Contacts of the helix formed by residues 17 - 25 (chain D) 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 TRP 17 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71C GLY 5.0 6.7 - - - -
12D ASP 3.7 15.9 - - - +
13D TRP 5.7 0.2 - - - -
15D GLY 3.5 0.6 - - - -
16D ARG* 1.3 122.7 - - + +
18D ASN* 1.3 63.6 + - - +
19D HIS* 3.2 3.1 - - - -
20D VAL* 3.0 21.0 + - + -
21D LYS* 3.0 29.7 + - + +
42D LEU* 3.5 30.7 - - + -
46D LEU* 4.0 23.6 - - + +
68D ALA 3.4 18.8 - - - -
69D LEU* 3.6 16.2 - - + -
71D GLY* 3.3 34.5 - - - -
72D PHE 5.3 0.7 - - - -
73D ARG* 4.1 9.4 - - - +
115D VAL* 5.4 1.8 - - + -
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Residues in contact with ASN 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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68C GLU* 3.9 22.2 + - - +
15D GLY* 2.8 41.1 - - - +
16D ARG 3.3 3.6 + - - -
17D TRP* 1.3 71.7 + - - +
19D HIS* 1.3 61.2 + - - +
20D VAL 2.8 11.8 + - - -
21D LYS* 3.5 21.2 + - - +
22D LYS* 3.6 38.9 + - - +
263H LYS* 5.4 6.3 - - - +
266H GLU* 5.2 4.8 + - - -
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Residues in contact with HIS 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C GLU* 3.4 55.9 + - + +
69C ASP* 5.7 2.1 + - - -
71C GLY 6.1 0.2 - - - -
72C ASN* 3.1 25.9 + - + +
487C ALA 5.4 0.8 + - - -
488C ALA* 4.1 11.5 - - + -
489C GLU* 3.0 54.9 + - - +
490C PRO* 4.2 11.9 - - + +
491C HIS 5.4 0.4 - - - +
16D ARG 4.6 3.3 + - - +
17D TRP* 3.2 1.8 - - - +
18D ASN* 1.3 77.2 + - + +
20D VAL* 1.3 66.9 + - + +
22D LYS* 5.5 2.9 - - - -
23D PHE* 3.8 18.1 - - - -
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Residues in contact with VAL 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D TRP* 3.0 29.8 + - + +
18D ASN 2.8 1.2 + - - -
19D HIS* 1.3 91.0 - - + +
21D LYS* 1.3 68.5 + - - +
22D LYS 3.1 1.6 - - - -
23D PHE* 3.0 18.8 + - - +
24D LEU* 3.3 23.3 + - + +
42D LEU* 4.5 8.3 - - + -
45D LEU* 5.1 0.2 - - + -
69D LEU 4.2 9.2 - - - +
70D SER* 3.4 28.7 - - - +
308D PHE* 3.6 22.7 - - + -
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Residues in contact with LYS 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 TRP* 3.0 28.9 + - - +
18D ASN* 4.1 14.1 - - - +
20D VAL* 1.3 77.3 - - - +
22D LYS* 1.3 54.1 + - + +
24D LEU* 2.7 12.6 + - - +
25D GLU* 2.5 73.3 + - + +
39D THR* 5.9 0.9 + - - -
42D LEU* 4.0 27.3 - - + +
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Residues in contact with LYS 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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68C GLU* 4.5 9.7 + - - -
445C VAL* 3.7 27.7 + - - +
447C ASN* 4.6 4.7 - - - +
484C ARG* 3.9 18.4 + - - +
485C TYR 3.8 19.7 - - - +
486C GLY* 3.7 15.3 + - - +
488C ALA* 3.8 12.0 - - + +
18D ASN* 3.7 37.5 + - - +
19D HIS* 5.4 3.0 + - - -
20D VAL 3.1 0.6 - - - -
21D LYS* 1.3 78.1 - - + +
23D PHE* 1.3 67.4 + - + +
25D GLU* 5.1 0.4 - - - -
26D ARG* 3.4 50.2 - - - +
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Residues in contact with PHE 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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157C GLY* 4.3 11.2 - - - -
158C LEU* 3.8 24.5 - - + -
484C ARG* 2.9 27.7 + - + +
485C TYR* 4.3 13.2 - + - -
488C ALA* 4.2 14.1 - - + -
490C PRO* 3.4 34.3 - - + -
19D HIS 3.8 15.3 - - - -
20D VAL* 3.0 14.4 + - - +
22D LYS* 1.3 84.0 - - + +
24D LEU* 1.3 61.7 + - - +
26D ARG 4.3 1.6 - - - -
35D PHE* 3.5 10.4 - - - -
308D PHE* 4.5 22.2 - + + -
314D ALA* 3.6 9.2 - - + +
315D TYR* 3.5 28.5 - + - -
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Residues in contact with LEU 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 VAL* 3.4 30.7 - - + +
21D LYS* 2.7 7.3 + - - +
23D PHE* 1.3 85.3 - - - +
25D GLU* 1.3 60.3 + - + +
26D ARG 3.4 0.2 - - - -
35D PHE* 3.5 10.8 - - + -
37D PRO* 3.5 6.8 - - - +
38D SER 3.2 24.3 + - - +
41D SER* 4.0 19.3 + - - -
42D LEU* 3.9 34.8 - - + +
45D LEU* 4.5 4.3 - - + -
308D PHE* 3.7 11.0 - - + -
312D THR* 3.4 42.6 - - + +
314D ALA* 4.4 2.2 - - + -
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Residues in contact with GLU 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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447C ASN* 2.9 27.8 + - - +
21D LYS* 2.5 62.4 + - + +
24D LEU* 1.3 75.7 - - + +
26D ARG* 1.3 60.5 + - + +
27D SER 4.1 0.2 + - - -
37D PRO* 3.8 15.7 - - - +
38D SER 3.7 18.0 - - - +
39D THR* 3.7 25.1 + - - +
42D LEU* 6.4 1.3 - - + -
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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