Contacts of the strand formed by residues 28 - 35 (chain A) in PDB entry 3KBF
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 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ILE* 3.9 22.4 - - + -
20A THR 3.6 5.6 - - - +
21A GLN* 4.3 10.3 - - - +
26A ASP 3.7 1.6 + - - -
27A GLN* 1.3 73.5 - - - +
29A VAL* 1.3 60.2 + - - +
30A ILE* 4.0 5.0 + - + +
99A THR* 3.2 5.9 - - - -
100A ASP* 2.9 33.6 + - - +
103A VAL* 3.3 35.2 + - + +
104A THR* 4.9 0.2 - - - -
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Residues in contact with VAL 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A TRP 3.6 1.6 - - - +
19A ILE* 3.2 4.5 - - - -
20A THR* 2.8 49.6 + - - +
27A GLN* 4.3 7.4 - - + +
28A ALA* 1.3 75.0 - - - +
30A ILE* 1.3 62.1 + - - +
31A GLU* 4.1 25.9 + - + +
97A LYS* 5.9 4.3 - - + -
98A LEU 3.6 9.4 - - - +
99A THR* 4.2 16.2 - - + -
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Residues in contact with ILE 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ILE* 3.6 24.5 - - + -
18A TRP 3.4 3.8 - - - +
19A ILE* 4.2 15.5 - - + -
28A ALA* 4.5 3.8 - - + +
29A VAL* 1.3 77.4 - - - +
31A GLU* 1.3 64.5 + - - +
44A PHE* 4.5 11.7 - - + -
83A LEU* 4.0 31.0 - - + -
96A ILE* 3.9 6.4 - - + +
97A LYS* 3.4 2.4 + - - -
98A LEU* 2.8 50.9 + - + +
100A ASP* 4.4 16.2 - - + -
103A VAL* 4.4 15.7 - - + -
116A MET* 4.0 12.6 - - + -
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Residues in contact with GLU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ILE* 4.5 5.2 - - - -
18A TRP* 2.8 53.3 + - + +
20A THR* 4.5 13.2 + - - +
29A VAL* 4.2 22.1 - - + +
30A ILE* 1.3 76.9 - - - +
32A GLY* 1.3 58.7 + - - +
96A ILE* 3.1 12.6 - - - +
97A LYS* 4.5 18.1 - - + +
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Residues in contact with GLY 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A THR 3.3 12.3 - - - -
17A ILE* 4.1 6.5 - - - -
18A TRP* 5.3 3.8 - - - -
31A GLU* 1.3 75.3 - - - +
33A GLU* 1.3 69.5 + - - +
95A LYS* 3.8 1.0 - - - +
96A ILE* 2.9 31.7 + - - +
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Residues in contact with GLU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLY* 3.2 3.5 - - - -
16A THR 3.0 31.0 + - - +
17A ILE* 4.1 0.6 - - - +
32A GLY* 1.3 80.3 - - - +
34A ILE* 1.3 65.3 + - - +
35A LYS* 4.3 1.6 - - - -
93A VAL* 3.9 15.9 - - + +
94A ALA 3.3 11.4 - - - +
95A LYS* 3.9 31.0 - - + +
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Residues in contact with ILE 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.5 7.0 - - + -
13A VAL* 3.5 24.0 - - + -
14A THR 3.4 13.7 - - - +
15A GLY* 4.7 4.3 - - - -
17A ILE* 4.1 7.9 - - + -
33A GLU* 1.3 80.1 - - - +
35A LYS* 1.3 63.1 + - - +
37A LEU* 3.7 17.7 - - + +
44A PHE* 4.1 14.1 - - + -
86A VAL* 4.7 4.0 - - + -
92A GLY 3.7 1.6 - - - +
93A VAL* 3.3 4.8 - - - +
94A ALA* 2.8 33.9 + - + +
96A ILE* 3.5 27.1 - - + -
118A VAL* 4.0 30.1 - - + -
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Residues in contact with LYS 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A THR 5.7 0.7 - - - +
13A VAL* 3.4 9.2 - - - +
14A THR* 2.8 53.6 + - - +
15A GLY* 4.7 1.1 - - - -
33A GLU* 6.1 1.6 - - + -
34A ILE* 1.3 72.8 - - - +
36A GLY* 1.3 64.0 + - - +
37A LEU 3.3 2.7 - - - -
92A GLY 3.5 4.7 - - - -
93A VAL* 4.1 19.5 - - + -
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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