Contacts of the helix formed by residues 6 - 28 (chain A) in PDB entry 1JRJ
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 PHE 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A GLY* 3.2 27.0 + - - -
5A THR* 1.3 75.4 - - - +
7A THR* 1.3 88.1 + - + +
8A SER 3.2 2.5 - - - -
9A ASP* 3.2 8.1 + - - +
10A LEU* 2.8 48.9 + - + +
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Residues in contact with THR 7 (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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4A GLY 4.6 3.7 + - - -
6A PHE* 1.3 104.5 - - + +
8A SER* 1.3 57.1 + - - +
10A LEU* 4.0 7.2 - - + -
11A SER* 2.9 33.3 + - - +
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Residues in contact with SER 8 (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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5A THR* 4.5 22.2 - - - +
6A PHE 3.2 0.8 - - - +
7A THR* 1.3 80.8 - - - +
9A ASP* 1.3 59.9 + - - +
11A SER* 3.8 9.4 + - - -
12A LYS* 3.8 13.0 + - - +
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Residues in contact with ASP 9 (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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5A THR 5.2 2.9 - - - +
6A PHE* 3.2 11.3 + - - +
8A SER* 1.3 76.7 - - - +
10A LEU* 1.3 60.5 + - - +
12A LYS* 3.3 9.1 + - - +
13A GLN* 2.9 45.3 + - - +
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Residues in contact with LEU 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* 2.8 41.5 + - + +
7A THR* 3.3 8.9 + - + +
9A ASP* 1.3 77.0 - - - +
11A SER* 1.3 62.4 + - - +
13A GLN* 3.3 15.6 + - + +
14A MET* 3.0 44.5 + - + +
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Residues in contact with SER 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A THR* 2.9 19.6 + - - +
8A SER* 3.9 6.7 - - - -
10A LEU* 1.3 78.4 - - - +
12A LYS* 1.3 62.3 + - - +
14A MET* 3.5 17.4 + - - +
15A GLU* 3.6 7.3 + - - +
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Residues in contact with LYS 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 SER 3.8 9.7 + - - +
9A ASP* 3.3 12.8 + - - +
11A SER* 1.3 77.6 - - - +
13A GLN* 1.3 65.7 + - + +
15A GLU* 3.0 14.7 + - + +
16A GLU* 2.9 36.3 - - - +
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Residues in contact with GLN 13 (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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9A ASP* 2.9 33.5 + - - +
10A LEU* 3.6 18.4 + - + +
12A LYS* 1.3 76.4 - - - +
14A MET* 1.3 63.6 + - - +
16A GLU* 3.1 13.6 + - + +
17A GLU* 3.0 23.8 + - - +
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Residues in contact with MET 14 (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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10A LEU* 3.0 32.7 + - + +
11A SER* 3.5 13.2 - - - +
13A GLN* 1.3 76.3 - - - +
15A GLU* 1.3 61.1 + - - +
17A GLU* 3.3 16.7 + - - +
18A ALA* 3.4 12.0 + - - +
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Residues in contact with GLU 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 SER 3.6 7.3 + - - +
12A LYS* 3.0 12.2 + - + +
14A MET* 1.3 75.7 - - - +
16A GLU* 1.3 71.8 + - - +
18A ALA* 3.3 19.0 + - - +
19A VAL* 3.3 21.0 + - - +
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Residues in contact with GLU 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 LYS* 2.9 49.7 + - - +
13A GLN* 3.1 14.9 + - + +
15A GLU* 1.3 81.6 - - - +
17A GLU* 1.3 64.7 + - - +
19A VAL* 3.1 21.1 + - + +
20A ARG* 3.3 17.3 + - - +
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Residues in contact with GLU 17 (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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13A GLN 3.0 12.0 + - - +
14A MET* 3.5 14.6 - - - +
15A GLU 3.3 0.2 - - - -
16A GLU* 1.3 76.4 - - - +
18A ALA* 1.3 61.9 + - - +
20A ARG* 3.2 37.9 + - - +
21A LEU* 3.2 29.5 + - + +
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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 MET 3.4 8.2 + - - +
15A GLU* 3.3 19.6 + - - +
