Contacts of the helix formed by residues 3 - 20 (chain A) in PDB entry 1MBU
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 ASN 3 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.5 4.2 + - - -
2A LEU* 1.3 75.8 - - - +
4A GLN* 1.3 66.7 + - - +
5A GLU* 3.3 11.5 + - - +
6A LEU* 3.0 24.3 + - - +
7A GLU* 3.0 20.4 + - - +
37A ASN* 5.3 0.2 + - - -
39A SER* 5.6 3.0 - - - -
102A GLU* 3.2 35.4 + - + +
103A VAL 3.0 18.3 + - - +
104A THR* 3.6 23.1 - - - +
105A GLY 5.1 0.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 4 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU 3.9 0.2 + - - -
3A ASN* 1.3 75.5 - - - +
5A GLU* 1.3 66.5 + - + +
7A GLU* 3.4 5.7 + - - +
8A LEU* 3.0 36.5 + - + +
48D GLN* 2.8 32.7 + - - -
55D VAL* 3.6 19.7 - - - +
107D YBT 6.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 5 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASN* 3.3 11.3 + - - +
4A GLN* 1.3 77.9 - - + +
6A LEU* 1.3 67.0 + - - +
8A LEU* 3.4 10.5 + - + +
9A SER* 3.0 24.8 + - - -
37A ASN* 3.6 11.9 - - - +
38A PRO* 3.3 40.1 - - + +
39A SER* 4.9 2.9 + - - -
----------------------------------------------------------
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 LEU* 4.1 15.0 - - + -
3A ASN* 3.0 20.1 + - - +
5A GLU* 1.3 75.8 - - - +
7A GLU* 1.3 55.1 + - - +
9A SER* 3.0 5.1 + - - -
10A LEU* 2.8 58.6 + - + +
34A LEU* 4.1 15.0 - - + -
37A ASN* 3.6 9.5 - - - +
88A LEU* 6.2 0.4 - - + -
103A VAL* 3.7 28.0 - - + +
104A THR 3.8 6.7 - - - +
105A GLY* 4.1 14.4 - - - +
108A VAL* 3.5 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 7 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 3.7 28.3 - - + +
3A ASN 3.0 16.3 + - - +
4A GLN* 3.5 8.3 - - - +
6A LEU* 1.3 77.9 - - - +
8A LEU* 1.3 55.9 + - - +
10A LEU* 3.3 8.6 + - - +
11A ASN* 2.9 50.3 + - - +
55D VAL* 3.8 21.1 - - + -
56D GLU* 2.7 24.9 - - - +
107D YBT 3.3 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLN* 3.0 29.2 + - + +
5A GLU* 3.6 10.1 - - + +
7A GLU* 1.3 75.6 - - - +
9A SER* 1.3 58.2 + - - +
11A ASN* 3.8 0.5 - - - +
12A MET* 2.9 63.5 + - + +
41D GLU* 4.3 21.5 - - + +
44D ILE* 3.8 29.6 - - + -
48D GLN* 5.1 2.2 - - - +
55D VAL* 3.9 14.5 - - + +
59D THR* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLU 3.0 13.8 + - - -
6A LEU* 3.0 15.3 + - - -
8A LEU* 1.3 77.5 - - - +
10A LEU* 1.3 62.6 + - - +
12A MET* 4.1 8.5 - - - +
13A ALA* 3.0 26.9 + - - +
33A ALA* 3.9 20.5 + - - +
34A LEU* 4.8 4.3 - - - -
36A SER 5.2 0.7 + - - -
37A ASN* 3.4 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 3.8 29.2 - - + -
6A LEU* 2.8 38.0 + - + +
7A GLU* 3.7 9.4 - - - +
9A SER* 1.3 74.5 - - - +
11A ASN* 1.3 61.4 + - - +
13A ALA* 3.7 5.4 - - + +
14A PHE* 3.0 29.9 + - - +
25A MET* 3.9 4.2 - - - +
30A LEU* 3.5 33.2 - - + -
84A PHE* 4.2 16.2 - - + -
88A LEU* 3.9 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLU* 2.9 51.9 + - - +
8A LEU 4.0 2.0 - - - +
