Contacts of the helix formed by residues 16 - 28 (chain D) in PDB entry 3RKR
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 ARG 16 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D GLY 4.0 5.2 + - - +
14D ALA 3.4 0.8 + - - -
15D SER* 1.3 90.0 + - - +
17D GLY* 1.3 71.1 + - - +
18D ILE 3.4 0.3 + - - -
19D GLY* 3.3 5.5 + - - -
20D ALA* 2.8 20.9 + - - -
241D SO4 6.0 0.2 + - - -
242D SO4 4.1 26.7 + - - +
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Residues in contact with GLY 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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16D ARG* 1.3 77.5 - - - +
18D ILE* 1.3 64.0 + - - -
20D ALA* 3.1 3.5 + - - +
21D ALA* 2.9 22.3 + - - +
24D ARG* 5.2 0.5 + - - -
209D PRO* 4.0 16.6 - - - +
242D SO4 3.2 14.4 - - - -
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Residues in contact with ILE 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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16D ARG 3.4 0.6 + - - -
17D GLY* 1.3 70.3 - - - -
19D GLY* 1.3 53.2 + - - +
21D ALA* 3.1 4.0 + - - +
22D ILE* 2.8 56.5 + - + +
90D ASN* 3.3 21.3 - - - +
141D ILE* 4.4 11.7 - - + -
207D ILE 5.7 2.0 - - - +
209D PRO* 4.2 21.1 - - + -
212D ILE* 3.6 43.1 - - + -
242D SO4 2.8 34.5 + - - +
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Residues in contact with GLY 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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11D VAL* 3.8 11.1 - - - +
13D GLY 3.5 9.0 - - - -
14D ALA* 3.8 9.6 - - - -
16D ARG 3.3 2.8 + - - -
18D ILE* 1.3 78.9 - - - +
20D ALA* 1.3 56.2 + - - +
22D ILE* 3.3 3.3 + - - +
23D ALA* 2.9 30.5 + - - +
90D ASN* 3.3 28.1 + - - -
242D SO4 4.7 1.0 + - - -
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Residues in contact with ALA 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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14D ALA 3.5 12.1 + - - -
16D ARG* 2.8 41.8 + - - +
17D GLY 3.4 2.5 - - - +
19D GLY* 1.3 70.1 - - - +
21D ALA* 1.3 64.3 + - - +
23D ALA* 3.1 7.1 - - - +
24D ARG* 3.0 49.2 + - - +
46D VAL* 3.8 11.8 - - + +
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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 GLY 2.9 13.1 + - - +
18D ILE 3.6 5.8 - - - +
20D ALA* 1.3 76.0 - - - +
22D ILE* 1.3 59.2 + - - +
24D ARG* 3.3 19.3 + - - +
25D LYS* 2.9 31.2 + - - +
209D PRO* 3.8 30.7 - - + +
210D ASP* 3.8 14.6 - - - +
213D ALA* 3.6 5.9 - - + +
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Residues in contact with ILE 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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11D VAL* 4.1 13.7 - - + -
18D ILE* 2.8 42.5 + - + +
19D GLY* 3.7 7.9 - - - +
21D ALA* 1.3 75.9 - - - +
23D ALA* 1.3 54.9 + - - +
25D LYS* 3.3 1.8 + - - +
26D LEU* 2.8 56.7 + - + +
88D VAL* 4.1 17.7 - - + -
90D ASN* 4.5 2.0 - - + +
141D ILE* 4.2 7.9 - - + -
212D ILE* 4.3 0.7 - - + -
213D ALA* 3.9 25.4 - - - +
216D VAL* 3.9 30.5 - - + -
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Residues in contact with ALA 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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11D VAL* 4.5 3.8 - - + +
14D ALA* 4.5 3.6 - - + +
19D GLY 2.9 13.4 + - - +
20D ALA* 3.1 11.0 - - - +
22D ILE* 1.3 77.1 - - - +
24D ARG* 1.3 61.9 + - - +
26D LEU* 4.9 0.2 - - - -
27D GLY 3.0 19.9 + - - -
33D VAL* 3.7 17.4 - - + +
35D LEU* 3.6 30.3 - - + -
46D VAL* 3.8 13.0 - - + -
50D ILE* 3.7 5.9 - - + +
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Residues in contact with ARG 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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17D GLY 5.2 0.6 + - - -
20D ALA* 3.0 38.9 + - - +
21D ALA* 3.7 28.4 - - - +
23D ALA* 1.3 71.9 - - - +
25D LYS* 1.3 62.5 + - - +
27D GLY* 3.5 0.5 + - - -
28D SER* 3.0 26.9 + - - -
46D VAL* 4.4 11.4 - - + +
49D GLU* 2.8 36.9 + - + +
50D ILE* 4.1 17.6 - - + +
210D ASP* 5.1 4.2 + - - -
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Residues in contact with LYS 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 17.3 + - - +
22D ILE 3.7 3.1 - - - +
24D ARG* 1.3 77.7 - - - +
26D LEU* 1.3 62.9 + - + +
28D SER* 3.0 26.5 + - - +
29D LEU* 3.5 26.1 + - - +
213D ALA* 3.7 28.7 - - + +
214D ASP* 3.5 23.5 + - - +
217D ALA* 3.9 22.4 - - + -
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Residues in contact with LEU 26 (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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4D LEU* 4.0 19.9 - - + +
9D ALA* 3.7 28.0 - - + -
11D VAL* 4.0 9.9 - - + -
22D ILE* 2.8 41.4 + - + +
23D ALA* 4.0 3.1 - - - +
25D LYS* 1.3 72.8 - - + +
27D GLY* 1.3 64.0 + - - +
29D LEU* 3.1 15.6 + - + +
30D GLY 3.5 0.3 + - - -
31D ALA* 3.3 20.0 + - + +
33D VAL* 4.1 9.9 - - + -
86D VAL* 4.2 4.3 - - + -
88D VAL* 4.1 11.4 - - + -
213D ALA 5.6 0.4 - - - +
216D VAL* 4.3 11.0 - - + -
217D ALA* 4.4 12.6 - - + +
220D ALA* 4.2 16.2 - - + -
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Residues in contact with GLY 27 (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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23D ALA 3.0 13.4 + - - -
24D ARG 4.0 0.9 - - - -
26D LEU* 1.3 71.1 - - - +
28D SER* 1.3 54.1 + - - +
29D LEU 3.0 4.5 - - - -
30D GLY* 2.8 26.2 + - - -
31D ALA 3.6 7.0 - - - +
33D VAL* 3.4 18.9 - - - +
50D ILE* 4.3 16.8 - - - -
55D GLY* 4.4 12.8 - - - -
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Residues in contact with SER 28 (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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2D SER* 4.2 8.8 + - - -
24D ARG 3.0 15.5 + - - -
25D LYS* 3.0 22.5 + - - +
27D GLY* 1.3 74.5 - - - +
29D LEU* 1.3 63.7 + - - +
30D GLY 3.3 1.1 - - - -
50D ILE* 5.8 0.2 - - - +
53D ALA* 6.0 7.9 - - - -
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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