Contacts of the helix formed by residues 4 - 26 (chain J) 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 THR 4 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I HIS* 5.8 0.4 - - + -
108I PHE* 5.4 2.6 + - - +
112I GLU* 3.0 23.6 + - - +
3J PHE* 1.3 82.8 - - + +
5J TYR* 1.3 64.8 + - - +
6J SER* 3.0 29.0 + - - +
7J TYR* 3.2 17.9 - - + +
8J LEU* 3.1 16.3 + - - +
10J ARG* 4.1 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 5 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I MET* 5.5 2.5 - - + -
112I GLU* 2.7 33.7 + - - +
115I LEU* 3.6 28.9 - - + -
116I VAL* 4.0 20.2 - - + -
123I GLU 4.1 0.2 + - - -
124I ASN* 2.6 37.4 + - - -
127I MET* 4.0 29.7 - - + +
128I LYS* 3.9 25.7 + - + -
3J PHE 4.9 1.6 - - - -
4J THR* 1.3 70.1 - - - +
6J SER* 1.3 63.7 + - - +
8J LEU* 2.9 28.5 + - + +
9J PHE* 3.0 36.5 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 6 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I MET* 3.7 26.1 - - - +
35I HIS* 3.7 13.8 - - - -
108I PHE* 6.0 4.9 - - - -
111I MET* 6.6 0.2 - - - -
112I GLU* 3.7 2.0 + - - -
4J THR* 3.0 16.2 + - - +
5J TYR* 1.3 78.3 - - - +
7J TYR* 1.3 57.2 + - - +
9J PHE* 3.3 2.1 + - - +
10J ARG* 2.6 65.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 7 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I ALA 4.3 16.3 + - - -
57I LEU* 5.6 0.4 - - - -
58I GLN* 3.8 13.3 + - - -
135I LEU* 5.0 9.7 - - + +
3J PHE* 4.0 15.7 - - + -
4J THR* 3.2 23.2 - - + +
6J SER* 1.3 80.2 + - - +
8J LEU* 1.3 81.1 + - + +
10J ARG* 3.4 17.7 - - - +
11J MET* 3.0 66.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 8 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128I LYS* 4.0 27.4 - - + +
131I LEU* 4.5 14.8 - - + -
132I THR* 5.1 6.7 - - - +
135I LEU* 4.7 6.0 - - + +
2J GLU* 4.5 5.4 - - + -
3J PHE* 3.6 20.6 - - + +
4J THR 3.1 17.5 - - - +
5J TYR* 2.9 35.5 + - + +
7J TYR* 1.3 100.2 - - + +
9J PHE* 1.3 64.1 + - + +
11J MET* 4.5 1.4 - - - +
12J ILE* 3.3 33.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 9 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I PHE* 5.0 13.7 - - + +
12I ILE* 4.9 18.6 - - + -
13I SER* 3.9 12.8 - - - +
16I MET* 3.6 33.7 - - + -
127I MET* 4.8 23.1 - - + -
131I LEU* 6.2 4.7 - - + -
5J TYR* 3.0 36.6 + + + -
6J SER 3.9 4.0 - - - +
8J LEU* 1.3 79.8 - - + +
10J ARG* 1.3 69.7 + - - +
11J MET 3.3 0.2 - - - -
12J ILE* 4.7 6.3 - - + +
13J SER* 3.3 25.3 + - - -
131J LEU* 5.7 8.7 - - + -
134J MET* 5.7 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 10 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I SER* 4.9 5.1 - - - -
31I ASN* 5.7 6.5 - - - +
32I GLU* 6.5 0.7 - - - +
35I HIS* 3.0 55.0 + - - +
57I LEU* 6.0 3.8 - - - +
59I ARG* 4.4 9.4 + - - +
4J THR* 4.1 3.4 - - - +
6J SER* 2.6 43.8 + - - +
7J TYR* 3.4 24.1 - - - +
9J PHE* 1.3 79.8 - - - +
11J MET* 1.3 82.7 + - + +
13J SER* 3.8 1.7 - - - -
14J HIS* 3.2 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 11 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57I LEU* 3.6 21.8 - - + +
58I GLN* 3.0 42.8 - - - +
59I ARG* 4.0 11.7 - - - +
135I LEU* 3.7 22.3 - - + +
7J TYR* 3.0 47.9 + - + +
8J LEU 4.6 0.2 - - - +
10J ARG* 1.3 111.2 - - + +
12J ILE* 1.3 59.7 + - - +
14J HIS* 3.9 3.9 - - - +
15J GLU* 2.9 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 12 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I PHE* 4.5 11.4 - - + -
131I LEU* 3.7 30.3 - - + +
134I MET* 4.3 8.3 - - + -
135I LEU* 3.8 33.2 - - + +
138I LEU* 4.6 5.8 - - + +
8J LEU* 3.3 20.4 + - + +
9J PHE* 4.5 8.1 - - + +
10J ARG 3.4 0.8 - - - -
11J MET* 1.3 73.7 - - - +
13J SER* 1.3 68.3 + - - +
15J GLU* 3.0 3.0 + - - +
16J MET* 2.9 47.4 + - + +
115J LEU* 5.2 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 13 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I PHE* 4.1 14.9 - - - +
10I ARG* 3.8 12.9 - - - +
13I SER* 3.0 28.7 + - - -
9J PHE 3.3 17.9 + - - -
10J ARG 3.8 1.8 - - - -
12J ILE* 1.3 81.5 - - - +
14J HIS* 1.3 63.1 + - - +
16J MET* 3.4 7.1 + - - +
17J LYS* 3.1 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 14 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58I GLN* 4.0 3.4 + - + -
59I ARG* 2.8 53.6 + - - +
60I THR* 6.3 0.8 - - - +
10J ARG 3.2 15.9 + - - +