16A GLU 3.2 0.6 - - - -
17A GLU* 1.3 78.4 - - - +
19A VAL* 1.3 61.9 + - + +
21A LEU* 3.3 9.5 + - - +
22A PHE* 3.0 23.3 + - - +
38A PRO 4.4 8.5 - - - +
39A SER* 5.8 4.5 - - - +
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Residues in contact with VAL 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 GLU* 3.3 22.9 - - - +
16A GLU* 3.1 14.3 + - + +
18A ALA* 1.3 77.2 - - + +
20A ARG* 1.3 52.0 + - - +
22A PHE* 3.2 12.0 + - + +
23A ILE* 2.8 58.1 + - + +
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Residues in contact with ARG 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 GLU* 3.3 12.9 + - - +
17A GLU* 3.2 33.4 + - - +
19A VAL* 1.3 79.3 - - - +
21A LEU* 1.3 57.2 + - + +
23A ILE* 3.3 14.4 + - + +
24A GLU* 2.9 29.2 + - - +
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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 GLU* 3.2 36.1 + - + +
18A ALA* 3.6 11.2 - - - +
20A ARG* 1.3 78.6 - - + +
22A PHE* 1.3 57.5 + - - +
24A GLU* 3.3 11.3 + - - +
25A TRP* 2.9 24.4 + - - +
38A PRO* 3.2 29.4 - - + +
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Residues in contact with PHE 22 (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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18A ALA 3.0 13.5 + - - +
19A VAL* 3.5 15.9 - - + +
21A LEU* 1.3 75.9 - - - +
23A ILE* 1.3 68.9 + - + +
25A TRP* 3.2 35.2 + + - +
26A LEU* 3.0 50.2 + - + +
37A PRO* 5.3 3.4 - - + -
38A PRO* 3.4 20.3 - - + +
39A SER* 6.1 1.1 - - - -
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Residues in contact with ILE 23 (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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19A VAL* 2.8 48.4 + - + +
20A ARG* 3.5 13.9 - - + +
21A LEU 3.3 0.2 - - - -
22A PHE* 1.3 82.2 - - + +
24A GLU* 1.3 63.4 + - - +
26A LEU* 3.2 10.4 + - + +
27A LYS* 3.1 35.5 + - + +
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Residues in contact with GLU 24 (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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20A ARG 2.9 16.3 + - - +
21A LEU* 3.6 11.4 - - - +
23A ILE* 1.3 77.3 - - - +
25A TRP* 1.3 63.7 + - - +
27A LYS* 3.2 14.5 + - + +
28A ASN* 3.2 24.4 + - + +
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Residues in contact with TRP 25 (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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21A LEU 2.9 9.1 + - - +
22A PHE* 3.2 27.8 + + - +
24A GLU* 1.3 77.6 - - - +
26A LEU* 1.3 87.3 + - + +
28A ASN* 2.6 45.0 - - - +
30A GLY 2.8 31.5 + - - -
31A PRO* 3.3 28.9 - - + -
33A SER* 5.1 0.2 - - - -
35A ALA* 3.0 27.5 + - + -
36A PRO* 3.2 13.2 + - + -
37A PRO* 3.4 35.7 - - + -
38A PRO* 3.3 23.6 - - + -
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Residues in contact with LEU 26 (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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22A PHE* 3.0 49.5 + - + +
23A ILE* 3.2 11.2 + - + +
25A TRP* 1.3 100.2 - - + +
27A LYS* 1.3 65.5 + - - +
29A GLY* 3.2 11.8 + - - -
30A GLY* 3.6 13.0 + - - +
31A PRO* 4.4 6.1 - - + -
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Residues in contact with LYS 27 (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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23A ILE* 3.1 26.1 + - + +
24A GLU* 3.2 16.3 + - + +
26A LEU* 1.3 78.3 - - - +
28A ASN* 1.3 59.6 + - - +
29A GLY* 3.1 0.9 + - - -
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Residues in contact with ASN 28 (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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24A GLU* 3.2 11.0 + - + +
25A TRP* 2.6 49.4 + - - +
27A LYS* 1.3 75.4 - - - +
29A GLY* 1.3 57.0 + - - +
30A GLY 3.3 0.2 + - - -
33A SER* 2.7 41.4 + - - +
35A ALA* 5.9 2.8 - - - +
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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
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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