - - -
36B GLU* 4.7 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ASP* 2.7 37.3 + - - +
28B ILE* 3.8 8.6 - - + +
30B LEU* 1.3 75.0 - - - +
32B ASP* 1.3 61.9 + - - +
33B GLY 3.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ILE* 3.0 18.5 + - - +
29B PHE* 3.5 6.1 - - - +
30B LEU 3.1 0.2 - - - -
31B ASP* 1.3 79.8 - - - +
33B GLY* 1.3 61.1 + - - +
34B VAL* 3.4 14.6 - - + +
29D THR* 5.0 5.5 + - - -
31D GLN* 6.1 0.9 - - - +
32D LEU* 3.3 33.4 + - + +
35D GLN* 6.1 0.2 - - - +
----------------------------------------------------------
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