11J MET* 3.9 4.0 - - - +
12J ILE 3.2 0.6 - - - -
13J SER* 1.3 80.3 - - - +
15J GLU* 1.3 65.9 + - - +
17J LYS* 3.3 7.4 + - - +
18J GLN* 2.8 61.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 15 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58I GLN* 5.0 13.9 - - - +
135I LEU* 4.5 6.3 - - + -
138I LEU* 3.6 46.8 - - + +
139I GLN 4.2 10.9 - - - -
11J MET 2.9 20.8 + - - +
12J ILE 3.0 3.5 + - - +
14J HIS* 1.3 87.3 - - - +
16J MET* 1.3 54.9 + - - +
18J GLN* 3.3 12.5 + - - +
19J LYS* 2.6 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 16 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I TYR* 5.3 1.1 - - + -
6I SER* 3.6 40.2 - - - +
9I PHE* 4.6 9.4 - - - -
10I ARG 6.1 0.2 - - - -
138I LEU* 4.4 12.1 - - + -
12J ILE* 2.9 37.2 + - + +
13J SER* 3.6 7.4 - - - +
15J GLU* 1.3 73.6 - - - +
17J LYS* 1.3 57.0 + - - +
19J LYS* 3.6 6.2 - - - +
20J ALA* 2.6 40.2 + - - +
111J MET* 4.3 28.6 - - + +
112J GLU* 5.5 0.7 - - - +
115J LEU* 4.0 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 17 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J SER 3.1 11.4 + - - +
14J HIS* 3.5 14.4 - - - +
16J MET* 1.3 76.8 - - - +
18J GLN* 1.3 61.0 + - - +
20J ALA* 3.9 0.2 - - - +
21J ASP* 2.9 41.8 + - - +
31J ASN* 3.7 28.0 - - - +
32J GLU* 4.9 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 18 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60I THR* 5.8 5.7 - - - +
14J HIS* 2.8 52.2 + - + +
15J GLU* 3.4 18.4 - - - +
17J LYS* 1.3 79.2 - - - +
19J LYS* 1.3 65.0 + - - +
21J ASP* 4.2 10.9 - - - +
22J GLN* 3.1 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 19 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138I LEU* 5.5 10.8 - - + -
15J GLU* 2.6 22.8 + - + +
16J MET* 3.6 6.7 - - - +
18J GLN* 1.3 74.8 - - - +
20J ALA* 1.3 63.3 + - - +
22J GLN* 3.4 9.1 + - - +
23J LYS* 3.2 25.2 + - + +
111J MET* 3.4 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 20 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J MET 2.6 21.9 + - - +
17J LYS* 3.9 0.4 - - - +
19J LYS* 1.3 71.7 - - - +
21J ASP* 1.3 53.6 + - - +
23J LYS* 3.0 4.3 + - - +
24J LEU* 2.6 46.9 + - + +
31J ASN* 3.8 22.9 - - + +
107J ILE* 6.3 0.4 - - - -
108J PHE* 4.5 9.9 - - + -
111J MET* 3.2 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 21 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17J LYS* 2.9 28.4 + - - +
18J GLN* 4.2 13.5 - - - +
19J LYS 3.4 0.4 - - - -
20J ALA* 1.3 74.7 - - - +
22J GLN* 1.3 53.2 + - + +
24J LEU* 3.3 5.0 - - - +
25J GLU* 2.5 37.9 + - - +
29J ILE 4.6 2.3 - - - +
30J THR* 3.5 8.9 - - - -
31J ASN* 2.8 40.7 + - - +
32J GLU* 5.2 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 22 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18J GLN* 3.1 31.5 + - - +
19J LYS* 3.7 8.0 - - - +
20J ALA 3.2 0.4 - - - -
21J ASP* 1.3 73.3 - - + +
23J LYS* 1.3 74.9 + - - +
25J GLU* 3.3 20.1 + - - +
26J GLN* 4.2 2.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19J LYS* 3.2 13.8 + - + +
20J ALA* 3.0 10.9 + - - +
22J GLN* 1.3 85.8 - - - +
24J LEU* 1.3 61.6 + - - +
25J GLU 3.8 0.2 + - - -
26J GLN* 4.1 13.7 - - - +
27J PHE* 4.1 9.2 - - - -
107J ILE* 4.1 24.7 - - + +
111J MET* 4.1 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J ALA* 2.6 27.6 + - + +
21J ASP 3.3 2.7 - - - +
23J LYS* 1.3 75.0 - - + +
25J GLU* 1.3 50.8 + - - +
26J GLN 3.0 6.3 - - - -
27J PHE* 2.7 32.0 + - + +
28J ASP 3.5 1.6 + - - -
29J ILE* 3.4 30.4 - - + +
30J THR 3.7 3.8 - - - +
31J ASN* 3.5 38.1 - - + +
104J PHE* 3.8 45.1 - - + +
107J ILE* 4.7 7.2 - - + -
108J PHE* 4.1 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 25 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J ASP 2.5 20.1 + - - +
22J GLN* 3.3 14.5 + - - +
24J LEU* 1.3 72.6 - - - +
26J GLN* 1.3 60.3 + - - +
27J PHE 3.1 1.7 + - - -
28J ASP* 3.2 13.8 + - - +
29J ILE 4.7 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 26 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J GLN 4.2 3.0 + - - +
23J LYS 4.1 11.3 + - - +
24J LEU 3.0 0.2 - - - -
25J GLU* 1.3 80.2 - - - +
27J PHE* 1.3 91.4 + - - +
28J ASP 3.5 0.6 + - - -
----------------------------------------------------------
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