Contacts of the helix formed by residues 161 - 166 (chain C) in PDB entry 1KYZ
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 THR 161 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152C ILE* 6.2 0.9 - - + -
154C PHE* 3.2 11.1 - - - -
155C ASN* 3.8 19.5 - - - +
160C MET* 1.3 84.0 - - - +
162C ALA* 1.3 63.9 + - - +
163C PHE* 3.6 11.1 + - - +
164C GLU* 3.1 35.9 + - - +
165C TYR 3.5 12.0 + - - -
325C PRO* 6.3 2.9 - - + -
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Residues in contact with ALA 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C PHE* 3.6 16.9 - - + -
155C ASN* 4.7 0.8 - - - +
161C THR* 1.3 72.8 - - - +
163C PHE* 1.3 60.4 + - + +
164C GLU 2.8 10.8 + - - -
165C TYR* 3.1 8.8 + - - +
166C HIS* 2.8 26.9 + - - -
323C HIS* 4.1 19.2 + - + +
366C FER 3.2 38.8 - - + +
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Residues in contact with PHE 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C THR* 3.6 9.2 + - - +
162C ALA* 1.3 78.7 - - + +
164C GLU* 1.3 61.6 + - + +
166C HIS* 4.1 15.6 - - - +
167C GLY 4.7 0.5 + - - -
270C ASP* 4.6 21.8 - - - -
271C TRP* 5.5 9.0 - + - -
325C PRO* 5.3 14.1 - - + -
366C FER 3.8 20.9 - + - -
1699C SAH 4.9 26.0 - + - -
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Residues in contact with GLU 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C MET* 3.1 41.3 - - + +
161C THR* 3.1 39.8 + - - +
162C ALA 2.8 1.2 + - - -
163C PHE* 1.3 78.5 - - + +
165C TYR* 1.3 66.4 + - - +
166C HIS 3.1 2.5 - - - -
167C GLY* 2.8 17.7 + - - -
168C THR* 4.1 0.5 + - - +
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Residues in contact with TYR 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C VAL* 3.5 35.8 - - + +
154C PHE* 3.8 20.0 - + + -
158C TYR* 3.2 39.2 - + - -
160C MET* 3.1 22.3 - - + +
161C THR 3.5 4.7 + - - +
162C ALA 3.1 6.3 + - - +
164C GLU* 1.3 77.8 - - - +
166C HIS* 1.3 54.8 + - + +
167C GLY 2.7 1.0 + - - -
168C THR* 2.7 44.9 + - - -
169C ASP* 3.6 24.5 + - + +
172C PHE* 4.0 14.8 - + + -
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Residues in contact with HIS 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C ALA* 2.8 27.0 + - + -
163C PHE* 4.1 13.0 + - - +
164C GLU 3.0 0.8 + - - -
165C TYR* 1.3 75.9 - - + +
167C GLY* 1.3 57.0 + - - +
168C THR 3.4 0.2 - - - -
169C ASP 3.8 17.9 + - - +
170C PRO* 5.0 0.7 - - - +
172C PHE* 4.3 13.0 - + - -
173C ASN* 3.5 38.0 + - - +
176C PHE* 3.5 40.4 - + + +
366C FER 3.5 32.8 - + - -
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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