10A LEU* 1.3 74.1 - - - +
12A MET* 1.3 60.3 + - + +
14A PHE* 3.3 12.3 + - - +
15A ALA* 2.9 27.7 + - - +
55D VAL* 3.7 16.3 - - + +
56D GLU* 3.8 25.0 + - - +
59D THR* 3.4 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 2.9 46.7 + - + +
9A SER* 4.2 7.2 - - - +
11A ASN* 1.3 69.4 - - - +
13A ALA* 1.3 61.2 + - - +
15A ALA* 3.1 2.4 + - - +
16A ARG* 2.8 55.5 + - - +
40D MET* 3.9 23.3 - - - +
41D GLU* 3.8 49.8 - - + +
44D ILE* 3.9 13.9 - - + -
59D THR* 5.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A SER 3.0 19.9 + - - +
10A LEU* 3.7 7.0 - - + +
12A MET* 1.3 75.2 - - - +
14A PHE* 1.3 58.2 + - - +
16A ARG* 3.4 11.8 + - - +
17A ALA* 3.0 28.8 + - - +
25A MET* 4.0 14.1 - - + +
29A HIS* 4.5 12.0 - - + +
30A LEU* 5.5 2.0 - - + -
33A ALA* 3.6 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU 3.0 16.3 + - - +
11A ASN* 3.6 12.8 - - - +
13A ALA* 1.3 77.6 - - - +
15A ALA* 1.3 63.0 + - - +
17A ALA* 3.2 3.7 + - - +
18A ARG* 2.9 52.9 + - - +
25A MET* 3.2 36.1 - - + +
78A THR* 3.6 38.6 - - + -
79A GLN* 4.9 3.1 - - - -
80A PRO* 5.0 6.3 - - + -
59D THR* 6.3 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASN 2.9 17.6 + - - +
12A MET 3.1 4.5 + - - +
14A PHE* 1.3 76.9 - - - +
16A ARG* 1.3 57.4 + - - +
18A ARG* 3.2 5.1 + - - +
19A GLU* 2.9 34.5 + - - +
40D MET* 4.2 7.2 - - + -
59D THR* 3.8 20.0 - - + -
62D MET* 3.8 17.7 - - + -
63D LEU* 4.1 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A MET* 2.8 44.6 + - - +
13A ALA* 3.8 8.8 - - - +
15A ALA* 1.3 73.7 - - - +
17A ALA* 1.3 64.9 + - - +
19A GLU* 3.2 9.1 + - - +
20A HIS* 2.9 44.2 + - + +
33A ALA* 6.3 0.8 - - - +
40D MET* 3.8 41.2 - - + +
41D GLU* 5.2 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA 3.0 17.2 + - - +
14A PHE* 3.6 6.1 - - - +
16A ARG* 1.3 75.4 - - - +
18A ARG* 1.3 64.6 + - - +
20A HIS* 3.1 4.0 + - - -
21A ARG 3.1 16.5 + - - -
22A HIS* 3.1 22.2 + - + -
24A PHE 4.8 0.7 - - - +
25A MET* 4.5 5.4 - - - -
29A HIS* 4.0 25.5 - - + +
78A THR* 4.0 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 2.9 53.0 + - - +
15A ALA* 3.6 7.4 - - - +
16A ARG 3.2 0.2 - - - -
17A ALA* 1.3 77.7 - - - +
19A GLU* 1.3 61.4 + - + +
21A ARG* 3.1 27.9 + - - +
77A ASP* 3.4 37.3 + - - +
78A THR* 3.3 26.2 + - - +
60D GLN* 6.3 1.2 - - - +
63D LEU* 3.7 28.5 - - + +
67D TYR* 3.9 7.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA 2.9 21.2 + - - +
16A ARG* 3.2 9.6 + - - +
18A ARG* 1.3 76.5 - - - +
20A HIS* 1.3 64.4 + - + +
21A ARG* 3.2 7.8 + - - +
40D MET* 3.6 26.3 - - - +
62D MET* 4.7 2.3 - - - +
63D LEU* 3.7 19.5 - - + +
66D HIS* 3.1 41.5 + - - +
67D TYR* 3.5 17.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG* 2.9 37.7 + - + +
17A ALA* 3.1 2.4 + - - +
19A GLU* 1.3 80.2 - - + +
21A ARG* 1.3 71.1 + - - +
22A HIS* 3.3 36.1 + - + +
68A VAL* 4.2 7.6 - - - +
----------------------------------------------------------
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