Contacts of the helix formed by residues 172 - 190 (chain C) in PDB entry 1KXT
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 172 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134C TRP* 3.4 37.3 + - - +
135C ASP* 3.1 23.3 + - - +
169C ALA* 3.1 17.2 + - + +
171C GLU* 1.3 90.8 - - + +
173C ASP* 1.3 59.5 + - - +
174C TYR* 4.2 17.7 - - - +
175C VAL* 3.2 8.8 + - + +
176C ARG* 3.0 28.7 + - - -
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Residues in contact with ASP 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C GLU 3.6 2.8 + - - -
172C LYS* 1.3 70.0 - - - +
174C TYR* 1.3 59.3 + - - +
176C ARG* 4.1 12.3 + - - +
177C SER* 2.7 54.8 + - - -
213C LYS* 3.5 19.8 + - - -
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Residues in contact with TYR 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C PRO* 2.6 33.6 + - - +
131C TYR* 4.1 6.5 - + - -
135C ASP* 3.3 36.8 - - - -
172C LYS* 3.2 18.8 - - - +
173C ASP* 1.3 80.9 + - - +
175C VAL* 1.3 59.8 + - - +
177C SER* 3.7 5.0 - - - -
178C MET* 2.9 56.5 + - + +
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Residues in contact with VAL 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C TYR* 4.3 7.2 - - + +
135C ASP* 4.0 37.5 - - + +
168C LEU* 3.9 18.2 - - + -
169C ALA 3.3 33.2 - - - +
170C LEU* 4.2 5.6 - - + -
172C LYS* 3.2 10.2 + - + +
173C ASP 3.2 0.4 - - - -
174C TYR* 1.3 77.2 - - + +
176C ARG* 1.3 68.0 + - - +
178C MET* 3.0 5.7 + - - +
179C ILE* 3.0 43.1 + - + +
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Residues in contact with ARG 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C LEU* 2.9 22.8 + - + +
171C GLU* 3.5 16.7 + - - +
172C LYS 3.0 24.2 + - - +
173C ASP* 3.7 12.3 + - - +
175C VAL* 1.3 76.9 - - - +
177C SER* 1.3 56.9 + - - +
179C ILE* 3.8 3.1 - - - +
180C ALA* 3.0 28.4 + - - +
205C GLY 4.7 1.0 + - - -
206C ASP* 2.7 36.9 + - - +
209C ALA* 3.4 26.4 - - + +
210C VAL* 3.6 30.4 - - + +
213C LYS* 4.1 14.6 - - - +
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Residues in contact with SER 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C ASP* 2.7 44.6 + - - -
174C TYR* 3.7 5.2 - - - -
176C ARG* 1.3 70.8 - - - +
178C MET* 1.3 57.0 + - - +
180C ALA* 3.3 1.4 + - - +
181C ASP* 2.7 42.0 + - - +
213C LYS* 3.5 20.8 + - - -
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Residues in contact with MET 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C TYR* 4.2 8.0 - - + -
129C VAL* 3.3 52.0 - - + +
130C PRO* 3.8 4.3 - - + -
131C TYR* 3.8 15.3 - - + +
174C TYR* 2.9 58.2 + - + +
175C VAL 3.0 4.2 + - - +
177C SER* 1.3 73.2 - - - +
179C ILE* 1.3 66.5 + - - +
181C ASP* 3.2 25.9 + - - +
182C TYR* 3.3 10.4 + - - +
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Residues in contact with ILE 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C TYR* 3.7 21.3 - - - +
99C ILE* 3.5 42.6 - - + +
131C TYR* 3.7 3.1 - - - +
168C LEU* 3.8 9.9 - - + -
170C LEU* 3.5 32.1 - - + -
175C VAL* 3.0 20.5 + - + +
176C ARG 3.8 3.8 - - - +
178C MET* 1.3 74.8 - - - +
180C ALA* 1.3 58.7 + - - +
182C TYR* 2.8 27.6 + - + +
183C LEU* 3.0 18.1 + - + +
210C VAL* 3.8 20.9 - - + -
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Residues in contact with ALA 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C ARG 3.0 19.2 + - - +
