Contacts of the helix formed by residues 10 - 25 (chain J) in PDB entry 1EA4
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 SER 10 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2H LYS* 3.3 19.1 + - - +
33H SER* 5.7 0.4 + - - -
9J LEU* 1.3 73.2 - - - +
11J GLU* 1.3 68.0 + - - +
12J SER* 3.8 12.1 - - - -
13J VAL* 2.8 10.2 + - - +
14J LEU* 2.7 21.6 + - - -
22K ARG 5.4 1.1 - - - -
25K GLY* 3.1 40.8 + - - -
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Residues in contact with GLU 11 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2H LYS* 4.9 5.5 - - - +
3H LYS* 2.9 46.0 - - + +
9J LEU 3.5 3.8 + - - -
10J SER* 1.3 69.4 - - - +
12J SER* 1.3 55.7 + - - +
14J LEU* 3.3 6.6 - - - +
15J GLU* 2.6 70.6 + - - +
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Residues in contact with SER 12 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H GLU* 5.6 0.4 + - - -
10J SER* 3.8 8.0 - - - -
11J GLU* 1.3 80.6 - - - +
13J VAL* 1.3 75.4 + - - +
15J GLU* 3.1 12.9 + - - +
16J ASN* 2.8 29.3 + - - +
22K ARG 4.5 7.3 + - - -
23K GLU 4.5 8.4 + - - -
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Residues in contact with VAL 13 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H SER* 4.6 11.4 - - - -
36H LEU* 4.1 27.8 - - + -
37H GLU* 3.5 30.0 + - - +
9J LEU* 4.7 6.1 - - + -
10J SER* 2.8 27.2 + - - +
12J SER* 1.3 85.8 + - - +
14J LEU* 1.3 55.0 + - - +
16J ASN* 3.2 8.2 + - - +
17J LEU* 2.7 36.3 + - - +
23K GLU 4.8 0.4 - - - +
24K MET 4.0 5.4 - - - +
25K GLY* 4.0 16.6 - - - +
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Residues in contact with LEU 14 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3H LYS* 3.5 44.6 - - + -
4H ARG 5.5 2.7 - - - +
5H LEU* 4.4 13.7 - - + -
9J LEU* 4.2 16.9 - - + +
10J SER 2.7 15.2 + - - +
11J GLU* 3.3 8.7 - - - +
13J VAL* 1.3 73.5 - - - +
15J GLU* 1.3 67.9 + - + +
17J LEU* 3.0 22.4 + - + +
18J GLU* 2.8 43.6 + - + +
28J LYS* 4.2 9.6 - - - -
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Residues in contact with GLU 15 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J GLU* 2.6 55.6 + - - +
12J SER* 3.3 10.9 - - - +
14J LEU* 1.3 73.1 - - + +
16J ASN* 1.3 61.6 + - - +
18J GLU* 2.8 10.9 + - - +
19J LYS* 2.6 57.6 + - - +
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Residues in contact with ASN 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H LEU* 4.8 6.7 - - - +
37H GLU* 4.7 9.3 + - - +
40H LYS* 3.1 42.8 - - - +
12J SER 2.8 15.5 + - - +
13J VAL* 3.5 11.2 + - - +
15J GLU* 1.3 72.6 - - - +
17J LEU* 1.3 71.0 + - - +
19J LYS* 2.9 12.2 + - - +
20J MET* 2.8 52.8 + - - +
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Residues in contact with LEU 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5H LEU* 4.3 3.8 - - + -
36H LEU* 4.2 19.7 - - + -
9J LEU* 3.7 28.5 - - + -
13J VAL 2.7 16.3 + - - +
14J LEU* 3.0 11.7 - - + +
16J ASN* 1.3 82.2 - - - +
18J GLU* 1.3 67.6 + - - +
19J LYS 2.8 0.2 + - - -
20J MET* 2.9 6.0 + - - +
21J ALA* 2.9 21.8 + - + +
28J LYS* 3.8 39.7 - - + +
31J MET* 3.8 30.1 - - + -
32J ILE* 4.3 9.9 - - + -
