Contacts of the helix formed by residues 2 - 23 (chain A) in PDB entry 1JS3
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 1.3 75.8 - - - +
3A ALA* 1.3 60.3 + - - +
4A SER* 2.9 15.7 + - - -
5A ASP* 2.9 34.8 + - - +
6A PHE* 2.8 27.9 + - - +
86B TYR* 3.4 7.6 - - - -
801B SO4 3.6 19.5 - - - +
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Residues in contact with ALA 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ASN* 1.3 75.1 - - - +
4A SER* 1.3 58.0 + - - +
6A PHE* 3.2 3.1 + - - +
7A ARG* 2.9 33.5 + - - +
18B ALA* 4.1 10.2 - - + +
22B GLU* 3.5 30.1 - - + +
86B TYR* 3.3 27.5 - - - +
801B SO4 3.1 19.0 + - - +
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Residues in contact with SER 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ASN* 2.9 19.4 + - - -
3A ALA* 1.3 76.0 - - - +
5A ASP* 1.3 66.8 + - - +
7A ARG* 3.3 24.7 + - - +
8A ARG* 3.3 12.8 + - - +
22B GLU* 4.7 4.1 + - - -
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Residues in contact with ASP 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.2 24.3 - - + -
2A ASN* 2.9 42.7 + - - +
4A SER* 1.3 79.1 + - - +
6A PHE* 1.3 58.3 + - - +
8A ARG* 3.2 14.8 + - - +
9A ARG* 2.9 36.8 + - + +
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Residues in contact with PHE 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.1 6.9 - - + +
2A ASN 2.8 11.4 + - - +
3A ALA 3.5 6.7 - - - +
4A SER 3.2 0.2 - - - -
5A ASP* 1.3 74.7 - - - +
7A ARG* 1.3 60.2 + - - +
10A GLY* 2.6 36.0 + - - +
14B VAL* 3.8 37.4 - - + +
17B MET* 3.7 37.7 - - + -
18B ALA* 4.3 8.1 - - + -
86B TYR* 3.3 49.4 - + + -
89B MET* 4.3 10.3 - - + -
90B LEU* 3.9 31.4 - - + -
93B MET* 4.6 6.3 - - - -
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Residues in contact with ARG 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ALA 2.9 19.8 + - - +
4A SER* 3.3 14.5 + - - +
6A PHE* 1.3 77.3 - - - +
8A ARG* 1.3 58.4 + - - +
11A LYS* 3.0 36.3 - - - +
14B VAL* 3.8 9.9 - - + -
15B ASP* 3.0 43.8 + - - +
18B ALA* 3.4 16.7 - - + +
19B ASP* 2.6 39.5 + - - +
22B GLU* 2.8 28.7 + - - -
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Residues in contact with ARG 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER 3.3 7.5 + - - +
5A ASP* 3.2 15.9 + - - +
6A PHE 3.1 1.0 - - - -
7A ARG* 1.3 78.8 - - - +
9A ARG* 1.3 102.4 + - - +
11A LYS* 3.3 7.3 + - - +
12A GLU* 3.2 36.2 + - + +
54A GLU* 3.9 5.1 + - - -
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Residues in contact with ARG 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.8 18.8 - - + -
5A ASP* 2.9 25.7 + - + +
8A ARG* 1.3 100.6 - - - +
10A GLY* 1.3 61.2 + - - +
12A GLU* 3.0 34.1 + - - +
13A MET* 2.7 30.7 + - - +
52A THR* 5.6 0.4 - - - -
53A PHE* 3.6 37.7 - - + +
54A GLU* 2.5 42.2 + - - -
90B LEU* 3.9 15.6 - - + +
368B MET* 6.4 0.2 - - - -
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Residues in contact with GLY 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PHE* 2.6 28.9 + - - -
9A ARG* 1.3 71.9 - - - +
11A LYS* 1.3 55.6 + - - +
13A MET* 3.3 3.2 + - - +
14A VAL* 2.9 30.5 + - - +
14B VAL* 3.7 16.6 - - - -
90B LEU* 3.6 18.7 - - - +
93B MET* 3.7 3.6 - - - +
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Residues in contact with LYS 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ARG* 3.0 23.6 + - - +
8A ARG* 3.3 6.2 + - - +
9A ARG 3.2 0.6 - - - -
10A GLY* 1.3 73.6 - - - +
12A GLU* 1.3 64.8 + - - +
14A VAL* 3.3 9.5 + - - +
15A ASP* 3.2 26.0 + - - +
11B LYS* 3.7 45.5 - - + +
14B VAL* 4.1 7.9 - - + -
15B ASP* 2.8 39.1 + - - -
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Residues in contact with GLU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG* 3.2 31.4 + - + +
9A ARG* 3.0 43.5 + - - +
11A LYS* 1.3 74.5 - - + +
13A MET* 1.3 65.1 + - - +
15A ASP* 3.1 9.8 + - - +
16A TYR* 2.9 22.4 + - - +
53A PHE* 3.6 16.3 - - + -
54A GLU* 4.5 2.6 - - - +
57A LEU* 5.1 6.4 - - + +
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Residues in contact with MET 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG 2.7 19.2 + - - +
10A GLY 3.5 6.1 - - - +
12A GLU* 1.3 73.2 - - - +
14A VAL* 1.3 63.5 + - - +
16A TYR* 3.1 20.0 + - - +
17A MET* 2.8 35.3 + - - +
53A PHE* 4.2 10.3 - - + -
57A LEU* 3.9 20.0 - - + -
90B LEU* 3.7 34.5 - - + +
93B MET* 3.9 21.1 - - + -
94B LEU* 4.1 20.9 - - + -
364B PHE* 3.9 22.9 - - + -
