Contacts of the helix formed by residues 4 - 24 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A GLU 4.2 1.0 + - - -
3A PHE* 1.3 76.9 - - + +
5A TYR* 1.3 63.3 + - - +
6A SER* 3.2 14.3 + - - +
7A TYR* 3.0 34.7 + - + +
8A LEU* 3.3 9.4 + - - +
10A ARG* 5.2 0.9 - - - +
112B GLU* 2.9 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 5 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A PHE 4.2 0.2 - - - -
4A THR* 1.3 72.1 - - - +
6A SER* 1.3 63.2 + - - +
8A LEU* 3.0 12.3 + - + +
9A PHE* 3.0 40.3 + + + -
134A MET* 3.0 44.9 - - + -
16B MET* 5.1 0.2 - - - -
112B GLU* 2.9 21.6 + - - +
115B LEU* 3.8 16.6 - - + -
116B VAL* 4.2 14.8 - - + -
119B LEU* 5.2 1.1 - - + +
124B ASN* 3.4 25.2 + - + +
127B MET* 3.0 31.6 - - + +
128B LYS* 2.8 48.0 - - + -
131B LEU* 4.6 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 6 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A THR* 3.2 17.0 + - - +
5A TYR* 1.3 80.0 - - - +
7A TYR* 1.3 66.4 + - - +
9A PHE* 4.2 0.8 - - - +
10A ARG* 2.8 40.7 + - - +
16B MET* 4.3 29.4 - - - +
35B HIS* 4.0 19.8 + - - -
108B PHE* 6.0 1.8 - - - -
112B GLU* 4.2 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 7 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A PHE* 3.9 44.4 - + + -
4A THR* 3.0 24.5 + - + +
6A SER* 1.3 81.1 + - - +
8A LEU* 1.3 66.1 + - + +
10A ARG* 3.6 25.5 - - - +
11A MET* 2.8 67.5 + - + +
56B ALA 4.2 15.6 + - - -
57B LEU* 6.4 0.7 - - + -
58B GLN* 4.8 6.8 - - - +
135B LEU* 4.4 11.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
3A PHE* 3.3 46.9 - - + +
4A THR 3.3 9.6 - - - +
5A TYR* 3.0 10.4 + - + +
7A TYR* 1.3 82.3 - - + +
9A PHE* 1.3 65.6 + - - +
12A ILE* 2.7 36.0 + - + +
128B LYS* 3.6 21.3 - - + +
131B LEU* 3.6 34.8 - - + -
132B THR* 4.5 15.5 - - + +
135B LEU* 4.6 11.9 - - + -
----------------------------------------------------------
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 TYR* 3.0 50.8 + + + +
6A SER 4.2 1.8 - - - +
8A LEU* 1.3 76.2 - - - +
10A ARG* 1.3 64.8 + - - +
12A ILE* 4.5 3.6 - - + -
13A SER* 2.9 28.9 + - - -
131A LEU* 3.8 29.8 - - + -
134A MET* 4.2 9.4 - - + -
9B PHE* 4.3 17.2 - + - +
12B ILE* 3.3 35.0 - - + -
13B SER* 4.3 14.1 - - - +
16B MET* 3.8 13.7 - - - -
115B LEU* 4.1 10.8 - - + -
131B LEU* 3.8 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A THR* 5.2 0.8 - - - +
6A SER* 2.8 38.8 + - - +
7A TYR* 3.6 24.5 - - - +
9A PHE* 1.3 80.9 - - - +
11A MET* 1.3 83.3 + - - +
13A SER* 3.3 3.5 + - - -
14A HIS* 3.3 20.8 + - - +
13B SER* 4.1 11.0 - - - +
31B ASN* 4.9 9.0 - - - +
32B GLU* 5.9 2.9 - - - +
35B HIS* 3.6 46.0 + - - +
57B LEU* 5.2 10.1 + - - +
59B ARG* 4.1 16.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 2.8 55.2 + - + +
10A ARG* 1.3 95.0 - - - +
12A ILE* 1.3 66.3 + - - +
14A HIS* 3.2 3.8 + - - +
15A GLU* 3.1 28.9 + - + +
56B ALA 4.4 0.4 - - - +
57B LEU* 2.7 37.5 - - - +
58B GLN* 3.7 21.1 - - + -
59B ARG* 3.8 16.6 - - - +
135B LEU* 3.7 23.1 - - + -
139B GLN* 6.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 2.7 30.7 + - + +
9A PHE* 3.9 4.3 - - - +
11A MET* 1.3 76.2 - - - +
13A SER* 1.3 66.3 + - - +
15A GLU 3.4 0.2 + - - -
16A MET* 3.2 23.4 + - + +
9B PHE* 3.7 37.5 - - + -
131B LEU* 3.7 48.2 - - + +
134B MET* 4.7 2.9 - - + -
135B LEU* 3.7 28.5 - - + +
138B LEU* 3.8 18.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE 2.9 13.0 + - - -
10A ARG 3.3 6.9 + - - -
12A ILE* 1.3 79.9 - - - +
14A HIS* 1.3 66.9 + - - +
16A MET* 3.3 7.3 + - - +
