Contacts of the helix formed by residues 13 - 29 (chain E) in PDB entry 1R4N
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 TYR 13 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9E LYS* 2.9 36.8 + - + +
10E GLU 3.8 3.4 - - - -
12E LYS* 1.3 90.2 + - + +
14E ASP* 1.3 60.7 + - - -
15E ARG 3.6 1.6 - - - -
16E GLN* 3.4 24.7 - - + +
17E LEU* 2.9 30.6 + - + +
25E GLN* 3.7 13.2 - - + +
29E GLU* 4.0 16.4 + - - -
51E LEU 3.5 9.4 - - - -
52E PRO 3.3 30.5 - - - -
53E GLY* 3.5 15.7 - - - -
97E ASN* 3.3 23.7 + - - -
99E ASP* 3.6 13.5 + - - +
89F ASN* 4.3 8.3 - - + -
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Residues in contact with ASP 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E GLU* 3.2 19.1 + - - +
11E GLN* 3.9 11.0 - - - +
12E LYS 3.0 5.6 + - - +
13E TYR* 1.3 71.1 - - - +
15E ARG* 1.3 72.9 + - + +
16E GLN 2.7 6.1 + - - -
17E LEU* 2.7 29.7 + - - +
18E ARG* 2.6 51.4 + - - +
86F SER* 5.1 3.8 - - - -
279F ARG* 4.3 10.0 + - - +
282F GLN* 3.6 15.0 - - - +
288F ILE* 5.3 1.1 - - - -
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Residues in contact with ARG 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E LYS 4.7 1.0 + - - -
14E ASP* 1.3 87.6 + - - +
16E GLN* 1.3 55.9 + - - +
18E ARG* 4.3 4.9 + - - +
19E LEU* 4.4 0.3 - - - +
7F ATP 2.4 34.8 + - - -
86F SER* 3.5 37.0 + - - +
89F ASN* 4.2 4.2 + - - +
90F ARG* 3.7 24.5 - - - +
286F LYS* 4.5 24.9 - - - +
288F ILE* 3.0 39.0 - - - +
289F ILE 4.1 9.2 - - - +
290F PRO* 3.3 10.3 - - - +
291F ALA 2.7 40.9 + - - +
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Residues in contact with GLN 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E TYR* 3.4 25.3 - - + +
14E ASP 2.7 2.0 + - - -
15E ARG* 1.3 74.7 - - - +
17E LEU* 1.3 68.1 + - - +
18E ARG 3.1 1.3 - - - -
19E LEU* 3.2 13.2 + - - +
20E TRP* 2.9 39.4 + - + -
25E GLN* 2.8 27.7 + - - +
52E PRO* 2.9 38.7 + - - +
89F ASN* 3.7 17.6 + - - +
291F ALA 3.6 4.5 - - - +
292F VAL* 3.3 24.8 - - + +
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Residues in contact with LEU 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E GLU* 4.5 21.5 - - + +
13E TYR* 2.9 28.5 + - + +
14E ASP* 2.7 7.7 + - - +
16E GLN* 1.3 74.7 - - - +
18E ARG* 1.3 57.9 + - - +
19E LEU 3.0 5.8 - - - -
20E TRP* 4.5 0.4 - - - +
21E GLY* 2.9 41.4 + - - +
22E ASP* 4.1 7.6 - - - +
25E GLN* 3.4 46.2 - - + +
279F ARG* 3.4 39.2 + - - +
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Residues in contact with ARG 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E ASP* 2.6 35.6 + - - +
15E ARG* 4.4 5.6 - - - +
16E GLN 3.1 0.6 - - - -
17E LEU* 1.3 78.5 - - - +
19E LEU* 1.3 64.8 + - - +
21E GLY 4.9 0.2 - - - -
279F ARG* 2.6 57.0 + - - +
280F LEU* 4.9 3.6 - - - +
282F GLN* 3.6 4.9 - - - +
283F GLY* 3.4 11.5 - - - +
288F ILE* 3.0 43.8 - - - +
290F PRO* 3.9 27.3 - - + +
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Residues in contact with LEU 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E ARG 4.4 3.4 - - - +
16E GLN 3.2 9.1 + - - +
17E LEU 3.0 1.0 - - - -
18E ARG* 1.3 84.0 - - - +
20E TRP* 1.3 65.5 + - + +
21E GLY 3.6 1.1 + - - -
175E HIS* 4.1 12.1 - - - -
513E PHE* 4.1 13.0 - - - -
184F GLY* 4.3 20.6 - - - -
185F PHE* 3.5 38.1 - - + -
290F PRO* 3.3 29.6 - - + -
291F ALA 4.5 3.8 - - - +
292F VAL* 3.6 28.3 - - + -
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Residues in contact with TRP 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E GLN* 2.9 49.2 + - + +
17E LEU* 4.5 0.6 - - + +
19E LEU* 1.3 79.6 - - + +
21E GLY* 1.3 70.8 + - - +
23E HIS* 4.5 1.6 - - - -
24E GLY* 3.0 7.8 + - - -
25E GLN* 3.0 38.7 + - + +
28E LEU* 3.7 14.8 - - + -
52E PRO* 4.4 4.0 - - + -
