Contacts of the helix formed by residues 31 - 51 (chain A) in PDB entry 1IOU
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 31 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLY* 2.9 2.3 + - - -
30A PHE* 1.3 117.7 - + - +
32A GLU* 1.3 74.8 + - + +
33A ARG 3.5 0.7 - - - -
34A SER* 4.6 6.5 + - - -
35A SER* 3.6 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PHE* 3.7 17.5 - - + -
29A GLY 3.6 2.9 + - - +
31A PHE* 1.3 84.9 - - + +
33A ARG* 1.3 58.4 + - - +
34A SER 3.1 2.9 - - - -
35A SER* 2.7 25.0 + - - -
36A VAL* 2.6 56.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LYS* 4.2 21.3 + - - +
25A LEU* 3.1 57.2 - - + +
28A PHE 3.2 7.5 + - - +
29A GLY 2.9 22.8 + - - +
30A PHE* 4.8 5.2 - - - +
31A PHE 3.5 0.2 - - - -
32A GLU* 1.3 77.3 - - - +
34A SER* 1.3 68.9 + - - +
37A GLY* 3.1 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE 5.9 0.8 - - - -
31A PHE 4.6 7.7 + - - +
32A GLU 3.1 0.6 - - - +
33A ARG* 1.3 90.4 + - - +
35A SER* 1.3 69.5 + - - +
37A GLY* 3.3 1.6 + - - -
38A GLN* 3.2 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE 3.6 3.9 + - - -
32A GLU* 2.7 38.2 + - - -
34A SER* 1.3 78.7 - - - +
36A VAL* 1.3 67.3 + - - +
38A GLN* 3.2 10.1 + - - +
39A PHE* 3.0 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 4.1 0.7 - - + -
28A PHE* 3.5 45.8 - - + -
32A GLU* 2.6 59.1 + - + +
35A SER* 1.3 71.3 + - - +
37A GLY* 1.3 50.0 + - - +
39A PHE* 2.6 35.0 + - + +
40A MET* 2.7 36.7 + - + +
64A TYR* 4.7 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LYS* 4.4 18.6 - - - -
25A LEU* 3.8 9.7 - - - +
33A ARG 3.1 20.5 + - - -
34A SER 3.7 0.9 - - - -
35A SER 3.2 0.2 - - - -
36A VAL* 1.3 75.7 - - - +
38A GLN* 1.3 62.6 + - - +
40A MET* 2.9 18.5 + - - +
41A THR* 3.0 20.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A SER* 3.2 27.8 + - - +
35A SER* 3.2 9.4 + - - +
37A GLY* 1.3 72.9 - - - +
39A PHE* 1.3 52.3 + - - +
41A THR* 4.8 4.3 - - - +
42A PHE* 2.8 42.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A SER 3.0 9.3 + - - +
36A VAL* 2.6 34.1 + - + +
38A GLN* 1.3 69.7 - - - +
40A MET* 1.3 67.0 + - + +
42A PHE* 4.1 7.5 - + - +
43A PHE* 3.1 56.5 + + - +
61A GLU* 3.6 32.1 - - + -
64A TYR* 4.9 14.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TYR* 3.2 33.2 - - + +
5A TYR* 3.3 41.3 - - + -
23A LYS* 5.9 1.3 - - + -
24A ASP 5.5 0.7 - - - +
25A LEU* 5.6 2.5 - - + -
28A PHE* 4.1 1.1 - - + -
36A VAL* 2.7 36.8 + - + +
37A GLY* 2.9 9.8 + - - +
39A PHE* 1.3 79.9 - - + +
41A THR* 1.3 51.2 + - - +
43A PHE* 3.2 2.0 + - - +
44A ALA 2.7 30.3 + - - -
64A TYR* 3.3 35.4 - - + -
80A ILE* 3.2 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A TYR* 3.3 32.8 - - - +
9A PHE* 4.9 7.0 - - + -
18A GLU* 5.8 7.4 - - + +
21A GLU* 3.7 23.5 + - + +
23A LYS* 4.9 2.9 - - - -
37A GLY 3.0 16.7 + - - -
38A GLN* 4.3 3.6 - - - -
40A MET* 1.3 71.4 - - - +
42A PHE* 1.3 55.6 + - - +
43A PHE 2.9 1.3 - - - -
44A ALA* 2.6 24.7 + - - +
45A GLU* 2.6 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLN* 2.8 26.3 + - + +