17A LYS* 3.1 20.6 + - - +
9B PHE* 3.8 18.6 - - - +
10B ARG* 4.7 5.4 - - - -
13B SER* 3.1 30.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ARG 3.3 14.5 + - - +
11A MET* 3.2 5.1 + - - +
12A ILE 3.1 0.8 - - - -
13A SER* 1.3 84.7 + - - +
15A GLU* 1.3 70.4 + - - +
17A LYS* 3.1 10.3 + - + +
18A GLN* 3.0 57.2 + - + +
58B GLN 4.0 3.4 - - - -
59B ARG* 2.9 41.5 + - - +
14G T 3.1 26.2 + - - -
15G C 2.8 22.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A MET* 3.1 17.9 + - + +
12A ILE 4.2 1.3 - - - +
14A HIS* 1.3 93.2 + - - +
16A MET* 1.3 56.1 + - - +
18A GLN* 3.5 14.0 - - - +
19A LYS* 2.6 38.0 + - - +
58B GLN* 3.7 18.4 - - + +
135B LEU* 4.7 6.3 - - + -
138B LEU* 4.1 23.2 - - + +
139B GLN* 3.1 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE 3.2 16.2 + - - +
13A SER* 3.5 10.3 - - - +
15A GLU* 1.3 76.9 - - - +
17A LYS* 1.3 59.3 + - - +
19A LYS* 4.6 0.4 - - - -
20A ALA* 2.8 33.9 + - - +
31A ASN* 5.5 0.2 - - - -
111A MET* 3.6 36.5 - - + +
112A GLU* 5.5 1.8 - - - +
115A LEU* 3.9 22.9 - - + -
5B TYR 4.7 0.2 - - - +
6B SER* 4.4 27.4 - - - +
9B PHE* 4.1 28.7 - - - -
138B LEU* 3.5 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER 3.1 11.9 + - - +
14A HIS* 3.2 14.1 - - + +
16A MET* 1.3 77.9 - - - +
18A GLN* 1.3 61.8 + - - +
20A ALA* 3.5 0.5 - - - +
21A ASP* 2.5 44.6 + - - +
31A ASN* 4.1 25.4 - - + +
32A GLU* 4.8 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A HIS* 3.0 55.0 + - + +
15A GLU* 3.0 21.1 + - - +
17A LYS* 1.3 82.3 - - - +
19A LYS* 1.3 61.1 + - - +
21A ASP* 3.6 11.8 + - - +
22A GLN* 2.9 43.4 + - + +
14G T 5.9 0.2 - - - +
15G C 3.8 28.7 - - - +
16G T 4.8 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLU 2.6 21.3 + - - +
18A GLN* 1.3 72.7 - - - +
20A ALA* 1.3 62.4 + - - +
22A GLN* 3.4 10.3 + - - +
23A LYS* 3.1 35.5 + - + +
111A MET* 3.9 17.7 - - + -
138B LEU* 5.3 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A MET 2.8 20.8 + - - +
17A LYS 3.6 2.2 - - - +
19A LYS* 1.3 79.0 - - - +
21A ASP* 1.3 62.2 + - - +
23A LYS* 3.4 4.6 + - - +
24A LEU* 3.0 31.0 + - + +
31A ASN* 3.7 22.0 - - + +
107A ILE* 5.0 2.2 - - + -
108A PHE* 4.6 11.0 - - + -
111A MET* 3.6 21.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LYS* 2.5 27.7 + - - +
18A GLN* 3.2 15.4 + - - +
20A ALA* 1.3 74.6 - - - +
22A GLN* 1.3 62.9 + - + +
24A LEU* 3.3 13.3 + - - +
25A GLU* 3.4 10.9 + - - +
29A ILE 4.8 2.5 - - - +
30A THR* 4.7 8.1 - - - +
31A ASN* 2.6 45.4 + - - +
32A GLU* 4.9 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLN* 2.9 27.5 + - + +
19A LYS* 3.8 9.1 - - - +
21A ASP* 1.3 75.9 - - + +
23A LYS* 1.3 63.7 + - + +
25A GLU* 3.0 24.5 + - - +
16G T 4.6 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LYS* 3.1 24.7 + - + +
20A ALA 3.7 3.1 - - - +
22A GLN* 1.3 77.8 - - + +
24A LEU* 1.3 58.5 + - - +
25A GLU 3.1 3.9 + - - -
26A GLN* 3.6 15.6 + - - +
107A ILE* 3.5 46.4 - - + +
110A GLU* 3.4 35.5 + - - +
111A MET* 4.4 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA* 3.0 22.7 + - - +
21A ASP* 3.8 4.3 - - - +
22A GLN 3.1 0.6 - - - -
23A LYS* 1.3 73.1 - - - +
25A GLU* 1.3 66.6 + - - +
26A GLN 2.8 4.1 + - - -
27A PHE* 2.9 25.5 + - + +
28A ASP 3.5 3.6 + - - -
29A ILE* 3.6 24.3 - - + +
30A THR 3.8 8.1 - - - +
31A ASN* 3.8 28.3 - - - -
34A GLY* 4.8 0.4 - - - -
104A PHE* 3.7 31.0 - - + -
107A ILE* 3.6 25.1 - - + -
108A PHE* 4.1 19.1 - - + -
----------------------------------------------------------
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