Contacts of the helix formed by residues 11 - 25 (chain D) 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 GLU 11 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D LEU 3.4 4.6 + - - -
10D SER* 1.3 68.4 - - - +
12D SER* 1.3 54.4 + - - +
14D LEU* 3.4 7.5 - - + +
15D GLU* 2.7 60.2 + - + +
1E MET 3.0 44.4 + - - +
2E LYS* 3.8 2.4 + - - +
3E LYS* 4.2 30.1 + - + +
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Residues in contact with SER 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D SER* 2.7 20.3 + - - -
11D GLU* 1.3 77.5 - - - +
13D VAL* 1.3 70.4 + - - +
15D GLU* 3.5 6.2 - - - +
16D ASN* 2.8 24.2 + - - +
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Residues in contact with VAL 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LEU* 3.7 22.2 - - + -
10D SER* 2.6 32.4 + - - +
12D SER* 1.3 78.1 + - - +
14D LEU* 1.3 65.0 + - - +
16D ASN* 3.0 7.0 + - + +
17D LEU* 2.7 21.6 + - + +
20D MET* 5.5 0.8 - - + +
33E SER* 4.1 19.1 - - - +
36E LEU* 4.0 20.6 - - + -
37E GLU* 3.1 32.8 - - + +
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Residues in contact with LEU 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D LEU* 4.5 18.8 - - + +
10D SER 2.8 15.4 + - - +
11D GLU* 3.4 11.4 - - + +
13D VAL* 1.3 74.7 - - - +
15D GLU* 1.3 62.5 + - + +
17D LEU* 2.9 24.4 + - + +
18D GLU* 2.7 37.5 + - + +
28D LYS* 5.4 4.5 - - - -
3E LYS* 3.1 38.6 - - + +
4E ARG 5.8 2.2 - - - +
5E LEU* 4.5 26.9 - - + -
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Residues in contact with GLU 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D GLU* 2.7 49.4 + - + +
12D SER* 3.5 5.7 + - - +
14D LEU* 1.3 76.7 - - + +
16D ASN* 1.3 64.7 + - - +
18D GLU* 3.0 15.0 + - + +
19D LYS* 2.8 22.0 + - - +
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Residues in contact with ASN 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D SER 2.8 16.6 + - - +
13D VAL* 3.4 11.7 - - + +
15D GLU* 1.3 71.1 - - - +
17D LEU* 1.3 52.9 + - - +
19D LYS* 2.9 16.8 + - - +
20D MET* 2.7 54.8 + - - +
37E GLU* 4.7 3.0 - - - +
40E LYS* 2.7 43.3 - - - +
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Residues in contact with LEU 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LEU* 4.7 11.9 - - + -
13D VAL 2.7 16.2 + - - +
14D LEU* 3.0 24.9 - - + +
16D ASN* 1.3 71.1 - - - +
18D GLU* 1.3 66.3 + - - +
19D LYS 2.8 0.9 + - - -
20D MET* 2.9 11.8 + - - +
21D ALA* 2.8 23.4 + - + +
28D LYS* 4.2 33.9 - - + +
31D MET* 3.5 35.4 - - + -
32D ILE* 4.5 15.7 - - + -
5E LEU* 4.8 3.6 - - + -
36E LEU* 3.8 21.3 - - + -
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Residues in contact with GLU 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LEU* 2.7 23.6 + - + +
15D GLU* 3.0 17.5 - - + +
17D LEU* 1.3 74.9 - - - +
19D LYS* 1.3 63.6 + - - +
21D ALA* 3.6 2.0 + - - +
22D ARG* 3.0 34.7 + - - +
28D LYS* 2.9 44.4 + - - +
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Residues in contact with LYS 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D GLU 2.8 12.0 + - - +
16D ASN* 2.9 20.4 + - - +
17D LEU 2.8 0.4 + - - -
18D GLU* 1.3 76.5 - - - +
20D MET* 1.3 63.4 + - - +
22D ARG* 3.1 27.0 + - - +
23D GLU* 2.5 65.5 + - - +
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Residues in contact with MET 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D VAL* 5.5 1.1 - - + +
16D ASN* 2.7 49.2 + - + +
17D LEU* 2.9 15.1 + - + +
19D LYS* 1.3 72.4 - - + +
21D ALA* 1.3 62.8 + - - +
23D GLU* 3.3 6.5 + - - +
24D MET* 3.0 20.4 + - + +
31D MET* 2.8 26.2 - - + +
36E LEU* 4.1 26.0 - - + +
37E GLU* 5.9 0.7 - - - +
39E TYR* 3.8 23.6 - - + -
40E LYS* 3.6 26.9 - - + -
43E GLN* 5.7 0.9 - - - -
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Residues in contact with ALA 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D LEU* 2.8 19.9 + - + +
18D GLU* 3.8 6.5 - - - +
20D MET* 1.3 72.3 - - - +
22D ARG* 1.3 64.0 + - - +
24D MET 3.1 2.6 + - - -
25D GLY 2.9 19.6 + - - -
26D LEU 2.9 28.8 + - - +
27D SER 3.9 15.7 - - - +
28D LYS* 4.4 8.7 - - + +
31D MET* 3.3 18.7 - - + +
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Residues in contact with ARG 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D GLU* 3.0 21.2 + - - +
19D LYS* 3.2 38.0 - - - +
21D ALA* 1.3 79.3 - - - +
23D GLU* 1.3 81.1 + - - +
25D GLY* 3.4 10.0 + - - -
26D LEU 4.3 1.3 + - - -
10G SER* 5.5 0.7 - - - -
12G SER* 4.4 9.9 + - - -
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Residues in contact with GLU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LYS* 2.5 67.8 + - - +
20D MET* 3.5 11.0 - - - +
22D ARG* 1.3 93.3 + - - +
24D MET* 1.3 63.4 + - + +
25D GLY 3.2 3.0 + - - -
37F GLU* 3.5 14.1 - - - +
12G SER* 5.0 6.2 + - - -
13G VAL* 4.9 4.0 - - - +
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Residues in contact with MET 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D MET* 3.0 15.4 + - + +
23D GLU* 1.3 79.5 - - + +
25D GLY* 1.3 63.9 + - - +
26D LEU* 3.2 24.5 + - + +
31D MET* 3.0 28.5 - - + +
34D VAL* 5.7 2.7 - - + -
39E TYR* 3.3 26.9 - - - +
43E GLN* 5.5 3.4 - - - +
33F SER* 4.1 7.8 - - - +
34F VAL* 4.7 17.5 - - + +
37F GLU* 3.8 43.5 - - + +
38F ASN* 5.5 0.7 - - + +
13G VAL* 4.3 3.5 - - - +
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Residues in contact with GLY 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ALA 2.9 5.4 + - - -
22D ARG* 3.4 8.6 + - - -
23D GLU 3.2 5.5 + - - -
24D MET* 1.3 78.4 - - - +
26D LEU* 1.3 64.8 + - - +
2F LYS* 3.4 17.9 + - - -
33F SER* 4.2 8.7 + - - -
10G SER* 3.3 26.1 + - - -
12G SER* 5.3 0.4 - - - -
13G VAL* 4.2 8.6 - - - +
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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