Contacts of the helix formed by residues 13 - 25 (chain A) in PDB entry 1JQE
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 GLY 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A LYS* 1.3 69.8 + - - +
15A TYR* 3.3 9.8 - - - +
16A VAL* 3.8 4.6 + - - +
17A GLU* 3.4 19.6 + - - +
93A GLU* 3.8 18.9 - - - +
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Residues in contact with LYS 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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13A GLY* 1.3 75.0 - - - +
15A TYR* 1.3 60.4 + - + +
17A GLU* 4.3 13.5 - - + +
18A SER* 2.6 41.2 + - - +
239A LEU* 6.2 3.8 - - + +
248A CYS* 6.3 3.4 - - - -
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Residues in contact with TYR 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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13A GLY 3.3 6.8 - - - +
14A LYS* 1.3 82.8 - - + +
16A VAL* 1.3 60.0 + - + +
18A SER* 3.5 5.2 - - - -
19A PHE* 3.0 28.8 + - - +
248A CYS* 6.1 5.2 - - - -
500A QUN 3.3 103.0 - + + +
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Residues in contact with VAL 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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13A GLY* 3.8 5.2 + - - +
14A LYS 3.3 0.2 - - - -
15A TYR* 1.3 77.3 - - + +
17A GLU* 1.3 64.1 - - - +
19A PHE* 3.3 3.8 + - - +
20A ARG* 3.0 21.4 + - + +
91A SER* 3.7 24.9 - - - +
93A GLU* 3.4 33.4 - - + +
94A GLN* 3.4 29.2 - - + +
97A LYS* 4.1 11.2 - - - +
400A SAH 5.4 0.2 - - - +
500A QUN 3.5 19.5 - - + -
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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 GLY 3.4 14.9 + - - +
14A LYS* 3.3 20.5 + - + +
16A VAL* 1.3 79.9 - - - +
18A SER* 1.3 64.2 + - - +
20A ARG* 3.3 8.3 + - - +
21A ARG* 3.0 23.2 + - - +
93A GLU* 4.8 4.2 + - - +
97A LYS* 5.7 2.2 - - - +
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Residues in contact with SER 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 LYS* 2.6 25.5 + - - -
15A TYR* 3.5 7.4 - - - -
17A GLU* 1.3 74.3 - - - +
19A PHE* 1.3 61.3 + - - +
21A ARG* 3.2 10.8 + - - +
22A PHE 3.1 16.8 + - - -
239A LEU 4.7 4.0 + - - -
240A LEU* 5.7 0.3 - - - +
242A ASP* 5.4 1.6 - - - +
243A PHE* 3.1 37.4 + - - +
500A QUN 4.4 4.8 - - - +
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Residues in contact with PHE 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 TYR 3.0 16.6 + - - +
16A VAL* 3.3 4.9 + - + +
18A SER* 1.3 74.0 - - - +
20A ARG* 1.3 62.3 + - - +
22A PHE* 3.1 26.6 + + - +
23A LEU* 2.9 62.6 + - + +
28A GLU* 3.9 14.1 - - - -
94A GLN* 4.8 7.2 - - - -
143A GLN* 5.0 7.0 - - + -
147A TYR* 5.7 1.8 - - - -
243A PHE* 3.9 16.1 - + - -
400A SAH 3.6 47.8 - - + -
500A QUN 4.0 26.0 - - + +
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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 VAL* 3.0 13.4 + - + +
17A GLU* 3.6 11.7 - - - +
18A SER 3.2 0.2 - - - -
19A PHE* 1.3 77.6 - - - +
21A ARG* 1.3 57.7 + - - +
23A LEU* 3.3 30.8 + - - +
24A ASN* 2.9 56.1 + - - +
29A HIS* 4.8 2.6 + - - -
63A ALA* 3.3 19.8 - - - +
65A GLU* 2.8 32.1 + - - -
94A GLN* 5.0 3.4 + - - +
97A LYS* 4.2 24.9 - - - +
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Residues in contact with ARG 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 3.0 13.7 + - - +
18A SER* 3.5 12.0 - - - +
19A PHE 3.2 0.2 - - - -
20A ARG* 1.3 76.2 - - - +
22A PHE* 1.3 64.2 + - - +
24A ASN* 3.2 8.2 + - - -
25A HIS* 2.7 38.2 + - + +
235A GLU* 5.2 6.9 + - - +
236A ASN* 2.9 42.3 + - - +
239A LEU* 3.1 50.4 - - - +
240A LEU* 3.8 13.0 - - + -
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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 SER 3.1 5.6 + - - +
19A PHE* 3.3 27.8 - + - +
21A ARG* 1.3 78.2 - - - +
23A LEU* 1.3 64.2 + - + +
25A HIS 2.9 11.1 + - - -
26A SER* 2.9 41.0 + - - -
28A GLU* 3.3 40.4 - - + -
143A GLN* 5.2 1.6 - - - -
179A TRP* 4.4 4.0 - + - -
224A MET* 3.6 34.1 - - + -
240A LEU* 4.5 9.2 - - - +
243A PHE* 3.5 42.8 - + + -
283A ASN* 3.7 17.0 - - - -
500A QUN 6.4 1.1 - - + -
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Residues in contact with LEU 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 PHE* 2.9 57.5 + - + +
20A ARG* 3.6 42.6 - - - +
22A PHE* 1.3 83.2 - - + +
24A ASN* 1.3 65.0 + - - +
26A SER* 3.1 24.8 + - - +
28A GLU* 4.2 12.2 + - + +
29A HIS* 3.6 41.3 + - + +
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Residues in contact with ASN 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 46.7 + - - +
21A ARG* 3.5 8.6 - - - +
23A LEU* 1.3 77.7 - - - +
25A HIS* 1.3 76.1 + - + +
26A SER 3.6 1.4 + - - +
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Residues in contact with HIS 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 ARG* 2.7 33.3 + - + +
22A PHE 2.9 5.6 + - - +
24A ASN* 1.3 94.1 + - + +
26A SER* 1.3 55.1 + - - +
224A MET* 3.5 4.6 - - + +
225A ASP* 2.7 57.9 + - + +
228A ASP* 4.7 2.9 + - - -
236A ASN* 3.1 44.3 + - - -
240A LEU* 4.3 11.0 - - + -
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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