Contacts of the helix formed by residues 164 - 173 (chain C) in PDB entry 1T7C
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 SER 164 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132C ALA* 3.8 22.8 - - - +
163C LEU* 1.3 76.5 - - - +
165C ASN* 1.3 65.2 + - - +
166C THR* 3.7 8.8 + - - -
167C ASN* 3.0 28.2 + - - +
168C CYS* 2.8 21.6 + - - +
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Residues in contact with ASN 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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163C LEU 3.8 1.5 + - - +
164C SER* 1.3 71.8 - - - +
166C THR* 1.3 58.2 + - - +
168C CYS* 3.6 6.6 - - - +
169C LYS* 2.8 56.0 + - - +
176C ILE* 4.2 11.8 - - - +
177C LYS 5.3 0.7 - - - +
180C MET 4.0 6.6 - - - +
181C ILE* 5.0 1.9 - - - -
182C CYS* 5.3 2.7 + - - -
230C ARG* 3.1 30.7 + - - +
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Residues in contact with THR 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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164C SER* 3.1 8.6 - - - -
165C ASN* 1.3 81.8 - - - +
167C ASN* 1.3 62.2 + - - +
169C LYS* 4.0 7.0 - - - +
170C LYS* 3.3 33.0 + - + +
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Residues in contact with ASN 167 (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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163C LEU* 3.6 26.8 - - + +
164C SER* 3.0 27.3 + - - +
166C THR* 1.3 73.9 - - - +
168C CYS* 1.3 66.1 + - - +
170C LYS* 3.3 36.8 + - - +
171C TYR* 4.3 0.7 + - - +
225C PRO* 5.0 4.5 - - - +
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Residues in contact with CYS 168 (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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163C LEU* 4.8 2.2 - - + +
164C SER 2.8 12.3 + - - +
165C ASN* 3.6 9.6 - - - +
167C ASN* 1.3 79.3 - - - +
169C LYS* 1.3 57.2 + - - +
171C TYR* 2.9 22.7 + - - +
172C TRP* 3.2 22.1 + - - -
176C ILE* 3.6 17.3 - - + -
182C CYS* 2.0 54.1 - - + -
225C PRO* 3.8 11.9 - - - -
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Residues in contact with LYS 169 (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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165C ASN* 2.8 38.2 + - + +
166C THR* 4.0 7.2 - - - +
167C ASN 3.4 0.2 - - - -
168C CYS* 1.3 66.6 - - - +
170C LYS* 1.3 59.1 + - - +
171C TYR 2.9 6.5 - - - -
172C TRP 4.2 0.7 - - - +
173C GLY* 2.8 49.0 + - - +
174C THR* 5.7 1.6 - - - +
176C ILE* 4.1 36.9 + - + -
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Residues in contact with LYS 170 (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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166C THR* 3.3 27.7 + - + +
167C ASN* 3.3 30.1 - - - +
168C CYS 3.0 1.2 + - - -
169C LYS* 1.3 77.9 - - - +
171C TYR* 1.3 57.7 + - + +
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Residues in contact with TYR 171 (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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167C ASN 5.3 0.9 - - - +
168C CYS 2.9 7.4 + - - +
169C LYS 2.9 1.2 - - - -
170C LYS* 1.3 81.8 - - + +
172C TRP* 1.3 99.6 + + - +
173C GLY 3.4 1.9 + - - -
217C SER* 5.9 1.0 - - - -
223C SER 5.9 0.9 - - - -
224C THR* 3.4 34.6 + - + +
225C PRO* 4.1 18.2 - - + -
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Residues in contact with TRP 172 (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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168C CYS* 3.2 27.9 + - - +
171C TYR* 1.3 103.2 - + - +
173C GLY* 1.3 65.5 + - - +
174C THR 3.4 0.5 + - - -
175C LYS* 3.1 29.7 + - + +
176C ILE* 3.6 26.7 - - + -
215C TRP* 3.6 27.4 - + + -
216C GLY* 3.7 21.8 - - - -
217C SER* 3.7 17.7 - - - -
218C SER 5.4 0.2 - - - -
224C THR* 3.6 18.4 - - + +
225C PRO* 2.9 24.8 + - + +
227C VAL* 4.0 4.8 - - + +
13D PRO* 6.1 0.9 - - + -
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Residues in contact with GLY 173 (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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169C LYS* 2.8 47.4 + - - +
171C TYR 3.4 2.0 + - - -
172C TRP* 1.3 76.9 - - - +
174C THR* 1.3 60.6 + - - -
175C LYS 3.1 4.9 + - - -
176C ILE* 3.4 8.1 + - - +
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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