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Residues in contact with GLU 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14J LEU* 2.8 32.7 + - + +
15J GLU* 2.8 13.9 + - - +
17J LEU* 1.3 72.9 - - - +
19J LYS* 1.3 85.8 + - + +
21J ALA* 3.5 5.9 + - - +
22J ARG* 3.0 44.4 + - - +
28J LYS* 3.6 31.2 + - - +
201W T 3.5 21.0 - - + +
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Residues in contact with LYS 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J GLU* 2.6 49.5 + - - +
16J ASN* 3.1 12.6 - - - +
17J LEU 2.8 0.8 + - - -
18J GLU* 1.3 99.9 + - + +
20J MET* 1.3 64.3 + - + +
22J ARG* 3.0 12.5 + - + +
23J GLU* 3.0 35.9 + - + +
201W T 3.5 23.5 - - - -
202W A 6.4 2.5 - - - -
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Residues in contact with MET 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H LEU* 4.3 26.7 - - + +
39H TYR* 3.7 35.0 - - + -
40H LYS* 4.2 12.6 - - + -
43H GLN* 6.2 2.5 - - - -
16J ASN* 2.8 50.4 + - - +
17J LEU* 3.7 6.3 - - - +
19J LYS* 1.3 69.9 - - + +
21J ALA* 1.3 65.5 + - - +
23J GLU* 3.2 15.2 + - - +
24J MET* 3.0 34.9 + - - +
31J MET* 3.9 14.1 - - + -
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Residues in contact with ALA 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J LEU 2.9 11.1 + - - +
18J GLU* 3.6 12.1 - - - +
20J MET* 1.3 75.6 - - - +
22J ARG* 1.3 67.6 + - - +
24J MET 3.0 2.9 + - - -
25J GLY 2.8 20.6 + - - -
26J LEU 3.1 29.4 + - - +
27J SER 4.3 5.6 - - - +
28J LYS* 4.5 8.3 - - + +
31J MET* 3.9 23.0 - - + -
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Residues in contact with ARG 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G LYS* 4.5 3.1 + - - -
18J GLU* 3.0 35.3 + - - +
19J LYS* 3.1 11.4 - - + +
21J ALA* 1.3 82.9 - - - +
23J GLU* 1.3 65.9 + - + +
25J GLY* 3.2 10.8 + - - -
28J LYS* 5.8 3.6 - - - +
201W T 3.7 17.8 + - - -
202W A 3.4 33.3 + - - -
203W A 4.1 39.3 + - - +
204W C 4.4 20.9 + - - +
221X T 5.8 1.0 + - - -
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Residues in contact with GLU 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G LYS* 3.6 14.3 + - - +
19J LYS* 3.0 32.6 + - - +
20J MET* 3.2 16.0 + - - +
22J ARG* 1.3 82.1 - - + +
24J MET* 1.3 65.3 + - + +
25J GLY 3.5 0.9 + - - -
204W C 4.3 13.7 - - - +
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Residues in contact with MET 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G ALA* 4.5 5.5 - - - +
39H TYR* 3.0 32.8 - - - +
43H GLN* 5.4 3.1 - - + +
20J MET* 3.0 21.4 + - - +
21J ALA 3.9 1.3 - - - +
23J GLU* 1.3 81.1 - - + +
25J GLY* 1.3 62.4 + - - +
26J LEU* 3.2 24.9 + - + +
31J MET* 3.7 22.2 - - + +
34J VAL* 5.7 1.8 - - + -
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Residues in contact with GLY 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G SER* 3.1 36.7 + - - -
30G ALA* 3.5 16.7 - - - +
21J ALA 2.8 5.4 + - - -
22J ARG 3.2 10.6 + - - -
23J GLU 3.3 1.6 + - - -
24J MET* 1.3 79.7 - - - +
26J LEU* 1.3 60.6 + - - +
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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