Contacts of the helix formed by residues 170 - 181 (chain D) in PDB entry 1KR2
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 LYS 170 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94D GLU* 4.7 14.1 - - - +
97D LYS* 5.8 4.4 - - - +
169D TRP* 1.3 72.5 - - - +
171D SER* 1.3 60.3 + - - +
172D GLU* 3.7 26.4 + - - +
173D ASP* 2.8 59.7 + - - +
174D ILE* 3.3 4.7 + - - +
273D ASN* 3.3 31.1 - - + +
812D TAD 4.6 2.0 + - - -
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Residues in contact with SER 171 (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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169D TRP 3.3 5.5 + - - -
170D LYS* 1.3 71.2 - - - +
172D GLU* 1.3 74.0 + - - +
174D ILE* 3.4 15.6 + - - +
175D THR* 3.1 24.1 + - - -
202D VAL* 5.3 4.7 - - - +
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Residues in contact with GLU 172 (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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170D LYS* 3.7 32.8 + - - +
171D SER* 1.3 91.2 + - - +
173D ASP* 1.3 66.4 + - - +
175D THR* 3.4 7.4 + - - -
176D GLN* 3.0 39.9 + - + +
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Residues in contact with ASP 173 (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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94D GLU* 3.5 31.9 - - - +
96D LEU* 3.4 30.5 - - + +
169D TRP* 5.0 7.6 - - + -
170D LYS* 2.8 45.0 + - + +
172D GLU* 1.3 77.9 - - - +
174D ILE* 1.3 55.7 + - - +
176D GLN* 2.9 6.1 + - - +
177D ILE* 2.7 44.3 + - + +
812D TAD 4.6 5.5 + - - +
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Residues in contact with ILE 174 (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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163D PHE* 3.8 61.7 - - + +
169D TRP* 3.9 28.9 - - + +
170D LYS 3.3 1.5 + - - +
171D SER* 3.4 19.5 + - - +
173D ASP* 1.3 75.4 - - - +
175D THR* 1.3 65.4 + - - +
177D ILE* 3.2 8.4 + - - +
178D VAL* 3.0 26.3 + - - +
202D VAL* 4.1 16.2 - - + -
203D LEU* 4.0 14.8 - - + -
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Residues in contact with THR 175 (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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171D SER 3.1 12.9 + - - -
172D GLU* 3.6 11.0 - - - -
173D ASP 3.2 0.4 - - - -
174D ILE* 1.3 78.9 - - - +
176D GLN* 1.3 60.9 + - + +
178D VAL* 3.5 1.4 - - - +
179D ALA* 2.8 37.8 + - + +
202D VAL* 3.4 25.1 - - + +
206D HIS* 4.4 16.4 - - - +
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Residues in contact with GLN 176 (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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96D LEU* 3.8 24.8 - - + +
100D ARG* 3.2 23.0 + - - +
172D GLU* 3.0 33.2 + - + +
173D ASP* 2.9 6.6 + - - +
175D THR* 1.3 78.2 - - + +
177D ILE* 1.3 61.7 + - - +
179D ALA* 4.6 0.4 - - - -
180D ASN* 2.7 57.4 + - - +
181D TYR* 3.7 1.0 - - - -
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Residues in contact with ILE 177 (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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95D THR* 4.1 15.5 - - + -
96D LEU* 4.0 22.9 - - + +
99D LEU* 3.8 18.8 - - + -
153D LEU* 4.5 4.0 - - + -
163D PHE* 5.0 6.3 - - + -
169D TRP* 3.7 32.1 - - + -
173D ASP* 2.7 26.8 + - + +
174D ILE* 3.6 6.5 - - - +
176D GLN* 1.3 72.3 - - - +
178D VAL* 1.3 63.8 + - + +
181D TYR* 3.0 32.3 + - - +
182D GLY 3.1 14.0 + - - +
183D LEU* 4.5 21.3 - - + -
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Residues in contact with VAL 178 (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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163D PHE* 4.6 4.5 - - + -
174D ILE 3.0 19.6 + - - +
175D THR* 3.5 8.5 - - - +
177D ILE* 1.3 81.9 - - + +
179D ALA* 1.3 60.6 + - - +
182D GLY* 4.0 5.8 + - - +
183D LEU* 4.3 16.2 - - + -
202D VAL* 4.3 11.4 - - + +
203D LEU* 3.6 25.4 - - + -
206D HIS* 3.8 27.7 - - + +
209D ASN* 2.9 33.8 - - - +
210D ILE* 4.0 16.2 - - + -
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Residues in contact with ALA 179 (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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175D THR* 2.8 29.5 + - + +
176D GLN* 4.3 0.9 - - - +
178D VAL* 1.3 78.3 - - - +
180D ASN* 1.3 70.0 + - - +
206D HIS* 3.5 35.2 - - + +
209D ASN* 3.8 7.3 - - - +
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Residues in contact with ASN 180 (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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150D LYS* 5.3 8.8 + - - +
176D GLN* 2.7 50.1 + - - +
179D ALA* 1.3 83.6 - - - +
181D TYR* 1.3 79.9 + - + +
209D ASN* 4.6 0.2 - - - -
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Residues in contact with TYR 181 (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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96D LEU* 3.7 21.7 - - + +
99D LEU* 3.8 43.5 - - + -
100D ARG* 3.5 34.8 + - - +
103D GLN* 4.0 24.1 - - + +
150D LYS* 5.1 4.0 - - - +
151D VAL* 3.5 22.0 - - + +
152D LYS* 2.9 32.3 + - - +
176D GLN 3.7 9.9 - - - -
177D ILE* 3.0 13.4 + - - +
180D ASN* 1.3 100.5 - - + +
182D GLY* 1.3 64.1 + - - +
209D ASN* 3.2 5.4 - - - +
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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