39A PHE* 4.1 9.9 - + - +
41A THR* 1.3 73.0 - - - +
43A PHE* 1.3 60.2 + + - +
45A GLU* 2.8 47.3 + - - +
46A THR* 3.0 25.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PHE* 3.1 56.6 + + - +
40A MET* 3.4 5.4 - - - +
41A THR 2.8 1.0 + - - -
42A PHE* 1.3 79.9 - + - +
44A ALA* 1.3 52.1 + - - +
46A THR* 3.1 15.5 + - + -
47A VAL* 2.7 40.8 + - - +
50A ARG* 5.5 3.4 - - - -
59A ILE* 3.7 42.4 - - + -
61A GLU* 4.3 20.4 - - + -
80A ILE* 4.7 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A TYR* 3.2 24.9 - - + -
9A PHE* 3.0 31.9 - - + -
40A MET 2.7 11.4 + - - +
41A THR 2.6 11.7 + - - +
43A PHE* 1.3 72.4 - - - +
45A GLU* 1.3 57.8 + - - +
47A VAL* 2.8 24.8 - - - +
48A ALA 3.3 7.1 + - - -
78A VAL* 3.4 11.7 - - + +
80A ILE* 3.5 8.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 3.4 21.7 - - + -
15A LYS* 5.8 5.2 - - + +
16A ALA* 2.7 24.4 - - - +
18A GLU* 6.0 3.3 - - + +
41A THR* 2.6 22.0 + - + +
42A PHE* 2.8 58.2 + - - +
44A ALA* 1.3 71.0 - - - +
46A THR* 1.3 61.7 + - - +
49A SER* 2.4 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PHE* 3.0 29.5 + - - -
43A PHE* 3.1 17.9 + - + +
45A GLU* 1.3 80.9 + - - +
47A VAL* 1.3 52.7 + - - +
49A SER* 2.6 14.6 + - - -
50A ARG* 2.6 65.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE 2.7 26.9 + - - +
44A ALA* 2.8 26.7 - - - +
46A THR* 1.3 71.7 - - - +
48A ALA* 1.3 48.7 + - - +
50A ARG* 2.5 18.8 + - - +
51A THR* 2.5 38.1 + - - -
57A GLN* 4.2 12.8 - - + +
59A ILE* 3.0 38.1 - - + -
66A GLY 3.7 0.2 - - - +
68A VAL* 3.0 23.3 - - + -
78A VAL* 3.4 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 3.1 45.3 - - + +
11A SER* 4.0 9.8 + - - +
16A ALA* 3.2 11.4 - - + +
44A ALA 3.3 4.0 + - - +
46A THR 3.3 0.4 - - - -
47A VAL* 1.3 77.9 - - - +
49A SER* 1.3 56.6 + - - +
51A THR* 2.6 32.9 - - - +
68A VAL* 5.5 0.2 - - - -
76A CYS* 4.6 7.4 - - + -
78A VAL* 3.6 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A SER* 5.9 0.7 - - - +
13A GLY 3.9 14.8 - - - +
14A GLU* 3.3 24.1 - - - +
15A LYS* 3.2 4.6 - - - +
16A ALA* 2.6 22.8 + - - +
45A GLU 2.4 23.4 + - - -
46A THR* 2.6 20.4 + - - -
48A ALA* 1.3 74.0 - - - +
50A ARG* 1.3 58.3 + - - -
51A THR 4.5 1.9 - - - -
52A GLY* 4.9 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE* 5.5 3.0 - - - -
46A THR* 2.6 40.3 + - + +
47A VAL* 2.5 27.6 + - - +
49A SER* 1.3 74.1 - - - +
51A THR* 1.3 55.5 + - - -
52A GLY 3.3 5.4 + - - -
55A GLU* 3.8 8.7 - - - +
57A GLN* 3.1 35.9 + - - +
59A ILE* 4.7 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A SER* 3.5 7.6 + - - -
47A VAL 2.5 21.4 + - - -
48A ALA* 2.6 24.6 - - - +
49A SER 4.5 1.1 - - - -
50A ARG* 1.3 72.3 - - - +
52A GLY* 1.3 56.4 + - - +
53A ALA 3.0 9.2 + - - -
55A GLU* 3.0 46.2 - - + +
57A GLN* 3.2 14.2 - - + +
68A VAL* 3.0 31.8 - - + +
70A ALA* 4.2 8.1 - - + -
76A CYS* 4.1 3.5 - - - -
----------------------------------------------------------
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