Contacts of the helix formed by residues 163 - 170 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C THR* 3.9 21.5 - - - +
38C VAL* 3.3 25.1 - - + -
39C GLY* 3.5 25.5 - - - -
41C VAL* 3.8 15.9 - - + +
42C ASP* 3.1 36.8 + - - -
48C ALA 6.1 0.2 - - - -
50C PHE* 3.6 30.1 - - + +
160D ARG* 3.8 17.3 - - - -
161D GLY* 3.6 12.7 - - - +
162D LYS* 1.3 77.6 - - - +
164D TYR* 1.3 104.9 + + + +
166D LYS* 3.0 13.7 + - - +
167D SER* 3.4 11.7 + - - -
169D LYS* 4.3 24.5 - - + -
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Residues in contact with TYR 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D ARG* 3.7 40.2 - - + -
161D GLY 3.2 13.4 + - - +
163D TRP* 1.3 101.0 - + + +
165D GLY* 1.3 57.8 + - - +
166D LYS 3.1 3.8 + - - -
167D SER* 2.8 22.1 + - - -
169D LYS* 3.7 33.0 + - + +
170D VAL* 3.6 27.9 - - + +
178D LEU* 3.8 19.7 - - + +
181D ASN* 3.2 22.5 + - - +
182D ILE* 3.9 9.6 - - + +
207D PRO 5.7 0.2 - - - -
227D ILE* 3.4 29.8 - - + -
312D AKG 5.5 1.1 - - - -
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Residues in contact with GLY 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313C EDO 5.1 2.6 + - - -
161D GLY 4.5 0.6 + - - -
162D LYS* 3.5 7.5 + - - +
163D TRP 3.2 0.6 - - - -
164D TYR* 1.3 79.0 - - - +
166D LYS* 1.3 63.6 + - - +
167D SER 3.5 0.4 - - - -
170D VAL* 3.4 27.9 - - - +
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Residues in contact with LYS 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C THR* 3.7 11.6 - - - +
50C PHE* 2.8 40.2 + - + +
51C PHE* 3.6 14.1 - - - -
52C THR* 4.2 13.8 - - + +
313C EDO 3.7 36.6 + - - +
314C CL 3.2 25.5 - - + +
162D LYS* 4.3 9.0 - - - +
163D TRP 3.0 10.6 + - - +
165D GLY* 1.3 81.4 - - - +
167D SER* 1.3 60.5 + - - +
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Residues in contact with SER 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C THR* 3.3 28.9 - - - -
163D TRP* 3.4 9.2 + - - -
164D TYR* 2.8 21.0 + - - -
166D LYS* 1.3 81.1 - - - +
168D TRP* 1.3 68.9 - - - +
169D LYS* 3.0 27.9 + - - +
170D VAL* 3.3 18.2 + - - +
171D ASP* 4.1 2.3 + - - +
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Residues in contact with TRP 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C THR* 4.5 5.5 + - - -
79D PRO* 3.7 34.5 - - + +
80D ASN* 3.5 33.4 - - - -
167D SER* 1.3 79.4 - - - +
169D LYS* 1.3 80.3 + - + +
170D VAL 3.2 0.4 - - - -
171D ASP* 2.9 34.3 + - - +
174D LYS* 3.7 30.7 - - + +
175D SER* 3.7 23.7 - - - -
181D ASN* 3.7 11.9 - - - -
311D NAD 2.7 54.9 + - - -
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Residues in contact with LYS 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D TYR* 4.8 6.1 - - - +
160D ARG* 6.1 0.6 - - - +
163D TRP* 4.3 20.3 - - + -
164D TYR* 3.7 42.6 + - + -
167D SER* 3.0 16.2 - - - +
168D TRP* 1.3 115.0 - - + +
170D VAL* 1.3 57.6 + - - +
175D SER* 2.8 21.8 + - - -
177D GLY* 5.0 4.0 - - - -
178D LEU* 5.4 0.5 + - - -
181D ASN* 3.6 17.7 - - - +
311D NAD 2.9 38.4 + - - -
312D AKG 4.8 11.6 + - - -
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Residues in contact with VAL 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D TYR* 3.6 37.7 - - + +
165D GLY* 3.4 30.7 - - - +
166D LYS 5.2 0.2 - - - -
167D SER 3.3 13.4 + - - +
169D LYS* 1.3 76.1 - - - +
171D ASP* 1.3 61.9 + - + +
172D GLU* 3.4 4.8 + - - +
175D SER* 4.5 0.7 - - - -
177D GLY* 6.1 1.8 - - - -
207D PRO* 5.4 9.0 - - + +
227D ILE* 5.5 0.4 - - + -
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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