Contacts of the helix formed by residues 163 - 170 (chain C) in PDB entry 3O9Z
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 TRP 163 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C TYR* 6.4 2.9 - + + -
160C ARG* 3.8 31.6 - - - -
161C GLY* 3.7 9.8 - - - +
162C LYS* 1.3 75.4 - - - +
164C TYR* 1.3 95.8 + + + +
166C LYS* 3.0 14.6 + - - +
167C SER* 3.4 14.1 + - - -
169C LYS* 4.3 20.9 - - + -
36D THR* 3.5 22.3 - - - +
37D ASN* 5.9 0.9 - - - -
38D VAL* 3.3 24.9 - - + -
39D GLY* 3.7 23.0 - - - -
41D VAL* 4.1 15.7 - - + -
42D ASP* 3.1 34.6 + - - -
50D PHE* 3.6 29.2 - - + +
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Residues in contact with TYR 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C ARG* 3.7 40.4 - - + -
161C GLY 3.1 15.3 + - - +
163C TRP* 1.3 93.7 - + + +
165C GLY* 1.3 57.5 + - - +
167C SER* 2.8 27.0 + - - -
169C LYS* 3.6 37.7 + - + +
170C VAL* 3.6 29.0 - - + +
178C LEU* 4.0 10.7 - - + +
181C ASN* 3.0 24.8 + - - +
182C ILE* 3.6 18.7 - - + +
227C ILE* 3.6 27.1 - - + -
312C AKG 5.5 0.2 - - - -
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Residues in contact with GLY 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C GLY 4.4 0.4 + - - -
162C LYS* 3.4 8.0 + - - +
163C TRP 3.2 0.8 - - - -
164C TYR* 1.3 78.1 - - - +
166C LYS* 1.3 65.3 + - - +
167C SER 3.4 0.7 - - - -
170C VAL* 3.4 28.2 - - - +
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Residues in contact with LYS 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 LYS* 3.9 7.6 + - - +
163C TRP 3.0 11.2 + - - +
165C GLY* 1.3 82.7 - - - +
167C SER* 1.3 59.6 + - - +
170C VAL* 5.2 0.2 - - - -
36D THR* 3.8 10.6 - - - +
50D PHE* 2.9 34.9 + - + +
51D PHE* 3.6 18.0 - - - -
52D THR* 4.2 19.7 - - + +
313D CL 3.2 31.6 - - + +
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Residues in contact with SER 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C TRP* 3.8 10.8 - - - -
164C TYR* 2.8 20.2 + - - -
166C LYS* 1.3 80.0 - - - +
168C TRP* 1.3 65.0 + - - +
169C LYS* 3.0 33.8 + - - +
170C VAL* 3.3 18.0 + - - +
171C ASP* 4.2 2.3 + - - +
36D THR* 3.5 26.2 - - - -
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Residues in contact with TRP 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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79C PRO* 3.7 37.0 - - + +
80C ASN* 3.5 40.2 - - - -
167C SER* 1.3 73.7 - - - +
169C LYS* 1.3 85.8 + - + +
170C VAL 3.1 0.4 - - - -
171C ASP* 3.0 29.7 + - - +
174C LYS* 3.9 27.9 - - + +
175C SER* 3.7 17.4 - - - -
181C ASN* 3.7 11.0 - - - -
311C NAD 2.7 58.7 + - - -
36D THR* 4.8 7.1 + - - -
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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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163C TRP* 4.3 17.4 - - + -
164C TYR* 3.6 45.6 + - + -
167C SER* 3.0 18.2 - - - +
168C TRP* 1.3 114.3 - - + +
170C VAL* 1.3 58.6 + - - +
171C ASP 3.4 0.2 - - - -
175C SER* 2.8 20.6 + - - -
177C GLY 5.0 3.8 - - - -
178C LEU* 5.4 0.3 + - - -
181C ASN* 3.8 12.9 + - - +
311C NAD 2.9 51.2 + - - -
312C AKG 4.8 6.3 + - - -
36D THR* 6.0 0.2 - - - -
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Residues in contact with VAL 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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164C TYR* 3.6 37.5 - - + +
165C GLY* 3.4 30.5 - - - +
166C LYS 5.2 0.2 - - - -
167C SER 3.3 14.7 + - - +
169C LYS* 1.3 75.7 - - - +
171C ASP* 1.3 61.5 + - + +
172C GLU* 3.4 4.7 + - - +
175C SER* 4.5 0.7 - - - -
177C GLY* 6.0 2.0 - - - -
207C PRO* 5.7 6.3 - - + +
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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