Contacts of the helix formed by residues 13 - 29 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A LYS* 2.9 36.5 + - + +
10A GLU* 3.8 3.4 - - - -
12A LYS* 1.3 89.4 + - + +
14A ASP* 1.3 60.5 + - - -
15A ARG 3.6 1.1 - - - -
16A GLN* 3.4 25.0 - - + +
17A LEU* 2.9 32.3 + - + +
25A GLN* 3.8 12.3 - - + +
29A GLU* 4.0 16.5 + - - -
51A LEU 3.5 8.7 - - - -
52A PRO 3.3 36.6 - - - -
53A GLY* 3.4 10.3 + - - -
97A ASN* 3.3 24.5 + - - -
99A ASP* 3.6 13.9 + - - +
89B ASN* 4.4 6.3 - - + -
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Residues in contact with ASP 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 GLU* 3.3 20.3 + - - +
11A GLN* 3.9 10.8 - - - +
12A LYS 3.0 5.8 + - - +
13A TYR* 1.3 71.6 - - - +
15A ARG* 1.3 78.3 + - + +
16A GLN 2.9 4.0 - - - -
17A LEU* 2.7 27.6 + - - +
18A ARG* 2.7 50.9 + - - +
86B SER* 5.2 3.8 - - - -
279B ARG* 4.2 11.8 + - - +
282B GLN* 3.6 14.1 - - - +
288B ILE* 5.5 0.4 - - - -
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Residues in contact with ARG 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LYS 4.7 1.0 + - - -
13A TYR 3.6 0.4 - - - -
14A ASP* 1.3 89.0 + - - +
16A GLN* 1.3 56.1 + - - +
18A ARG* 4.2 5.6 + - - +
19A LEU* 4.3 0.9 - - - +
5B ATP 2.6 44.8 + - - -
86B SER* 3.4 34.2 + - - +
89B ASN* 4.1 5.1 + - - +
90B ARG* 3.8 22.7 - - - +
282B GLN* 6.0 0.8 - - - +
286B LYS* 4.4 24.5 - - - +
288B ILE* 3.0 37.9 - - - +
289B ILE 4.3 5.6 - - - +
290B PRO* 3.5 10.2 - - - +
291B ALA 2.9 39.1 + - - +
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Residues in contact with GLN 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 TYR* 3.4 29.1 + - + +
14A ASP 2.8 2.2 + - - -
15A ARG* 1.3 75.6 - - - +
17A LEU* 1.3 65.4 + - - +
18A ARG 3.0 2.2 - - - -
19A LEU* 3.2 13.1 + - - +
20A TRP* 2.8 46.0 + - + -
25A GLN* 2.9 19.1 + - - +
52A PRO* 2.9 38.9 + - - +
89B ASN* 3.8 18.0 + - - +
291B ALA 3.8 3.6 - - - +
292B VAL* 3.3 25.6 - - + +
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Residues in contact with LEU 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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10A GLU* 4.5 22.0 - - + +
13A TYR* 2.9 27.2 + - + +
14A ASP* 2.7 8.5 + - - +
16A GLN* 1.3 75.2 - - - +
18A ARG* 1.3 57.4 + - - +
19A LEU 3.0 5.8 + - - -
20A TRP* 4.5 0.7 - - - +
21A GLY* 2.9 41.1 + - - +
22A ASP* 4.1 9.0 - - + +
25A GLN* 3.4 46.0 - - + +
279B ARG* 3.3 40.3 + - - +
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Residues in contact with ARG 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 ASP* 2.7 35.7 + - - +
15A ARG* 4.3 6.1 - - - +
16A GLN 3.0 0.8 - - - -
17A LEU* 1.3 78.5 - - - +
19A LEU* 1.3 64.4 + - - +
21A GLY 4.9 0.2 - - - -
279B ARG* 2.5 57.9 + - - +
280B LEU* 4.8 3.8 - - - +
282B GLN* 3.6 6.1 - - - +
283B GLY* 3.5 11.9 - - - +
288B ILE* 3.2 41.6 - - - +
290B PRO* 4.0 27.6 - - + +
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Residues in contact with LEU 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 ARG 4.3 3.8 - - - +
16A GLN 3.2 8.0 + - - +
17A LEU 3.0 0.6 - - - -
18A ARG* 1.3 84.7 - - - +
20A TRP* 1.3 66.1 + - + +
21A GLY 3.6 1.2 + - - -
175A HIS* 4.1 12.1 - - - -
513A PHE* 4.1 13.0 - - - -
184B GLY* 4.4 18.8 - - - -
185B PHE* 3.5 36.8 - - + -
290B PRO* 3.2 30.7 - - + -
291B ALA 4.5 3.4 - - - +
292B VAL* 3.5 31.0 - - + -
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Residues in contact with TRP 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 GLN* 2.8 48.5 + - + +
17A LEU* 4.5 1.1 - - + +
19A LEU* 1.3 78.5 - - + +
21A GLY* 1.3 78.3 + - - +
23A HIS* 4.0 2.4 - - - -
24A GLY* 3.1 7.9 + - - -
25A GLN* 3.1 31.2 + - + +
28A LEU* 3.7 14.6 - - + +
52A PRO* 4.4 4.5 - - + -
175A HIS* 5.4 0.7 - - - -
503A GLN* 4.3 7.4 - - - -
506A ILE* 3.7 43.1 - - + -
510A THR* 4.9 2.5 - - + -
512A GLN* 2.8 41.2 + - + +
