Contacts of the helix formed by residues 2 - 24 (chain B) in PDB entry 1JS6
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 ASN 2 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLU* 5.0 2.6 + - - -
86A TYR* 3.4 13.5 - - - -
454A LYS* 4.2 13.0 - - - +
1B MET* 1.3 75.7 - - - +
3B ALA* 1.3 66.1 + - - +
4B SER* 2.8 35.8 + - - +
5B ASP* 2.5 33.6 + - - +
6B PHE* 3.1 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 3 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA* 4.1 15.8 - - + +
22A GLU* 2.9 40.6 - - + +
86A TYR* 3.5 25.5 + - - +
454A LYS* 3.7 8.3 - - - +
2B ASN* 1.3 74.0 - - - +
4B SER* 1.3 60.7 + - - +
6B PHE* 3.2 3.5 + - - +
7B ARG* 3.1 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 4 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLU* 4.0 4.5 + - - -
2B ASN* 2.8 27.1 + - - +
3B ALA* 1.3 78.5 - - - +
5B ASP* 1.3 75.4 + - - +
7B ARG* 3.1 24.5 + - - +
8B ARG* 3.4 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 5 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.4 25.9 - - + +
2B ASN* 2.5 30.5 + - - +
4B SER* 1.3 85.7 + - - +
6B PHE* 1.3 57.7 + - - +
8B ARG* 3.1 15.4 + - - +
9B ARG* 2.8 38.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 6 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 3.7 27.7 - - + +
17A MET* 3.5 45.8 - - + -
18A ALA* 4.5 9.0 - - + -
86A TYR* 3.1 52.5 - + + -
89A MET* 4.4 10.3 - - + -
90A LEU* 3.9 29.8 - - + -
93A MET* 4.9 7.0 - - - -
1B MET* 3.1 12.5 - - + +
2B ASN 3.1 3.9 + - - +
3B ALA 3.2 6.7 + - - +
5B ASP* 1.3 73.4 - - - +
7B ARG* 1.3 60.8 + - - +
10B GLY* 2.6 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 7 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 3.9 9.0 - - - -
15A ASP* 3.1 37.6 + - - +
18A ALA* 3.2 34.2 - - + +
19A ASP* 2.9 28.3 + - - -
22A GLU* 2.6 30.9 + - - -
3B ALA 3.1 17.0 + - - +
4B SER* 3.1 12.6 + - - +
6B PHE* 1.3 75.4 - - - +
8B ARG* 1.3 65.1 + - - +
11B LYS* 3.1 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B SER 3.4 6.9 + - - +
5B ASP* 3.1 17.3 + - - +
7B ARG* 1.3 83.8 - - - +
9B ARG* 1.3 109.9 + - - +
11B LYS* 3.0 11.0 + - - +
12B GLU* 3.0 32.0 + - + +
54B GLU* 4.1 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 9 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 3.9 13.9 - - + -
368A MET* 6.3 0.4 - - - -
1B MET* 4.2 16.8 - - + -
5B ASP* 2.8 27.6 + - + +
8B ARG* 1.3 113.6 - - - +
10B GLY* 1.3 63.7 + - - +
12B GLU* 2.9 23.7 + - - +
13B MET* 2.9 22.7 + - - +
52B THR* 4.5 2.6 - - - +
53B PHE* 3.5 38.4 - - + +
54B GLU* 2.7 40.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 10 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 4.0 10.5 - - - -
90A LEU* 3.6 18.9 - - - +
93A MET* 3.9 4.3 - - - +
6B PHE* 2.6 33.8 + - - -
9B ARG* 1.3 74.6 - - - +
11B LYS* 1.3 59.2 + - - +
13B MET* 3.4 3.6 + - - +
14B VAL* 3.2 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 11 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 3.5 56.3 - - + -
14A VAL* 4.3 7.6 - - + -
15A ASP* 2.8 41.3 + - - -
7B ARG* 3.1 26.3 + - - +
8B ARG* 3.0 6.1 + - - +
10B GLY* 1.3 73.8 - - - +
12B GLU* 1.3 67.2 + - - +
14B VAL* 3.2 16.3 + - - +
15B ASP* 3.2 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 12 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ARG* 3.0 36.7 + - + +
9B ARG* 2.9 25.0 + - - +
11B LYS* 1.3 76.6 - - + +
13B MET* 1.3 65.0 + - - +
15B ASP* 3.0 11.9 + - - +
16B TYR* 2.9 21.2 + - - +
53B PHE* 3.3 30.8 - - + -
54B GLU* 5.3 2.8 - - - +
57B LEU* 5.5 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 3.8 33.4 - - + +
93A MET* 3.9 20.6 - - + -
94A LEU* 4.2 18.4 - - + -
364A PHE* 4.0 19.1 - - + -
9B ARG 2.9 10.6 + - - +
10B GLY 3.5 9.6 - - - +
12B GLU* 1.3 77.7 - - - +
