Contacts of the helix formed by residues 4 - 23 (chain A) in PDB entry 4ESF
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 LEU 4 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASN* 1.3 83.2 - - - +
5A THR* 1.3 60.0 + - - +
6A GLU 3.4 2.5 - - - -
7A MET* 3.2 18.5 + - + -
8A LEU* 2.8 40.0 + - + +
38A GLY 5.0 6.7 - - - +
39A PHE* 4.2 27.8 - - + -
41A GLU* 4.0 11.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 5 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASN* 3.2 26.0 + - - +
4A LEU* 1.3 78.0 - - - +
6A GLU* 1.3 64.0 + - - +
8A LEU* 3.7 5.1 - - - +
9A LYS* 2.7 38.6 + - - +
41A GLU* 5.3 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 6 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASN* 5.3 1.0 + - - +
4A LEU 3.4 0.6 - - - -
5A THR* 1.3 83.6 + - - +
7A MET* 1.3 63.9 + - - +
9A LYS* 3.5 43.9 + - - +
10A GLY 4.2 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 7 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.2 20.2 + - + +
6A GLU* 1.3 80.3 - - - +
8A LEU* 1.3 60.6 + - - +
9A LYS 3.6 0.2 + - - -
10A GLY* 4.3 5.2 + - - -
11A SER* 4.8 7.3 + - - -
----------------------------------------------------------
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 LEU* 2.8 26.4 + - + +
5A THR* 4.0 4.0 - - - +
7A MET* 1.3 76.7 - - - +
9A LYS* 1.3 65.9 + - - +
10A GLY 3.4 0.2 - - - -
11A SER* 3.0 23.5 + - - +
12A LEU* 3.0 41.2 + - + +
15A CYS* 5.0 4.3 - - - -
39A PHE* 3.8 51.8 - - + -
42A VAL* 4.2 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A THR* 2.7 20.2 + - - +
6A GLU* 3.5 40.1 + - - +
7A MET 3.4 0.4 - - - -
8A LEU* 1.3 76.9 - - - +
10A GLY* 1.3 58.7 + - - +
11A SER 3.0 5.9 + - - -
12A LEU* 3.3 19.1 + - + +
13A GLU* 4.5 2.4 + - - +
----------------------------------------------------------
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 GLU 4.2 4.4 + - - -
7A MET 4.3 4.0 + - - -
8A LEU 3.4 1.0 - - - -
9A LYS* 1.3 77.4 - - - +
11A SER* 1.3 59.3 + - - +
13A GLU 5.5 0.4 - - - -
89A PHE* 4.9 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A MET 4.8 4.5 + - - -
8A LEU* 3.0 20.7 + - - -
10A GLY* 1.3 77.5 + - - +
12A LEU* 1.3 65.3 + - - +
13A GLU 3.4 2.5 - - - -
14A GLY 3.4 4.8 + - - -
15A CYS* 3.2 26.1 + - - -
89A PHE* 3.5 20.4 - - - -
93A TRP* 4.1 24.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.0 41.6 + - + +
9A LYS* 3.3 13.2 + - - +
11A SER* 1.3 75.9 - - - +
13A GLU* 1.3 67.5 + - - +
15A CYS* 3.2 6.2 + - + +
16A VAL* 3.0 27.9 + - + +
34A LEU* 4.3 28.9 - - + -
39A PHE* 5.3 0.2 - - + -
42A VAL* 4.7 13.7 - - + -
46A THR* 3.6 23.8 - - + -
47A VAL* 6.1 0.4 - - + -
50A ILE* 3.5 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LYS 4.5 2.6 + - - +
10A GLY 6.4 0.2 - - - -
11A SER 3.4 0.8 - - - -
12A LEU* 1.3 80.2 - - - +
14A GLY* 1.3 57.0 + - - +
16A VAL* 3.3 5.0 + - - +
17A LEU* 3.0 32.8 + - + +
50A ILE* 4.0 19.0 - - + +
53A ARG* 2.0 49.2 + - - +
54A LEU* 3.5 30.9 - - + +
57A LYS* 3.2 22.1 + - - +
59A LEU* 4.5 4.3 - - - +
85A GLU* 5.1 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A SER 3.4 4.4 + - - -
