Contacts of the helix formed by residues 3 - 16 (chain A) in PDB entry 1MUK
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 3 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 1.3 69.5 - - - +
4A MET* 1.3 59.9 + - - -
6A LEU* 3.4 10.5 - - - +
7A THR* 2.6 45.4 + - - -
48A GLU* 3.9 14.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 4 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER 2.5 4.8 + - - -
3A SER* 1.3 79.2 - - - +
5A ILE* 1.3 62.5 + - + +
7A THR* 3.9 3.5 - - - -
8A GLN* 3.3 24.9 + - + +
37A PHE* 4.3 17.3 - - + -
41A ASP* 3.9 30.5 - - - +
44A LYS* 4.1 28.0 - - + -
45A ALA* 4.0 13.9 - - + -
48A GLU* 3.1 30.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 5 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 2.7 24.5 + - - +
4A MET* 1.3 70.5 - - + +
6A LEU* 1.3 60.3 + - - +
8A GLN* 3.2 1.4 + - - -
9A PHE* 2.9 35.4 + - + +
13A ILE* 4.4 2.2 - - + -
37A PHE* 3.7 18.4 - - + -
45A ALA* 4.0 22.7 - - + +
48A GLU* 5.6 0.2 - - - +
156A LEU* 3.7 30.7 - - + -
159A LEU* 4.0 20.6 - - + +
160A VAL* 3.8 33.4 - - + -
163A ALA* 4.4 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 6 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 2.8 33.6 - - - +
3A SER* 3.4 11.8 + - - +
5A ILE* 1.3 73.9 - - - +
7A THR* 1.3 57.7 + - - +
10A GLY* 2.9 32.2 + - - -
13A ILE* 3.6 26.2 - - + -
163A ALA* 3.8 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 7 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A SER* 2.6 34.1 + - - -
4A MET* 3.9 4.7 - - - +
6A LEU* 1.3 75.4 - - - +
8A GLN* 1.3 64.9 + - + +
10A GLY* 4.3 2.3 + - - -
11A PRO* 5.3 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A MET* 3.3 15.4 + - - +
5A ILE 3.2 2.2 + - - -
7A THR* 1.3 87.0 - - + +
9A PHE* 1.3 76.5 + - + +
11A PRO* 5.5 2.2 - - - +
29A ASP 6.0 0.3 - - - -
30A ALA* 5.5 1.4 - - - -
33A ALA* 3.9 31.2 + - - +
36A MET* 5.9 3.0 - - - +
37A PHE* 3.1 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 2.9 28.1 + - + +
8A GLN* 1.3 81.6 - - + +
10A GLY* 1.3 67.2 + - - +
11A PRO* 3.4 4.5 - - - -
12A PHE* 2.9 9.0 + + + +
13A ILE* 2.8 37.5 + - + +
30A ALA* 3.5 13.9 - - + -
33A ALA* 3.5 27.6 - - + -
34A PHE* 3.4 53.2 - + - -
37A PHE* 3.9 26.9 - + - -
156A LEU* 4.7 2.2 - - + -
160A VAL* 3.5 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 2.9 25.6 + - - -
7A THR 4.3 0.8 + - - -
8A GLN 3.6 0.6 - - - -
9A PHE* 1.3 78.0 - - - +
11A PRO* 1.3 69.1 - - - +
13A ILE* 3.1 16.8 + - - +
14A GLU* 3.2 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A THR 5.3 3.8 - - - +
8A GLN 5.5 1.6 - - - +
9A PHE* 3.8 2.9 - - - +
10A GLY* 1.3 87.2 - - - +
12A PHE* 1.3 60.3 + - - +
14A GLU* 3.5 8.7 + - + +
15A SER* 3.2 22.0 + - - -
20A THR* 4.7 5.2 - - - +
26A VAL* 3.7 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 2.9 12.0 + + - +
11A PRO* 1.3 76.4 - - - +
13A ILE* 1.3 65.0 + - - +
15A SER* 2.7 23.8 + - - -
16A ILE* 3.2 45.7 + - + +
22A GLN* 5.7 1.1 - - - -
26A VAL* 3.5 13.3 - - + +
27A PHE* 3.8 32.3 - + - -
30A ALA* 3.5 28.0 - - + -
34A PHE* 4.4 1.8 - + - -
160A VAL* 3.9 25.1 - - + -
843A TRP* 3.7 11.4 - + + -
844A ALA* 4.1 9.0 - - - -
847A CYS* 3.7 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 4.2 4.3 - - + +
6A LEU* 3.6 24.2 - - + -
9A PHE* 2.8 40.2 + - + +
10A GLY* 3.3 8.1 - - - +
12A PHE* 1.3 77.4 - - - +
14A GLU* 1.3 65.3 + - + +
16A ILE* 3.4 10.7 - - + +
17A SER* 3.0 28.5 + - - +
160A VAL* 3.6 16.4 - - + +
161A ALA 5.2 0.7 - - - +
163A ALA* 3.6 26.0 - - + +
164A GLY* 3.5 33.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLY 3.2 16.4 + - - +
11A PRO* 4.0 6.6 - - + +
12A PHE 3.2 0.4 - - - -
13A ILE* 1.3 81.5 - - + +
15A SER* 1.3 59.7 + - - +
16A ILE 3.2 0.2 - - - -
17A SER* 3.4 9.0 + - - -
19A ILE* 3.0 56.4 + - + +
20A THR* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PRO 3.2 12.5 + - - -
12A PHE* 2.7 30.6 + - - -
14A GLU* 1.3 76.9 - - - +
16A ILE* 1.3 63.8 + - - +
17A SER 3.3 1.1 + - - -
18A GLY 4.3 0.2 - - - -
20A THR* 3.3 18.5 - - - +
21A ASP 3.3 22.4 - - - -
22A GLN* 3.3 28.4 - - - +
26A VAL* 4.5 5.8 - - - +
878A VAL* 3.8 10.0 - - - +
879A LYS 4.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 3.3 59.9 - - + +
13A ILE* 3.4 13.2 - - + +
15A SER* 1.3 82.6 - - - +
17A SER* 1.3 58.5 + - - +
18A GLY 3.5 1.3 - - - -
22A GLN* 4.6 8.1 - - - +
160A VAL* 4.8 1.8 - - + -
161A ALA* 4.4 8.5 - - - -
840A ARG* 3.1 51.4 - - + +
843A TRP* 4.0 20.4 - - + -
844A ALA* 4.4 9.2 - - + -
878A VAL* 4.0 10.7 - - + +
886A TRP* 3.7 9.5 - - - -
----------------------------------------------------------
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