Contacts of the strand formed by residues 13 - 21 (chain D) in PDB entry 2CKE
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D VAL* 2.9 24.8 + - + +
10D GLU* 3.0 26.0 - - - +
11D ASP 3.6 0.4 - - - -
12D PHE* 1.3 87.2 - - + +
14D ASP* 1.3 61.4 + - - +
15D ILE* 3.5 18.0 + - + +
30D CYS* 3.9 15.0 - - + -
31D ARG 3.3 7.2 - - - +
32D GLU* 3.5 45.8 + - + -
33D LYS* 4.0 6.2 - - - +
39D TYR* 4.2 5.8 - + - -
80D HIS* 3.3 23.9 - - - -
81D ASP* 4.1 8.0 + - - +
83D TYR* 3.6 29.6 + + - -
92D ILE* 3.6 28.5 - - + +
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Residues in contact with ASP 14 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D TYR* 1.3 69.9 - - - +
15D ILE* 1.3 63.0 + - - +
30D CYS* 3.3 4.7 - - - -
31D ARG* 2.9 48.9 + - + +
33D LYS* 3.2 32.6 + - - +
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Residues in contact with ILE 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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9D VAL* 4.6 14.1 - - + -
10D GLU* 4.6 15.7 - - + +
13D TYR* 3.5 18.7 + - + +
14D ASP* 1.3 75.5 - - - +
16D GLY* 1.3 62.0 + - - +
28D LYS* 3.7 35.4 - - + +
29D LYS 4.0 1.6 - - - +
30D CYS* 4.0 16.6 - - + -
41D ALA* 4.9 2.9 - - + -
43D PHE* 4.1 24.7 - - + -
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Residues in contact with GLY 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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14D ASP 3.9 0.2 + - - -
15D ILE* 1.3 77.1 - - - +
17D GLU* 1.3 73.3 + - - +
18D GLU 3.9 0.2 + - - -
28D LYS* 3.7 18.2 - - - +
29D LYS* 2.7 20.3 + - - -
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Residues in contact with GLU 17 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D GLY* 1.3 74.4 - - - -
18D GLU* 1.3 68.1 + - - +
19D LEU* 3.3 9.6 - - + +
28D LYS* 4.3 0.2 - - - -
29D LYS* 2.9 29.0 + - + +
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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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16D GLY 3.9 0.2 + - - -
17D GLU* 1.3 77.9 + - - +
19D LEU* 1.3 64.8 + - - +
20D GLY* 3.6 16.1 - - - +
21D SER* 3.5 21.6 - - - -
26D ILE* 3.8 19.4 - - + +
27D VAL 3.5 13.7 - - - +
28D LYS* 4.2 10.5 - - + +
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Residues in contact with LEU 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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17D GLU* 3.3 22.9 - - + +
18D GLU* 1.3 77.7 - - - +
20D GLY* 1.3 57.4 + - - +
27D VAL* 2.8 12.5 + - + +
28D LYS 4.6 1.6 - - - -
29D LYS* 3.7 28.5 - - + +
40D ALA* 4.8 3.6 - - + -
95D LEU* 3.7 20.4 - - + -
97D SER* 6.0 2.5 - - - -
1302D IQU 3.3 51.1 + - + +
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Residues in contact with GLY 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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18D GLU* 3.6 11.3 - - - +
19D LEU* 1.3 78.7 - - - +
21D SER* 1.3 64.6 + - - -
27D VAL* 2.9 26.9 + - - +
1302D IQU 3.2 21.8 + - - -
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Residues in contact with SER 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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53C ARG* 4.2 11.5 + - - +
18D GLU* 3.5 20.6 - - - -
20D GLY* 1.3 76.6 - - - -
22D GLY* 1.3 63.4 + - - +
25D ALA 3.5 11.7 + - - -
26D ILE* 4.2 12.9 - - - +
27D VAL* 5.6 0.2 - - - -
1302D IQU 3.6 21.2 + - - -
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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