Contacts of the helix formed by residues 7 - 27 (chain M) in PDB entry 4LLL
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 TYR 7 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M SER* 1.3 82.2 - - - +
8M LEU* 1.3 61.5 + - - +
9M PHE 3.3 0.5 + - - -
10M ARG* 3.4 18.2 + - - +
11M MET* 3.8 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 8 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M SER* 3.1 8.8 + - - +
7M TYR* 1.3 78.6 - - - +
9M PHE* 1.3 60.0 + - - +
11M MET* 2.8 35.6 + - + +
12M ILE* 3.7 3.5 + - - +
131O LEU* 6.2 6.1 - - + -
132O THR* 6.4 2.5 - - - -
135O LEU* 5.6 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 9 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M SER* 3.0 27.4 + - - +
8M LEU* 1.3 78.5 - - - +
10M ARG* 1.3 63.7 + - - +
11M MET 3.3 0.3 + - - -
12M ILE* 3.4 18.5 + - - +
13M SER* 4.1 2.6 + - - -
131M LEU* 6.6 0.4 - - + -
134M MET* 6.2 7.2 - - + -
9O PHE* 3.6 26.1 - + + +
12O ILE* 3.2 50.0 - - + -
13O SER* 4.0 7.3 - - - -
16O MET* 4.0 18.8 - - - -
131O LEU* 6.1 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 10 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M SER 3.9 2.5 + - - +
7M TYR* 3.4 12.2 + - - +
8M LEU 3.2 0.6 - - - -
9M PHE* 1.3 84.0 - - + +
11M MET* 1.3 62.6 + - + +
13M SER* 3.1 20.0 + - - -
14M HIS* 3.4 9.6 + - - +
13O SER* 5.5 4.3 - - - -
16O MET* 5.9 3.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 11 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7M TYR 3.8 12.8 - - - +
8M LEU* 2.8 21.1 + - + +
10M ARG* 1.3 78.6 - - + +
12M ILE* 1.3 61.3 + - - +
14M HIS* 3.2 29.6 + - - +
15M GLU* 3.5 13.0 + - - +
135O LEU* 5.6 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 12 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8M LEU 3.7 3.1 + - - +
9M PHE* 3.4 13.5 + - + +
10M ARG 3.2 0.8 - - - -
11M MET* 1.3 79.3 - - - +
13M SER* 1.3 62.7 + - - +
14M HIS 3.4 0.2 + - - -
15M GLU* 3.6 3.7 + - - +
16M MET* 3.3 27.8 + - + +
9O PHE* 3.8 27.1 - - + -
131O LEU 6.1 0.7 - - - +
134O MET* 6.1 3.4 - - + -
135O LEU* 5.2 18.3 - - + +
138O LEU* 5.6 4.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 13 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9M PHE 4.1 1.9 + - - -
10M ARG* 3.1 12.1 + - - -
12M ILE* 1.3 79.2 - - - +
14M HIS* 1.3 56.8 + - - +
16M MET* 3.2 18.5 + - - +
17M LYS* 2.8 31.8 + - - +
9O PHE* 4.6 3.7 + - - -
10O ARG* 4.8 6.2 + - - -
13O SER* 3.9 28.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 14 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10M ARG 3.4 6.4 + - - +
11M MET* 3.2 27.2 + - + +
13M SER* 1.3 78.0 - - - +
15M GLU* 1.3 69.9 + - - +
17M LYS* 3.4 6.9 + - + +
18M GLN* 3.0 54.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 15 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11M MET 3.5 11.5 + - - +
12M ILE* 3.6 4.0 + - - +
13M SER 3.4 0.2 - - - -
14M HIS* 1.3 92.0 + - + +
16M MET* 1.3 60.9 + - - +
18M GLN* 3.8 20.5 - - - +
19M LYS* 3.1 26.7 + - - +
111M MET* 5.2 0.2 - - - +
135O LEU 5.4 0.7 - - - +
138O LEU* 4.1 28.9 - - + +
139O GLN 3.9 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 16 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M ILE 3.3 15.9 + - - +
13M SER* 3.2 13.0 + - - +
14M HIS 3.2 0.4 - - - -
15M GLU* 1.3 77.2 - - + +
17M LYS* 1.3 64.9 + - - +
19M LYS* 3.3 11.3 + - - +
20M ALA* 3.3 11.8 + - - +
108M PHE* 6.0 0.2 - - - -
111M MET* 3.6 30.8 - - - +