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Residues in contact with VAL 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLY 2.9 19.2 + - - +
11A LYS* 3.4 10.3 - - - +
12A GLU 3.2 0.4 - - - -
13A MET* 1.3 77.9 - - - +
15A ASP* 1.3 62.5 + - - +
17A MET* 3.3 9.4 + - - +
18A ALA* 3.0 22.0 + - - +
93A MET* 4.5 0.4 - - + -
6B PHE* 3.8 25.1 - - + +
7B ARG* 3.8 31.6 - - - +
10B GLY* 3.7 26.9 - - - +
11B LYS* 4.1 5.8 - - + +
14B VAL* 4.1 2.9 - - + -
93B MET* 3.7 15.0 - - + -
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Residues in contact with ASP 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LYS 3.2 5.7 + - - +
12A GLU* 3.1 11.8 + - - +
14A VAL* 1.3 78.6 - - - +
16A TYR* 1.3 57.5 + - - +
18A ALA* 4.4 0.2 - - - -
19A ASP* 2.8 42.0 + - - +
7B ARG* 3.1 32.6 + - - +
11B LYS* 2.8 37.3 + - - -
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Residues in contact with TYR 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLU 2.9 13.7 + - - +
13A MET* 3.1 19.3 + - - +
15A ASP* 1.3 77.1 - - - +
17A MET* 1.3 57.6 + - - +
19A ASP* 3.4 9.8 + - + +
20A TYR* 2.9 32.5 + - + +
27A ARG* 4.6 1.2 + - - -
57A LEU* 4.2 33.7 - - + -
60A VAL* 3.5 24.4 - - + +
61A GLU* 2.8 31.0 + - + -
65A MET* 3.6 14.7 - - + +
94B LEU* 3.7 31.4 - - + -
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Residues in contact with MET 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A MET* 2.8 30.7 + - - +
14A VAL* 3.6 8.1 - - - +
16A TYR* 1.3 76.8 - - + +
18A ALA* 1.3 65.9 + - - +
20A TYR* 3.4 3.5 + - - +
21A LEU* 3.1 32.9 + - + +
89A MET* 3.8 26.2 - - + -
93A MET* 5.3 2.0 - - + -
6B PHE* 3.7 25.1 - - + -
93B MET* 3.3 58.1 - - + +
94B LEU* 4.6 1.3 - - - -
97B ALA* 3.7 20.4 - - + -
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Residues in contact with ALA 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL 3.0 16.4 + - - +
17A MET* 1.3 75.9 - - - +
19A ASP* 1.3 57.2 + - - +
21A LEU* 4.0 0.5 - - - +
22A GLU* 2.8 34.5 + - - +
86A TYR* 4.6 9.9 + - - -
3B ALA* 4.2 11.8 - - + +
6B PHE* 4.3 9.2 - - + -
7B ARG* 3.4 41.3 - - + +
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Residues in contact with ASP 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ASP* 2.8 31.5 + - - +
16A TYR* 3.6 10.4 - - + +
18A ALA* 1.3 73.0 - - - +
20A TYR* 1.3 57.1 + - - +
22A GLU* 3.9 2.2 - - - +
23A GLY* 2.9 28.9 + - - -
7B ARG* 2.6 34.5 + - - +
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Residues in contact with TYR 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A TYR* 2.9 27.1 + - + +
17A MET* 3.6 4.9 - - - +
18A ALA 3.3 0.2 - - - -
19A ASP* 1.3 77.0 - - - +
21A LEU* 1.3 84.0 + - + +
23A GLY 3.7 0.9 - - - -
24A ILE* 3.0 40.4 + - + +
27A ARG* 3.9 25.0 + - - +
65A MET* 3.5 26.5 - - + -
68A VAL* 4.3 4.5 - - - +
70A HIS* 2.6 47.8 + + - +
72A HIS* 5.5 0.6 + + - -
94B LEU* 6.3 1.1 - - + -
97B ALA* 3.4 29.2 - - + -
98B ILE* 3.8 18.7 + - + -
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Residues in contact with LEU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A MET 3.1 23.1 + - - +
18A ALA 4.1 0.2 - - - +
20A TYR* 1.3 90.8 - - + +
22A GLU* 1.3 59.8 + - - +
24A ILE* 3.2 13.1 - - + +
72A HIS* 4.3 20.9 - - + -
84A SER* 4.7 9.4 - - - +
86A TYR* 3.4 35.9 - - + +
89A MET* 4.2 11.7 - - + -
453A ARG* 4.9 4.5 - - - +
454A LYS* 2.4 35.0 + - - +
97B ALA* 3.6 38.1 - - + +
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Residues in contact with GLU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA 2.8 21.5 + - - +
19A ASP* 3.9 3.4 - - - +
21A LEU* 1.3 75.8 - - - +
23A GLY* 1.3 58.9 + - - +
24A ILE* 3.6 0.7 + - - +
25A GLU* 4.9 3.3 + - - +
86A TYR* 4.7 0.4 + - - -
454A LYS* 4.0 5.9 + - - +
802A SO4 4.5 7.5 + - - +
3B ALA* 3.5 23.7 - - + +
4B SER* 4.7 4.7 + - - -
7B ARG* 2.8 31.3 + - - -
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Residues in contact with GLY 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASP 2.9 19.8 + - - -
20A TYR 3.7 2.2 - - - -
22A GLU* 1.3 73.1 - - - +
24A ILE* 1.3 57.4 + - - +
25A GLU* 3.1 4.3 - - - -
26A GLY* 2.9 23.7 + - - -
27A ARG* 4.1 6.1 + - - +
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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
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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) + - + + + + + -
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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