Contacts of the strand formed by residues 150 - 156 (chain F) in PDB entry 1KR2
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 LYS 150 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7F THR* 4.3 25.6 + - + +
8F GLU 2.8 12.9 + - - +
9F VAL* 3.4 9.3 - - + +
10F VAL* 2.9 24.8 + - - +
103F GLN* 3.7 6.7 - - - +
148F VAL 4.4 7.4 - - - +
149F PRO* 1.3 75.5 - - - +
151F VAL* 1.3 61.9 + - - +
152F LYS* 4.0 22.8 - - - +
181F TYR 5.8 0.9 - - - +
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Residues in contact with VAL 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F VAL* 3.3 16.6 - - + +
12F LEU* 3.7 28.0 - - + -
47F ILE* 6.0 0.2 - - + -
99F LEU* 3.9 18.3 - - + +
102F HIS* 4.3 14.4 - - + -
103F GLN* 3.1 26.8 + - + +
106F LEU* 4.6 10.7 - - + +
149F PRO 3.9 1.4 + - - -
150F LYS* 1.3 73.1 - - - +
152F LYS* 1.3 64.7 + - - +
181F TYR* 3.5 40.7 - - + +
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Residues in contact with LYS 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F VAL* 3.6 29.8 - - + -
10F VAL 2.8 8.7 + - - +
11F LEU* 3.7 3.0 - - + +
12F LEU 2.9 24.4 + - - -
35F MET* 5.0 4.0 - - + -
41F TYR* 4.7 16.2 + - - -
99F LEU* 4.6 2.9 - - - -
150F LYS* 4.0 23.7 - - - +
151F VAL* 1.3 79.6 - - - +
153F LEU* 1.3 61.3 + - - +
154F LEU 3.4 0.5 + - - -
181F TYR 3.0 25.4 + - - +
182F GLY* 3.8 11.0 - - - +
184F ILE* 4.0 24.7 - - + -
209F ASN* 2.9 32.7 + - - +
211F HIS* 5.1 3.2 + - + -
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Residues in contact with LEU 153 (chain F).
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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12F LEU* 3.4 16.2 - - + +
14F CYS* 4.2 21.1 - - + +
95F THR* 3.7 33.2 - - + -
99F LEU* 4.1 22.5 - - + +
152F LYS* 1.3 70.8 - - - +
154F LEU* 1.3 66.8 + - - +
155F CYS* 4.8 1.3 - - + -
159F LEU* 4.5 19.7 - - + -
163F PHE* 5.9 1.3 - - + -
169F TRP* 5.3 1.3 - - + -
177F ILE* 4.6 8.5 - - + -
182F GLY 3.0 8.9 + - - +
183F LEU* 3.5 30.6 - - + +
184F ILE* 2.8 28.1 + - - +
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Residues in contact with LEU 154 (chain F).
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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11F LEU* 4.5 10.3 - - + -
12F LEU 2.7 24.2 + - - +
13F ALA* 3.8 18.2 - - + +
14F CYS 4.6 1.6 + - - +
27F LEU* 4.0 25.6 - - + +
28F PHE* 3.6 59.5 - - + +
31F ALA* 4.1 17.3 - - + -
152F LYS 3.4 1.6 + - - -
153F LEU* 1.3 75.4 - - - +
155F CYS* 1.3 75.6 + - - +
184F ILE* 3.4 13.7 - - + +
186F VAL* 4.1 13.0 - - + -
814F TAD 4.2 2.8 + - - +
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Residues in contact with CYS 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F LEU* 4.5 7.4 - - - -
153F LEU* 4.8 3.4 - - + -
154F LEU* 1.3 80.7 - - - +
156F GLY* 1.3 63.8 + - - +
159F LEU* 4.1 22.7 - - + -
160F LEU* 4.8 3.4 - - - -
183F LEU* 4.2 26.7 - - - -
184F ILE 2.9 13.2 + - - +
185F CYS* 3.2 13.0 - - - -
186F VAL* 2.7 36.0 + - - +
814F TAD 3.2 20.2 - - - +
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Residues in contact with GLY 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F CYS* 1.3 78.7 - - - +
157F ALA* 1.3 65.9 + - - -
158F ASP* 3.2 3.6 + - - -
159F LEU* 3.3 10.2 + - - +
160F LEU 3.4 7.8 + - - -
185F CYS* 3.5 8.5 - - - -
186F VAL 3.2 11.4 - - - -
814F TAD 3.1 36.4 + - - -
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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