Contacts of the helix formed by residues 6 - 22 (chain B) in PDB entry 2ISZ
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 ASP 6 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.2 33.8 + - + +
4B LEU* 2.8 10.8 + - - -
5B VAL* 1.3 77.1 - - - +
7B THR* 1.3 59.2 + - - +
8B THR* 3.3 10.7 + - - -
9B GLU* 3.2 37.2 + - - +
10B MET* 3.0 30.7 + - - +
106B HIS* 3.7 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 7 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET 4.7 0.6 - - - +
2B ASN* 2.6 31.0 + - - +
4B LEU* 3.8 11.1 - - + +
6B ASP* 1.3 69.5 + - - +
8B THR* 1.3 66.8 + - - +
10B MET* 3.3 1.2 + - - -
11B TYR* 2.9 48.9 + - + -
44B THR* 3.8 18.4 - - + +
19E C 3.7 26.5 + - - +
20E C 2.8 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ASP* 3.3 8.2 + - - -
7B THR* 1.3 80.5 - - - +
9B GLU* 1.3 61.9 + - + +
11B TYR* 3.2 9.8 + - - +
12B LEU* 3.0 30.5 + - + +
44B THR* 5.5 0.7 - - - +
48B MET* 3.7 16.9 - - + +
53B LEU* 3.4 32.1 - - + -
71B LEU* 4.7 5.8 - - + -
19E C 4.2 16.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 9 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ASP* 3.2 24.2 + - - +
8B THR* 1.3 78.3 - - + +
10B MET* 1.3 57.7 + - - +
12B LEU* 3.1 7.5 + - - +
13B ARG* 2.8 32.2 + - - +
71B LEU* 3.8 27.6 - - + +
75B VAL* 3.5 30.5 - - + +
78B LYS* 6.1 0.6 - - - -
105B GLU 5.0 0.2 - - - -
106B HIS* 3.1 48.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 10 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 3.5 31.4 - - + +
6B ASP 3.0 16.9 + - - +
7B THR 3.8 3.6 - - - +
9B GLU* 1.3 76.5 - - - +
11B TYR* 1.3 57.1 + - - +
13B ARG* 4.0 21.3 - - - +
14B THR* 2.6 39.5 + - - +
34B LEU* 3.8 24.9 - - + -
102B CYS* 3.9 9.9 - - - -
105B GLU* 3.0 6.7 - - - +
106B HIS* 3.2 14.8 - - + +
1002B NI 2.3 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 11 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 4.5 1.6 - - + -
7B THR* 2.9 37.5 + - + +
8B THR 3.4 9.2 - - - +
9B GLU 3.1 0.2 - - - -
10B MET* 1.3 76.2 - - - +
12B LEU* 1.3 63.7 + - - +
14B THR* 3.4 5.6 + - - -
15B ILE* 3.1 30.9 + - + +
30B ILE* 3.9 29.4 - - + +
34B LEU* 3.6 22.4 - - + -
36B GLN* 2.6 28.2 + - - -
40B THR 4.2 0.3 + - - -
41B VAL* 3.4 31.2 + - + +
44B THR* 3.6 30.5 + - + -
45B VAL* 4.1 7.9 - - + -
48B MET* 3.6 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 12 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B THR* 3.0 27.2 + - + +
9B GLU* 3.6 6.1 - - + +
11B TYR* 1.3 73.7 - - - +
13B ARG* 1.3 66.8 + - - +
15B ILE* 3.0 11.4 + - - +
16B TYR 3.0 16.1 + - - -
48B MET* 3.8 17.3 - - + -
53B LEU* 4.0 11.7 - - + +
64B LEU* 3.6 21.8 - - + +
68B GLY* 3.6 23.6 - - - +
71B LEU* 3.2 44.0 - - + -
72B ALA* 3.8 21.3 - - + +
75B VAL* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLU 2.8 19.8 + - - +
10B MET* 4.0 22.2 - - - +
12B LEU* 1.3 74.1 - - - +
14B THR* 1.3 59.4 + - - +
16B TYR* 3.0 8.8 + - + +