513A PHE* 4.3 10.3 - + + -
185B PHE* 4.4 16.2 - + - -
292B VAL* 4.2 22.0 - - + -
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Residues in contact with GLY 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 LEU* 2.9 27.3 + - - +
18A ARG 4.9 0.2 - - - -
19A LEU 3.6 1.8 + - - -
20A TRP* 1.3 91.2 - - - +
22A ASP* 1.3 67.6 + - - -
23A HIS* 3.2 13.2 - - - -
25A GLN 3.2 10.0 + - - -
279B ARG* 4.8 3.4 - - - -
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Residues in contact with ASP 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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10A GLU* 4.3 4.2 - - - +
17A LEU* 4.1 14.7 - - + +
21A GLY* 1.3 71.3 - - - -
23A HIS* 1.3 53.6 + - - +
25A GLN* 3.2 5.0 + - - +
26A GLU* 2.7 42.1 + - + +
279B ARG* 2.9 36.7 + - - -
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Residues in contact with HIS 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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20A TRP 4.0 11.7 - - - -
21A GLY* 4.1 8.7 - - - -
22A ASP* 1.3 81.2 + - - +
24A GLY* 1.3 72.9 + - - +
26A GLU* 3.2 16.7 + - - +
27A ALA* 3.0 21.8 + - - +
173A GLU* 3.0 34.2 + - - -
382A LEU* 5.7 3.9 - - + +
512A GLN* 3.4 13.2 + - + -
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Residues in contact with GLY 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 TRP* 3.1 28.4 + - - -
23A HIS* 1.3 79.2 - - - +
25A GLN* 1.3 65.7 + - - +
27A ALA* 2.9 8.3 + - - +
28A LEU* 2.8 21.3 + - - +
510A THR* 3.7 13.3 - - - +
512A GLN* 3.3 14.1 - - - -
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Residues in contact with GLN 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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13A TYR* 3.8 16.5 - - + -
16A GLN* 2.9 23.3 + - - -
17A LEU* 3.4 27.4 - - + +
20A TRP* 3.1 15.9 + - - +
21A GLY 3.2 5.3 + - - -
22A ASP* 3.2 10.1 - - - +
24A GLY* 1.3 74.4 - - - +
26A GLU* 1.3 54.9 + - - +
28A LEU* 2.9 6.5 + - - +
29A GLU* 2.6 77.3 + - - +
52A PRO 3.3 19.0 + - - -
53A GLY* 4.6 0.6 + - - -
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Residues in contact with GLU 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 ASP* 2.7 23.3 + - + +
23A HIS* 3.2 21.0 + - - +
24A GLY 3.1 0.2 - - - -
25A GLN* 1.3 75.5 - - - +
27A ALA* 1.3 62.8 + - - +
29A GLU* 3.4 9.2 + - - +
30A SER* 3.1 25.8 + - - -
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Residues in contact with ALA 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 HIS 3.0 10.6 + - - +
24A GLY* 2.9 13.7 + - - +
26A GLU* 1.3 69.5 - - - +
28A LEU* 1.3 67.3 + - - +
30A SER* 3.1 15.7 + - - -
31A ALA* 3.3 8.1 + - - +
509A ILE* 3.6 26.5 - - + +
510A THR* 4.3 9.2 - - - +
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Residues in contact with LEU 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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16A GLN* 4.6 0.4 - - - +
20A TRP* 3.7 35.9 - - + +
24A GLY 2.8 12.2 + - - +
25A GLN* 3.3 11.0 - - - +
27A ALA* 1.3 77.9 - - - +
29A GLU* 1.3 59.3 + - - +
30A SER 2.8 6.4 + - - -
31A ALA* 3.1 9.0 + - - +
49A LEU* 5.4 2.0 - - + +
52A PRO* 4.1 20.4 - - + +
53A GLY 4.7 0.4 - - - -
54A ILE* 3.5 34.5 - - + +
55A GLY 3.0 15.1 + - - -
506A ILE* 4.4 18.8 - - + -
509A ILE* 3.7 24.4 - - + +
510A THR* 4.5 4.9 - - + +
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Residues in contact with GLU 29 (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 LYS* 4.0 24.6 + - - +
13A TYR* 4.0 19.4 + - - -
25A GLN* 2.6 60.3 + - - +
26A GLU* 3.9 8.2 - - - +
28A LEU* 1.3 69.7 - - - +
30A SER* 1.3 60.2 + - - +
31A ALA 3.6 0.2 - - - -
53A GLY 4.0 10.1 - - - +
55A GLY* 3.3 22.3 - - - +
99A ASP* 5.7 1.0 - - - +
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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