6O SER* 2.8 32.5 - - - +
9O PHE* 3.6 33.2 - - + -
10O ARG* 3.5 40.2 + - + +
138O LEU* 5.9 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 17 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13M SER 2.8 16.4 + - - +
14M HIS* 3.7 9.4 - - + +
16M MET* 1.3 74.7 - - - +
18M GLN* 1.3 61.5 + - + +
20M ALA* 3.0 7.3 + - - +
21M ASP* 2.8 29.2 + - - +
10O ARG* 4.1 18.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 18 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M HIS* 3.0 50.7 + - + +
15M GLU* 3.8 22.6 - - - +
17M LYS* 1.3 77.0 - - + +
19M LYS* 1.3 52.8 + - - +
21M ASP* 3.3 9.7 - - + +
22M GLN* 2.6 55.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 19 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M GLU 3.1 19.7 + - - +
16M MET* 3.5 9.2 - - - +
17M LYS 3.1 0.6 - - - -
18M GLN* 1.3 77.6 - - - +
20M ALA* 1.3 58.7 + - - +
22M GLN* 3.6 8.7 + - - +
23M LYS* 3.4 20.1 + - - +
111M MET* 4.4 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 20 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16M MET 3.3 8.3 + - - +
17M LYS* 3.0 10.6 + - - +
19M LYS* 1.3 73.9 - - - +
21M ASP* 1.3 59.5 + - - +
22M GLN 3.0 4.4 + - - -
23M LYS* 3.3 5.2 + - - +
24M LEU* 2.9 41.0 + - + +
104M PHE* 4.5 10.4 - - + -
108M PHE* 4.7 21.5 - - + -
111M MET* 5.6 0.8 - - + +
10O ARG* 5.6 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 21 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17M LYS 2.8 18.9 + - - +
18M GLN* 3.3 13.7 - - + +
20M ALA* 1.3 72.6 - - - +
22M GLN* 1.3 60.5 + - - +
24M LEU* 4.2 10.3 - - - +
25M GLU* 3.1 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 22 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M GLN* 2.6 41.7 + - + +
19M LYS* 3.7 9.9 - - - +
20M ALA 3.0 0.6 - - - -
21M ASP* 1.3 76.1 - - - +
23M LYS* 1.3 55.3 + - - +
25M GLU* 3.0 9.7 + - - +
26M GLN* 2.8 48.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M LYS 3.4 10.3 + - - +
20M ALA* 3.3 6.6 + - - +
22M GLN* 1.3 78.1 - - - +
24M LEU* 1.3 63.3 + - - +
26M GLN* 3.2 13.9 + - - +
27M PHE* 3.0 40.6 + - + -
103M ALA 6.5 0.7 - - - -
104M PHE* 4.0 23.8 - - + -
107M ILE* 5.6 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20M ALA* 2.9 26.0 + - + +
21M ASP* 4.2 7.9 - - - +
23M LYS* 1.3 75.8 - - - +
25M GLU* 1.3 57.5 + - - +
28M ASP* 2.9 21.7 + - - -
29M ILE* 3.0 52.8 + - + +
30M THR 4.0 5.8 - - - +
31M ASN* 3.6 35.4 - - - +
34M GLY* 4.9 2.7 - - - -
104M PHE* 3.4 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 25 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21M ASP 3.1 21.9 + - - +
22M GLN* 3.0 12.8 + - - +
24M LEU* 1.3 76.3 - - - +
26M GLN* 1.3 66.8 + - - +
28M ASP* 3.3 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 26 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22M GLN* 2.8 32.1 + - + +
23M LYS* 3.2 11.4 + - - +
25M GLU* 1.3 76.5 - - - +
27M PHE* 1.3 88.7 + - + +
28M ASP* 3.4 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 27 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M LYS* 3.0 37.5 + - + +
24M LEU* 5.1 0.2 - - - -
26M GLN* 1.3 97.1 - - + +
28M ASP* 1.3 70.7 + - - +
29M ILE* 3.4 15.7 + - + +
74M LYS* 4.8 4.0 + - - +
76M LEU* 4.9 3.5 - - - +
100M LEU* 3.5 36.8 - - + -
103M ALA* 4.4 25.4 - - + -
104M PHE* 4.3 8.5 - + - -
----------------------------------------------------------
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