17B ASP* 2.8 53.0 + - - -
72B ALA* 4.3 4.8 - - - +
75B VAL* 4.3 9.4 - - + -
76B MET* 3.6 48.3 - - + +
79B HIS* 3.3 21.9 + - - -
98B HIS* 4.4 15.7 + - - -
102B CYS* 4.2 5.5 - - - -
105B GLU* 2.8 47.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B MET* 2.6 31.1 + - - +
11B TYR* 3.8 6.3 - - - -
12B LEU 3.2 0.4 - - - -
13B ARG* 1.3 76.7 + - - +
15B ILE* 1.3 57.9 + - - +
17B ASP* 3.3 15.4 + - + +
18B LEU* 3.1 40.0 + - + +
30B ILE* 4.3 17.3 - - + -
33B ARG* 4.0 27.5 - - + +
34B LEU* 3.6 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TYR* 3.1 17.8 + - + +
12B LEU 3.0 8.4 + - - +
14B THR* 1.3 75.6 - - - +
16B TYR* 1.3 62.1 + - - +
18B LEU* 3.5 9.3 + - + +
19B GLU* 3.1 31.0 + - - +
25B PRO* 4.1 11.7 - - + -
30B ILE* 4.2 15.7 - - + -
54B LEU* 3.8 23.1 - - + -
62B LEU* 4.0 35.2 - - + +
64B LEU* 3.7 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU 3.0 11.3 + - - +
13B ARG* 3.0 15.2 + - + +
15B ILE* 1.3 74.3 - - - +
17B ASP* 1.3 59.5 + - - +
19B GLU* 3.2 10.3 + - + +
20B GLU* 2.8 52.0 + - + +
64B LEU* 5.0 1.5 - - + +
69B ARG* 4.5 17.0 - - - -
72B ALA* 4.4 14.8 - - + -
73B ILE* 3.8 28.0 - - + +
76B MET* 3.5 34.8 - - + -
133B PRO* 3.2 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ARG* 2.8 41.5 + - - +
14B THR* 3.3 16.2 + - - +
16B TYR* 1.3 72.5 - - - +
18B LEU* 1.3 57.0 + - - +
20B GLU* 3.2 7.6 + - - +
21B GLU* 3.0 41.2 + - - +
33B ARG* 4.3 16.0 + - - +
76B MET* 2.9 25.7 - - - +
80B ARG* 4.9 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B THR* 3.1 30.0 + - + +
15B ILE* 3.9 7.9 - - + +
16B TYR 3.3 0.4 - - - -
17B ASP* 1.3 75.7 - - - +
19B GLU* 1.3 57.7 + - - +
21B GLU* 3.4 3.3 + - - +
22B GLY 3.0 6.9 + - - -
23B VAL* 2.8 63.5 + - + +
25B PRO* 4.2 14.4 - - + -
26B LEU 4.8 0.4 - - - +
29B ARG* 3.5 35.2 - - + -
30B ILE* 4.7 5.4 - - + +
33B ARG* 3.6 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE* 3.1 33.2 + - - +
16B TYR* 3.6 8.1 - - + +
18B LEU* 1.3 76.2 - - - +
20B GLU* 1.3 63.6 + - - +
22B GLY* 3.2 12.1 + - - -
23B VAL 4.5 1.6 - - - -
25B PRO* 3.7 20.4 - - + +
62B LEU 4.9 2.8 - - - +
63B GLU* 4.2 9.4 - - - +
64B LEU* 4.3 2.1 + - - +
69B ARG* 3.0 39.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TYR* 2.8 38.1 + - + +
17B ASP* 3.2 10.2 + - - +
19B GLU* 1.3 79.4 - - - +
21B GLU* 1.3 62.8 + - + +
22B GLY* 4.7 0.2 - - - -
80B ARG* 2.8 43.6 + - - -
130B ASN* 4.0 10.5 + - - -
131B PRO* 4.5 13.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ASP* 3.0 22.7 + - - +
18B LEU* 3.9 4.3 - - - +
20B GLU* 1.3 79.3 - - + +
22B GLY* 1.3 59.9 + - - +
23B VAL* 4.0 15.1 - - + +
33B ARG* 2.7 41.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU 3.0 3.9 + - - -
19B GLU* 3.2 12.4 + - - -
20B GLU 3.3 0.6 + - - -
21B GLU* 1.3 80.9 - - - +
23B VAL* 1.3 59.8 + - - +
24B THR 4.1 0.7 + - - -
----------------------------------------------------------
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