Contacts of the strand formed by residues 105 - 111 (chain B) in PDB entry 1KO1
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 LEU 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B HIS* 3.8 2.5 + - - -
10B ILE* 3.3 22.7 - - + -
12B VAL* 3.5 25.4 - - + -
73B ALA* 4.2 13.7 - - + -
98B LEU* 3.7 24.2 - - + +
99B ARG* 4.5 9.9 - - + +
102B ASN* 3.4 19.9 - - + +
103B PRO 3.1 9.4 + - - +
104B ASN* 1.3 80.9 - - - +
106B SER* 1.3 68.8 + - - +
107B PHE* 3.3 38.4 - - + -
150B ASP* 3.3 19.1 - - - +
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Residues in contact with SER 106 (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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9B HIS* 3.4 11.6 + - - -
10B ILE 2.8 6.3 + - - +
11B TYR* 3.0 36.3 - - - -
12B VAL* 2.7 33.6 + - - +
105B LEU* 1.3 78.9 - - - +
107B PHE* 1.3 60.4 + - - +
150B ASP* 3.2 22.7 - - - -
152B LEU* 4.6 7.3 - - - +
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Residues in contact with PHE 107 (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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12B VAL* 3.2 34.5 - - + +
14B MET* 3.9 22.2 - - + -
89B ALA* 4.3 1.6 - - + -
95B ARG* 3.5 48.5 - - + -
98B LEU* 3.9 12.1 - - + -
99B ARG* 3.4 36.3 - - - -
105B LEU* 3.3 26.0 - - + -
106B SER* 1.3 75.5 - - - +
108B ILE* 1.3 66.0 + - - +
109B TYR 3.8 0.7 - - - -
150B ASP* 2.9 12.2 + - - +
151B VAL* 4.1 10.3 - - + -
152B LEU* 2.8 28.9 + - - +
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Residues in contact with ILE 108 (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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11B TYR* 3.9 19.7 - - + -
12B VAL 2.8 8.8 + - - -
13B LEU* 3.3 30.1 - - + +
14B MET* 3.0 22.3 + - - -
107B PHE* 1.3 77.4 - - - +
109B TYR* 1.3 61.8 + - - +
110B LEU* 3.4 6.4 + - + +
152B LEU* 3.2 7.4 - - + +
154B VAL* 3.7 31.6 - - + -
167B THR* 3.7 23.1 - - + +
170B VAL* 3.7 24.0 - - + -
171B ILE* 3.8 16.4 - - + -
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Residues in contact with TYR 109 (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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14B MET* 3.6 29.6 - - + -
15B GLY* 4.0 14.1 - - - -
16B VAL 5.2 0.7 - - - -
107B PHE 3.8 1.4 - - - -
108B ILE* 1.3 69.1 - - - +
110B LEU* 1.3 81.0 + - - +
111B LYS* 3.1 32.4 + - + +
112B GLY 5.1 2.8 + - - -
138B PHE* 5.6 1.2 - - - -
141B LEU* 3.2 29.1 - - + +
143B GLU* 2.5 44.6 + - + -
144B PRO* 4.1 13.2 - - + -
151B VAL* 4.2 7.6 - - + -
152B LEU 2.7 14.6 + - - +
153B VAL* 3.6 14.7 - - + +
154B VAL 2.9 26.6 + - - -
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Residues in contact with LEU 110 (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 LEU* 4.1 11.4 - - + -
14B MET 3.0 14.9 + - - +
15B GLY* 4.0 1.6 - - - -
16B VAL 4.9 0.2 + - - -
19B SER* 3.7 32.8 + - - +
21B LYS* 3.6 35.2 - - + +
24B VAL* 4.1 17.0 - - + -
108B ILE* 3.4 8.2 + - + +
109B TYR* 1.3 78.6 - - - +
111B LYS* 1.3 59.5 + - - +
112B GLY 4.1 0.7 + - - -
117B ILE* 5.6 0.3 - - - +
154B VAL* 3.7 17.5 - - + -
156B ILE* 3.5 15.0 - - + -
163B VAL* 3.7 26.0 - - + -
167B THR* 4.2 9.2 - - - +
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Residues in contact with LYS 111 (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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109B TYR* 3.1 31.6 + - + +
110B LEU* 1.3 72.5 - - - +
112B GLY* 1.3 64.8 + - - +
113B ASP* 6.0 2.0 - - - -
143B GLU* 3.5 25.9 + - - +
153B VAL* 3.9 23.8 - - + +
154B VAL 2.8 16.3 + - - +
155B ASP* 3.7 7.1 - - - +
156B ILE* 3.0 24.5 + - - +
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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