Contacts of the helix formed by residues 157 - 167 (chain N) in PDB entry 1KYO
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 VAL 157 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154N ILE* 3.9 20.4 - - + -
156N PHE* 1.3 78.0 - - + +
158N GLY* 1.3 68.3 + - - +
159N ASN 3.6 0.9 - - - -
160N ASP* 2.8 32.5 + - + +
161N ILE* 3.1 28.2 + - + -
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Residues in contact with GLY 158 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151N PHE 3.7 12.9 - - - +
152N SER* 4.0 9.0 - - - -
154N ILE* 3.0 27.4 + - - -
155N PRO 5.1 0.4 - - - -
156N PHE 3.2 3.4 - - - -
157N VAL* 1.3 75.2 - - - +
159N ASN* 1.3 66.7 + - - +
161N ILE* 2.9 20.3 + - - +
162N VAL* 3.2 10.9 + - - +
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Residues in contact with ASN 159 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152N SER* 4.3 17.5 + - - -
155N PRO 5.9 0.6 + - - -
156N PHE 5.0 2.2 + - - -
157N VAL 3.6 0.8 - - - -
158N GLY* 1.3 73.4 - - - +
160N ASP* 1.3 61.8 + - - +
162N VAL* 3.2 11.3 + - - +
163N SER* 2.9 31.3 + - - -
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Residues in contact with ASP 160 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156N PHE 4.6 2.9 - - - +
157N VAL* 2.8 27.8 + - + +
159N ASN* 1.3 77.5 - - - +
161N ILE* 1.3 64.7 + - + +
163N SER* 3.4 7.5 + - - -
164N TRP* 2.9 26.4 + - - +
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Residues in contact with ILE 161 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151N PHE* 4.4 17.3 - - + -
154N ILE* 4.4 12.8 - - + -
157N VAL* 3.1 38.8 + - + +
158N GLY* 2.9 7.8 + - - +
160N ASP* 1.3 75.9 - - + +
162N VAL* 1.3 63.8 + - - +
164N TRP* 3.2 19.2 + - + +
165N LEU* 3.0 36.2 + - + +
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Residues in contact with VAL 162 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148N THR* 3.7 18.4 - - - +
149N ASN* 3.8 11.0 - - - +
151N PHE* 3.9 2.9 - - + -
152N SER* 3.4 39.7 - - - +
158N GLY 3.2 8.9 + - - +
159N ASN* 3.5 8.3 - - - +
160N ASP 3.2 0.6 - - - -
161N ILE* 1.3 75.1 - - - +
163N SER* 1.3 57.4 + - - +
165N LEU* 3.1 11.9 + - - +
166N TRP* 3.0 62.8 + - + +
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Residues in contact with SER 163 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E THR* 5.4 0.2 - - - -
84E ALA* 5.3 2.3 + - - +
159N ASN 2.9 20.1 + - - -
160N ASP* 3.4 10.2 + - - -
162N VAL* 1.3 71.9 - - - +
164N TRP* 1.3 60.7 + - - +
166N TRP* 4.2 10.1 - - - -
167N GLY* 2.8 26.6 + - - -
168N GLY 3.6 21.1 + - - -
169N PHE* 5.8 0.2 - - - -
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Residues in contact with TRP 164 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E ILE* 3.1 50.1 + - + +
82E MET* 3.3 37.2 - - + +
83E THR* 3.5 31.6 - - + +
160N ASP 2.9 19.9 + - - +
161N ILE* 3.3 19.3 - - + +
163N SER* 1.3 77.6 + - - +
165N LEU* 1.3 94.6 + - + +
167N GLY* 3.2 8.4 + - - -
178N ARG* 3.2 16.6 + - - -
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Residues in contact with LEU 165 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E MET* 5.2 5.6 - - + -
148N THR* 4.4 17.5 - - + +
151N PHE* 3.9 28.3 - - + -
161N ILE* 3.0 28.9 + - + +
162N VAL* 3.1 8.9 + - - +
164N TRP* 1.3 95.8 - - + +
166N TRP* 1.3 66.1 + - - +
175N THR* 4.3 4.0 - - - +
178N ARG* 3.1 30.6 + - - +
179N PHE* 5.0 5.0 - - + -
182N LEU* 6.5 0.4 - - + -
525N SMA 3.9 31.0 - - + -
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Residues in contact with TRP 166 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145N THR* 4.5 4.5 - - + -
148N THR* 2.8 29.8 + - + -
149N ASN* 3.6 30.1 - - - -
162N VAL* 3.0 31.8 + - + +
163N SER* 4.0 12.3 - - - +
165N LEU* 1.3 78.5 - - - +
167N GLY* 1.3 62.7 + - - +
168N GLY* 3.7 11.2 - - - +
169N PHE 3.3 20.0 - - - -
170N SER* 3.3 34.9 - - - +
171N VAL* 3.3 28.4 - - + +
174N PRO* 3.6 2.9 - - - +
175N THR* 3.2 40.8 + - + +
178N ARG* 3.8 0.9 + - - -
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Residues in contact with GLY 167 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E MET 3.7 11.4 - - - -
84E ALA* 3.7 21.0 - - - +
85E THR 4.6 0.9 + - - -
88E VAL* 4.3 4.0 - - - +
163N SER 2.8 13.2 + - - -
164N TRP 3.2 2.2 + - - -
165N LEU 3.2 2.2 - - - -
166N TRP* 1.3 79.0 - - - +
168N GLY* 1.3 56.8 - - - +
174N PRO* 3.6 20.6 - - - +
178N ARG* 3.4 19.0 + - - -
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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