Contacts of the strand formed by residues 17 - 24 (chain B) in PDB entry 7KAC
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 17 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B PRO 3.1 12.8 + - - +
14B ARG* 3.4 26.9 - - - +
15B ASP 3.7 0.4 - - - -
16B HIS* 1.3 85.1 - - + +
18B ASP* 1.3 60.7 + - - +
19B LEU* 4.0 3.7 + - + +
34B ALA* 4.2 12.8 - - + -
35B ARG 3.3 5.8 - - - +
36B ASP* 3.4 44.6 + - + -
37B LYS* 3.7 7.2 - - - -
43B VAL* 3.6 31.3 - - + +
45B LEU* 4.4 14.4 - - + -
78B HIS* 4.3 8.7 - - - +
81B TYR* 3.4 30.7 + + - -
90B CYS* 3.4 26.0 - - - -
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Residues in contact with ASP 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B TYR* 1.3 71.0 - - - +
19B LEU* 1.3 64.9 + - - +
20B LEU* 3.6 13.2 + - + +
34B ALA* 3.3 3.5 - - - -
35B ARG* 2.9 38.7 + - + +
37B LYS* 3.3 39.3 + - - +
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Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B PRO* 6.4 0.4 - - + -
14B ARG* 4.5 21.9 - - + +
17B TYR* 4.0 3.4 + - + +
18B ASP* 1.3 71.2 - - - +
20B LEU* 1.4 65.2 + - - +
32B PHE* 3.9 34.1 - - + -
33B LYS 3.8 2.0 - - - +
34B ALA* 4.2 3.1 - - + -
45B LEU* 3.7 28.9 - - + -
88B TRP* 4.2 25.8 - - + -
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Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ASP* 3.8 23.8 - - + +
19B LEU* 1.4 77.7 - - - +
21B GLN* 1.3 63.9 + - + +
33B LYS* 2.9 36.1 + - + +
34B ALA* 4.3 1.1 - - - -
35B ARG* 4.3 20.0 - - + +
42B LEU* 3.8 28.7 - - + -
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Residues in contact with GLN 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU* 5.4 0.8 - - - +
20B LEU* 1.3 80.6 - - + +
22B ARG* 1.3 71.6 + - - +
23B LEU* 4.6 11.8 - - + +
32B PHE* 3.4 9.2 - - - +
33B LYS* 2.9 57.5 + - + +
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Residues in contact with ARG 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B GLN* 1.3 82.4 + - - +
23B LEU* 1.3 64.5 + - - +
24B GLY* 3.3 25.6 + - - +
25B GLY* 3.6 24.7 - - - +
26B GLY 4.5 1.4 - - - +
30B GLU* 4.4 10.2 - - + +
31B VAL 3.7 6.7 - - - +
32B PHE* 3.8 25.0 - - + -
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B GLN* 3.6 14.6 + - - +
22B ARG* 1.3 75.9 - - - +
24B GLY* 1.3 59.2 + - - +
31B VAL* 2.9 19.0 + - + +
32B PHE 3.8 6.7 - - - +
33B LYS* 3.7 39.0 - - + +
44B ALA* 4.8 1.3 - - + -
93B PHE* 4.1 5.2 - - + -
401B W9D 3.7 73.1 - - + +
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Residues in contact with GLY 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ARG* 3.3 25.3 + - - -
23B LEU* 1.3 80.5 - - - +
25B GLY* 1.3 57.9 + - - -
30B GLU* 3.5 0.5 - - - -
31B VAL 2.9 24.5 + - - +
401B W9D 3.6 15.6 - - - -
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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