14B VAL* 1.3 56.4 + - - +
16B TYR* 3.2 23.2 + - - +
17B MET* 2.8 33.6 + - - +
53B PHE* 4.0 11.6 - - + -
57B LEU* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PHE* 3.7 34.9 - - + +
7A ARG* 4.0 18.6 - - - +
10A GLY* 3.9 13.2 - - - +
11A LYS* 4.2 5.2 - - + +
14A VAL* 3.9 15.9 - - + -
93A MET* 3.5 17.7 - - + -
10B GLY 3.2 16.1 + - - +
11B LYS* 3.4 9.6 - - - +
12B GLU 3.1 0.6 - - - -
13B MET* 1.3 76.6 - - - +
15B ASP* 1.3 57.5 + - - +
17B MET* 3.2 10.5 + - - +
18B ALA* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ARG* 3.1 31.9 + - - +
11A LYS* 2.9 37.3 + - - -
11B LYS 3.2 4.8 + - - +
12B GLU* 3.0 11.8 + - - +
14B VAL* 1.3 78.2 - - - +
16B TYR* 1.3 58.2 + - - +
18B ALA* 3.3 0.7 + - - -
19B ASP* 2.8 41.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
94A LEU* 3.6 31.0 - - + -
12B GLU 2.9 11.0 + - - +
13B MET* 3.3 22.0 - - - +
15B ASP* 1.3 74.8 - - - +
17B MET* 1.3 69.2 + - - +
19B ASP* 3.1 11.7 + - + +
20B TYR* 2.9 31.2 + - + +
57B LEU* 4.2 30.5 - - + -
60B VAL* 3.4 24.9 - - + +
61B GLU* 3.3 37.8 + - + +
65B MET* 3.7 12.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PHE* 3.5 28.5 - - + -
93A MET* 3.4 62.6 - - + +
94A LEU* 4.8 0.9 - - - -
97A ALA* 3.7 19.7 - - + -
13B MET* 2.8 25.9 + - - +
14B VAL* 3.5 8.7 - - - +
16B TYR* 1.3 80.6 - - + +
18B ALA* 1.3 62.8 + - - +
20B TYR* 3.3 3.3 + - - +
21B LEU* 2.9 35.3 + - + +
89B MET* 4.0 24.0 - - + -
93B MET* 5.4 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ALA* 4.1 15.1 - - + +
6A PHE* 4.5 9.8 - - + -
7A ARG* 3.2 45.5 - - + +
14B VAL 2.9 15.4 + - - +
17B MET* 1.3 76.6 - - - +
19B ASP* 1.3 56.3 + - - +
21B LEU* 3.8 0.9 - - - +
22B GLU* 2.8 33.6 + - - +
86B TYR* 4.9 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ARG* 3.0 26.2 + - - +
15B ASP* 2.8 34.2 + - - +
16B TYR* 3.5 11.6 - - + +
18B ALA* 1.3 73.2 - - - +
20B TYR* 1.3 65.0 + - - +
22B GLU* 3.0 4.5 + - - +
23B GLY* 2.8 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 6.4 1.6 - - + -
97A ALA* 3.7 24.5 - - + -
98A ILE* 3.9 22.0 + - + -
16B TYR* 2.9 25.5 + - + +
17B MET* 3.6 4.3 - - - +
19B ASP* 1.3 77.3 - - - +
21B LEU* 1.3 80.1 + - + +
23B GLY 3.7 1.0 - - - -
24B ILE* 3.0 42.5 + - + +
27B ARG* 4.0 23.7 + - + +
65B MET* 3.4 28.9 - - + -
68B VAL* 4.5 2.9 - - - +
70B HIS* 2.5 46.6 + + - +
71B TRP 5.4 0.2 + - - -
72B HIS* 5.4 0.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ALA* 3.9 26.0 - - + +
17B MET* 2.9 34.9 + - + +
18B ALA 4.1 0.7 - - - +
20B TYR* 1.3 101.2 - - + +
22B GLU* 1.3 65.8 + - - +
23B GLY 3.4 0.7 + - - -
24B ILE* 3.4 30.7 + - + +
72B HIS* 4.6 11.4 - - + -
84B SER* 5.3 4.5 - - - +
86B TYR* 3.6 31.9 - - + +
89B MET* 4.9 7.4 - - + -
453B ARG* 5.3 7.0 - - - +
454B LYS* 5.0 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ASN* 5.1 3.3 + - - -
3A ALA* 3.0 29.9 - - + +
4A SER* 4.1 7.1 + - - -
7A ARG* 2.5 30.1 + - - -
18B ALA 2.8 20.5 + - - +
19B ASP* 3.5 3.9 - - - +
21B LEU* 1.3 75.9 - - - +
23B GLY* 1.3 57.4 + - - +
24B ILE* 3.8 0.5 + - - +
25B GLU* 5.0 2.3 + - - +
454B LYS* 5.4 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ASP 2.8 14.3 + - - -
20B TYR 3.7 2.0 - - - -
22B GLU* 1.3 76.9 - - - +
24B ILE* 1.3 58.4 + - - +
25B GLU* 3.0 4.3 - - - -
26B GLY* 2.8 25.6 + - - -
27B ARG* 4.1 4.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR* 3.0 46.6 + - + +
21B LEU* 3.4 19.0 + - + +
22B GLU 3.5 0.6 - - - +
23B GLY* 1.3 76.1 - - - +
25B GLU* 1.3 61.9 + - + +
26B GLY 3.0 0.4 - - - -
27B ARG* 3.0 35.9 + - + +
70B HIS* 4.2 5.4 - - + -
72B HIS* 3.3 50.3 - - + +
73B SER* 3.5 16.8 - - - +
74B PRO* 4.3 5.6 - - + -
----------------------------------------------------------
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