Contacts of the strand formed by residues 25 - 32 (chain D) in PDB entry 2A27
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 ALA 25 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D GLY* 3.1 32.7 + - - +
24D PHE* 1.3 80.2 - - + +
26D ILE* 1.3 66.9 + - - +
27D VAL* 4.1 2.7 - - + -
42D LYS* 3.8 39.3 - - + -
43D PHE 3.5 9.2 - - - +
44D ILE* 3.9 9.9 - - + -
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Residues in contact with ILE 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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18D GLU* 4.0 20.6 - - - +
21D SER* 3.8 22.0 - - - -
22D GLY 5.1 1.8 - - - +
24D PHE 5.5 1.8 - - - +
25D ALA* 1.3 78.4 - - - +
27D VAL* 1.3 62.2 + - - +
28D LYS* 4.3 18.2 - - - -
43D PHE* 3.1 45.5 + - + +
45D LYS* 5.6 11.7 - - - +
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Residues in contact with VAL 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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18D GLU* 3.6 5.2 - - - +
19D LEU* 2.9 40.1 + - + -
20D GLY 3.6 25.5 + - - +
21D SER* 4.3 0.2 - - - +
22D GLY 6.1 0.2 - - - +
25D ALA* 4.1 2.4 - - + -
26D ILE* 1.3 73.8 - - - +
28D LYS* 1.3 68.1 + - - +
40D ALA* 4.1 24.9 - - + -
41D ALA 3.7 7.6 - - - +
42D LYS* 3.8 31.2 - - + +
93D LEU* 6.2 0.7 - - + -
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Residues in contact with LYS 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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15D ILE* 3.6 27.2 - - + +
16D GLY 4.1 8.9 + - - +
17D GLU 3.3 13.9 - - - +
18D GLU* 4.0 15.3 - - - -
19D LEU* 4.0 5.4 - - - +
26D ILE* 4.3 23.1 - - + +
27D VAL* 1.3 84.1 - - - +
29D LYS* 1.3 66.8 + - - +
40D ALA* 3.6 1.0 - - - -
41D ALA* 2.8 39.3 + - - +
43D PHE* 4.3 12.3 - - + -
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Residues in contact with LYS 29 (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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15D ILE* 3.8 1.4 - - - -
16D GLY* 3.1 23.6 + - - -
17D GLU* 3.0 33.2 + - + +
19D LEU* 3.5 29.2 - - + +
28D LYS* 1.3 76.9 - - - +
30D CYS* 1.3 72.2 + - - +
38D GLU* 3.8 26.3 + - - +
39D TYR 3.8 8.3 - - - +
40D ALA* 4.7 1.1 - - - +
95D LEU* 4.2 20.9 - - + +
97D SER* 5.7 5.4 - - - -
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Residues in contact with CYS 30 (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* 3.9 21.5 - - + -
14D ASP 3.0 19.3 - - - +
15D ILE* 4.2 7.2 - - + -
29D LYS* 1.3 80.1 - - - +
31D ARG* 1.3 66.2 + - - +
38D GLU* 3.4 11.1 - - - +
39D TYR* 2.9 56.3 + - - +
40D ALA 4.2 1.3 - - - -
41D ALA* 4.1 22.9 - - + -
92D ILE* 4.5 3.1 - - - -
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Residues in contact with ARG 31 (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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153C PRO* 5.3 10.1 - - - +
154C ILE* 3.9 22.3 - - - +
13D TYR* 3.4 3.5 - - - -
14D ASP* 3.0 49.5 + - + +
30D CYS* 1.3 81.3 - - - +
32D GLU* 1.3 77.1 - - - +
33D LYS* 3.3 2.1 + - - -
36D GLY* 2.8 34.6 + - - -
37D LEU 3.4 9.2 - - - +
38D GLU* 3.1 32.7 + - + +
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Residues in contact with GLU 32 (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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121C LYS* 5.0 3.5 + - - -
125C ASP* 5.9 0.2 - - - -
12D PHE* 4.3 4.0 - - + +
13D TYR* 3.4 32.7 + - + -
31D ARG* 1.3 73.7 - - - +
33D LYS* 1.3 61.2 + - - +
34D SER* 3.5 23.6 + - - +
35D THR* 3.0 28.3 + - - +
36D GLY* 3.0 28.8 + - - -
37D LEU* 2.9 13.1 + - - +
39D TYR* 3.7 9.9 + - + -
80D HIS* 3.3 34.3 + - - -
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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