175E HIS* 5.0 0.7 - - - -
503E GLN* 4.3 7.0 - - - -
506E ILE* 3.7 43.7 - - + -
510E THR* 4.9 3.1 - - + -
512E GLN* 2.8 40.5 + - + +
513E PHE* 4.4 9.9 - + + -
185F PHE* 4.3 15.9 - + - -
292F VAL* 4.0 22.7 - - + -
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Residues in contact with GLY 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E LEU* 2.9 28.2 + - - +
19E LEU 3.6 2.2 + - - -
20E TRP* 1.3 90.7 - - - +
22E ASP* 1.3 67.4 + - - -
23E HIS* 3.2 13.2 - - - -
25E GLN 3.2 9.9 + - - -
279F ARG* 4.7 3.6 - - - -
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Residues in contact with ASP 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E GLU* 4.3 3.6 - - - +
17E LEU* 4.1 14.8 - - + +
21E GLY* 1.3 72.3 - - - -
23E HIS* 1.3 54.4 + - - +
25E GLN* 3.2 5.6 + - - +
26E GLU* 2.7 41.7 + - + +
279F ARG* 2.7 38.6 + - - +
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Residues in contact with HIS 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E TRP 4.0 11.4 - - - -
21E GLY* 4.0 9.2 - - - -
22E ASP* 1.3 80.6 + - - +
24E GLY* 1.3 74.5 + - - +
26E GLU* 3.1 18.3 + - - +
27E ALA* 3.0 19.4 + - - +
173E GLU* 3.0 34.4 + - - -
382E LEU* 5.7 4.9 - - + +
512E GLN* 3.4 13.0 + - + -
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Residues in contact with GLY 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E TRP* 3.0 29.2 + - - -
23E HIS* 1.3 78.9 - - - +
25E GLN* 1.3 64.4 + - - +
27E ALA* 2.9 8.4 + - - +
28E LEU* 2.8 21.0 + - - +
510E THR* 3.7 13.2 - - - +
512E GLN* 3.3 14.8 - - - -
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Residues in contact with GLN 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E TYR* 3.7 17.2 - - + -
16E GLN* 2.8 23.2 + - - -
17E LEU* 3.4 27.8 - - + +
20E TRP* 3.0 17.0 + - - +
21E GLY 3.2 4.6 + - - -
22E ASP* 3.2 9.9 - - - +
24E GLY* 1.3 74.5 - - - +
26E GLU* 1.3 53.8 + - - +
28E LEU* 3.0 6.7 + - - +
29E GLU* 2.6 76.6 + - - +
52E PRO 3.3 20.0 + - - -
53E GLY* 4.6 0.4 - - - -
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Residues in contact with GLU 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ASP* 2.7 22.9 + - + +
23E HIS* 3.2 20.1 + - - +
24E GLY 3.1 0.2 - - - -
25E GLN* 1.3 74.5 - - - +
27E ALA* 1.3 63.4 + - - +
29E GLU* 3.4 8.8 + - - +
30E SER* 3.1 25.3 + - - -
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Residues in contact with ALA 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E HIS 3.0 9.7 + - - +
24E GLY* 2.9 12.9 + - - +
26E GLU* 1.3 69.5 - - - +
28E LEU* 1.3 68.7 + - - +
30E SER* 3.0 16.1 + - - -
31E ALA* 3.3 8.3 + - - +
509E ILE* 3.7 26.0 - - - +
510E THR* 4.3 9.4 - - - +
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Residues in contact with LEU 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E GLN* 4.6 0.2 - - - +
20E TRP* 3.7 35.4 - - + +
24E GLY 2.8 11.9 + - - +
25E GLN* 3.4 10.8 - - - +
27E ALA* 1.3 76.5 - - - +
29E GLU* 1.3 58.4 + - - +
30E SER 2.8 6.6 + - - -
31E ALA* 3.1 9.0 + - - +
49E LEU* 5.4 1.8 - - + +
52E PRO* 4.1 19.3 - - + +
53E GLY 4.7 0.4 - - - -
54E ILE* 3.4 33.9 - - + +
55E GLY 3.0 14.8 + - - -
506E ILE* 4.4 18.8 - - + -
509E ILE* 3.8 25.3 - - + +
510E THR* 4.5 5.3 - - + +
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Residues in contact with GLU 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E LYS* 4.0 24.2 + - - +
13E TYR* 4.0 19.8 + - - -
25E GLN* 2.6 60.0 + - - +
26E GLU* 3.9 7.9 - - - +
28E LEU* 1.3 70.1 - - - +
30E SER* 1.3 58.8 + - - +
53E GLY 4.0 10.9 - - - +
55E GLY* 3.3 23.7 - - - +
99E ASP* 5.7 1.2 - - - +
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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