12A LEU 3.2 0.6 - - - -
13A GLU* 1.3 76.7 - - - +
15A CYS* 1.3 58.8 + - - +
17A LEU* 3.3 11.7 + - - +
18A GLU* 2.8 30.1 + - - +
86A LEU* 3.8 4.0 - - - +
89A PHE* 3.6 39.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 5.0 3.4 - - - -
11A SER* 3.2 25.9 + - - -
12A LEU* 3.6 11.7 - - + +
14A GLY* 1.3 74.1 - - - +
16A VAL* 1.3 58.0 + - - +
18A GLU* 3.2 9.1 + - - +
19A ILE* 2.9 34.1 + - + +
34A LEU* 4.2 20.0 - - + -
37A LEU* 5.8 4.0 - - + -
39A PHE* 4.9 15.7 - - - -
89A PHE* 4.0 8.9 - - - -
90A TRP* 5.4 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 3.0 19.1 + - + +
13A GLU 3.4 8.1 - - - +
15A CYS* 1.3 72.6 - - - +
17A LEU* 1.3 60.2 + - - +
19A ILE* 2.9 9.3 + - - +
20A ILE* 2.8 50.4 + - + +
30A ILE* 4.2 21.3 - - + -
34A LEU* 4.2 13.7 - - + -
47A VAL* 5.0 3.8 - - + -
50A ILE* 3.9 28.0 - - + -
51A LEU* 4.2 9.2 - - + -
54A LEU* 4.0 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLU* 3.0 24.5 + - + +
14A GLY* 3.5 14.4 - - - +
16A VAL* 1.3 75.5 - - - +
18A GLU* 1.3 63.3 + - - +
20A ILE* 3.4 3.1 + - - -
21A SER* 3.0 23.6 + - - -
54A LEU* 4.0 32.1 - - + -
59A LEU* 4.5 11.7 - - + -
78A LEU* 3.5 32.4 - - + +
82A GLY 4.3 8.7 - - - +
85A GLU* 4.1 25.1 - - + +
86A LEU* 4.0 22.7 - - + +
89A PHE* 5.5 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLY 2.8 13.8 + - - +
15A CYS* 3.4 11.0 - - - +
17A LEU* 1.3 77.2 - - - +
19A ILE* 1.3 62.7 + - + +
21A SER* 2.7 27.2 + - - -
22A ARG* 2.9 48.0 + - - +
86A LEU* 3.4 20.3 - - + +
90A TRP* 2.8 39.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A CYS* 2.9 18.7 + - + +
16A VAL* 2.9 6.2 + - - +
18A GLU* 1.3 78.9 - - + +
20A ILE* 1.3 63.2 + - - +
21A SER 3.2 1.0 + - - -
22A ARG* 3.2 25.3 + - + +
23A ARG* 4.1 4.3 + - - +
25A THR* 4.5 6.0 - - + +
29A GLU* 5.5 1.1 - - + +
30A ILE* 4.1 33.4 - - + +
33A HIS* 4.0 43.3 - - + +
34A LEU* 3.6 38.1 - - + -
37A LEU* 6.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 2.8 42.0 + - + +
17A LEU* 3.9 5.4 - - - +
19A ILE* 1.3 72.0 - - - +
21A SER* 1.3 61.3 + - - +
23A ARG* 3.1 17.0 + - - +
25A THR* 3.9 11.9 - - + -
30A ILE* 3.9 17.5 - - + -
51A LEU* 3.8 19.5 - - + -
54A LEU* 4.0 13.0 - - + -
60A VAL* 4.3 9.2 - - + -
76A TYR* 3.6 13.0 - - + +
77A SER* 3.5 38.6 - - - +
78A LEU* 3.8 8.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU 3.0 7.9 + - - -
18A GLU* 2.7 29.9 + - - -
19A ILE 3.1 0.6 - - - -
20A ILE* 1.3 78.3 - - - +
22A ARG* 1.3 63.8 + - - +
23A ARG* 3.4 1.6 + - - -
78A LEU* 3.4 31.8 - - - +
86A LEU* 3.8 12.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 2.9 50.1 + - - +
19A ILE* 3.2 14.0 + - - +
21A SER* 1.3 80.0 - - - +
23A ARG* 1.3 70.6 + - + +
33A HIS* 4.8 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE 4.1 1.5 + - - +
20A ILE 3.1 15.9 - - - +
21A SER 3.3 3.4 - - - -
22A ARG* 1.3 89.3 - - + +
24A GLU* 1.3 90.1 + - - +
25A THR* 3.2 13.5 + - - +
29A GLU* 2.9 36.2 + - - -
77A SER* 5.3 0.4 - - - -
----------------------------------------------------------
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