Contacts of the helix formed by residues 32 - 45 (chain A) in PDB entry 1O9H
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 PRO 32 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TYR* 6.0 0.7 - - - +
30A ALA 4.2 2.7 - - - +
31A PHE* 1.3 110.2 - - + +
33A VAL* 1.3 66.7 + - - +
34A ARG* 4.5 2.7 - - + +
35A LEU* 3.2 22.1 + - + +
36A ALA 3.1 7.4 + - - -
235A ARG* 3.4 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 6.4 1.6 - - + -
13A SER* 3.6 37.7 - - - +
16A LEU* 4.1 27.8 - - + +
17A ALA* 5.7 0.9 - - - -
31A PHE 3.3 1.9 + - - +
32A PRO* 1.3 70.5 - - - +
34A ARG* 1.3 62.9 + - - +
36A ALA* 3.1 17.0 + - - +
37A THR* 3.1 15.2 + - + +
64A TYR* 3.8 22.4 - - - +
68A VAL* 4.4 11.4 - - + +
72A LEU* 4.3 14.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TYR* 3.1 45.5 - - + +
7A ALA* 2.8 38.6 + - + +
8A VAL 3.4 18.0 + - - -
10A ARG* 3.5 55.9 - - + +
11A ILE 5.9 0.2 - - - +
32A PRO* 3.2 2.8 - - + +
33A VAL* 1.3 81.1 - - - +
35A LEU* 1.3 60.8 + - - +
37A THR* 3.4 15.9 - - + +
38A GLU* 3.4 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TYR* 4.4 7.5 + - - +
31A PHE* 3.6 26.5 - - + -
32A PRO* 3.2 18.5 + - + +
34A ARG* 1.3 77.6 - - - +
36A ALA* 1.3 64.0 + - - +
38A GLU* 3.4 5.6 + - + +
39A ILE* 3.1 43.3 + - + +
213A THR* 4.9 0.4 - - + -
230A LEU* 4.4 10.5 - - + -
232A ILE* 4.1 37.7 - - + +
235A ARG* 3.6 41.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE* 3.3 8.4 - - + -
32A PRO 3.1 10.5 + - - +
33A VAL* 3.1 10.2 + - - +
35A LEU* 1.3 74.0 - - - +
37A THR* 1.3 63.4 + - - +
38A GLU 3.0 5.6 + - - -
39A ILE* 3.3 6.3 + - - +
40A PHE* 3.1 23.7 + - - +
65A LEU* 3.6 30.5 - - + -
68A VAL* 4.3 9.4 - - + -
69A LEU* 3.8 14.6 - - + +
173A LEU* 4.7 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ALA* 4.0 13.0 - - + -
11A ILE* 6.5 0.7 - - + -
33A VAL* 3.1 10.9 + - + +
34A ARG* 3.4 21.5 - - + +
36A ALA* 1.3 78.5 - - - +
38A GLU* 1.3 56.6 + - - +
40A PHE* 3.9 2.0 - - - -
41A GLN* 2.9 40.7 + - - +
69A LEU* 4.1 3.5 - - - +
72A LEU* 3.8 19.2 - - + +
73A HIS* 2.8 29.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TYR* 3.4 23.4 - - + -
5A ARG 3.2 14.2 + - - -
6A HIS* 3.2 12.6 + - - -
7A ALA* 3.0 26.8 + - + -
34A ARG 3.4 18.4 + - - +
35A LEU* 3.4 9.4 + - + +
36A ALA 3.0 0.4 - - - -
37A THR* 1.3 76.0 - - - +
39A ILE* 1.3 67.1 + - - +
40A PHE 3.1 1.3 - - - -
41A GLN* 3.6 0.9 + - - +
42A ARG* 2.5 70.2 + - - +
230A LEU* 4.7 4.5 - - + -
232A ILE* 4.4 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE* 3.9 15.7 - - + -
35A LEU* 3.1 29.5 + - + +
36A ALA* 3.3 4.2 + - - +
38A GLU* 1.3 77.4 - - - +
40A PHE* 1.3 57.5 + - - +
42A ARG* 3.7 8.5 + - - +
43A ALA* 3.1 25.3 + - - +
173A LEU* 4.3 14.8 - - + -
211A ALA* 3.5 29.4 - - + -
213A THR* 3.8 33.9 - - + +
230A LEU* 4.7 7.9 - - + -
237A ALA* 4.4 14.6 - - + -
239A LEU* 4.3 10.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA 3.1 16.4 + - - +
37A THR 4.2 2.7 - - - +
38A GLU 3.1 0.4 - - - -
39A ILE* 1.3 75.2 - - - +
41A GLN* 1.3 62.7 + - - +
43A ALA* 3.0 7.1 + - - +
44A LEU* 2.9 61.1 + - + +
53A VAL* 5.0 1.3 - - + -
55A LEU* 4.5 15.9 - - + -
69A LEU* 4.1 16.2 - - + -
73A HIS* 3.5 47.8 - + + -
76A SER* 4.5 4.9 - - - -
77A LEU* 3.5 29.6 - - + -
171A VAL* 4.6 14.8 - - + -
173A LEU* 4.2 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A HIS* 3.4 51.6 + - + +
7A ALA* 4.3 1.4 - - - +
37A THR* 2.9 36.5 + - - +
40A PHE* 1.3 77.2 - - + +
42A ARG* 1.3 57.8 + - - +
44A LEU* 3.2 16.2 + - + +
45A ALA* 3.1 27.2 + - - +
73A HIS* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 5.4 0.6 + - - -
3A ALA 2.8 31.5 + - - +
5A ARG* 3.7 36.7 - - - +
6A HIS* 3.6 20.0 - - + +
38A GLU* 2.5 40.2 + - - +
39A ILE* 3.8 5.2 - - - +
41A GLN* 1.3 73.4 - - - +
43A ALA* 1.3 65.3 + - - +
45A ALA* 3.5 12.0 + - - +
46A ARG* 3.6 17.8 + - - +
228A GLU* 3.0 29.8 + - - +
229A ARG 3.9 4.6 + - - -
230A LEU* 3.1 44.6 - - - +
239A LEU* 4.2 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE 3.1 14.4 + - - +
40A PHE* 3.0 12.8 + - - +
42A ARG* 1.3 74.5 - - - +
44A LEU* 1.3 64.0 + - - +
46A ARG* 3.1 17.1 + - - +
47A LEU* 3.7 10.8 + - - +
171A VAL* 4.0 27.6 - - + -
173A LEU* 5.9 0.2 - - + -
209A VAL* 4.0 22.8 - - + +
211A ALA* 5.0 6.5 - - + -
239A LEU* 4.4 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE* 2.9 50.9 + - + +
41A GLN* 3.2 18.4 + - + +
43A ALA* 1.3 75.1 - - - +
45A ALA* 1.3 58.1 + - - +
46A ARG 3.1 4.9 + - - -
47A LEU* 3.1 30.1 + - + +
49A GLY 5.1 1.0 - - - +
51A GLY 5.6 0.2 - - - +
53A VAL* 3.6 31.4 - - + -
73A HIS* 5.8 0.7 - - - +
76A SER* 4.3 16.8 - - - +
171A VAL* 4.4 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 6.1 1.3 - - - +
6A HIS* 4.6 10.1 - - + +
41A GLN 3.1 15.0 + - - +
42A ARG* 3.8 9.9 - - - +
43A ALA 3.2 0.8 - - - -
44A LEU* 1.3 75.4 - - - +
46A ARG* 1.3 62.7 + - + +
47A LEU 3.5 3.4 - - - +
----------------------------------------------------------
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