177C SER* 3.6 5.2 - - - +
179C ILE* 1.3 76.5 - - - +
181C ASP* 1.3 54.6 + - - +
183C LEU* 3.9 5.2 - - - +
184C ASN* 2.7 43.3 + - - +
210C VAL* 4.1 15.5 - - + +
213C LYS* 3.6 34.3 - - + -
214C LEU* 4.8 1.6 - - + -
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Residues in contact with ASP 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C SER* 2.7 34.2 + - - +
178C MET* 3.3 24.1 - - - +
179C ILE 3.1 0.2 - - - -
180C ALA* 1.3 75.1 - - - +
182C TYR* 1.3 65.3 + - - +
184C ASN* 3.9 8.1 + - - +
185C LYS* 3.0 24.4 + - - +
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Residues in contact with TYR 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C PRO* 3.1 27.9 - - + +
46C ASN* 3.3 24.8 + - + +
67C TYR* 3.5 56.3 - + + -
69C LEU* 3.7 19.7 - - + -
95C VAL* 4.2 2.5 - - + +
96C ASP 4.9 0.9 + - - -
97C ALA* 4.9 11.2 - - + -
98C VAL 5.2 1.8 - - - -
99C ILE* 5.0 8.1 - - + -
178C MET 3.3 5.6 + - - +
179C ILE* 2.8 11.3 + - + +
181C ASP* 1.3 79.1 - - - +
183C LEU* 1.3 78.3 + - + +
185C LYS* 3.1 27.3 + - - +
186C LEU* 3.1 29.1 + - + +
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Residues in contact with LEU 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ALA* 3.9 22.0 - - + -
99C ILE* 5.0 5.8 - - + -
179C ILE* 3.0 31.0 + - + +
180C ALA 3.9 1.6 - - - +
182C TYR* 1.3 89.8 - - + +
184C ASN* 1.3 56.1 + - - +
186C LEU* 3.2 10.7 + - + +
187C ILE* 2.9 31.5 + - - +
194C PHE* 3.5 37.4 - - + -
196C ILE* 5.5 6.1 - - + -
210C VAL* 4.2 14.8 - - + -
211C LEU* 5.8 2.5 - - + -
214C LEU* 3.7 23.1 - - + -
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Residues in contact with ASN 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C ALA* 2.7 28.5 + - - +
181C ASP* 4.0 7.7 + - - +
182C TYR 3.3 0.2 - - - -
183C LEU* 1.3 70.5 - - - +
185C LYS* 1.3 67.6 + - - +
187C ILE* 3.6 4.0 - - - +
188C ASP* 2.9 32.9 + - - +
213C LYS* 3.0 22.3 + - - +
214C LEU* 3.2 10.2 - - - +
215C HIS* 2.9 57.1 + - + +
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Residues in contact with LYS 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C TYR* 2.9 30.5 + - - +
68C LYS* 4.5 4.0 - - - +
69C LEU* 3.7 29.5 - - + +
76C GLU* 5.0 8.5 - - - +
80C ARG* 5.4 2.9 - - - +
181C ASP 3.0 12.6 + - - +
182C TYR* 3.1 20.0 + - - +
184C ASN* 1.3 77.0 - - - +
186C LEU* 1.3 52.3 + - - +
188C ASP* 3.5 7.0 + - - +
189C ILE* 2.7 51.3 + - + +
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Residues in contact with LEU 186 (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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45C PRO* 5.0 1.6 - - + -
69C LEU* 3.8 32.8 - - + -
79C PHE* 4.2 14.8 - - + -
95C VAL* 4.1 13.0 - - + -
182C TYR* 3.1 47.3 + - + +
183C LEU* 3.3 12.6 - - + +
185C LYS* 1.3 78.8 - - + +
187C ILE* 1.3 66.5 + - - +
189C ILE* 3.0 15.8 + - + +
190C GLY 3.1 9.2 + - - -
191C VAL* 3.2 26.4 - - + +
194C PHE* 3.8 21.3 - - + -
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Residues in contact with ILE 187 (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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183C LEU 2.9 22.0 + - - +
184C ASN* 3.3 15.9 + - - +
186C LEU* 1.3 73.2 - - - +
188C ASP* 1.3 63.7 + - - +
190C GLY* 2.7 28.4 + - - -
191C VAL 4.0 9.4 - - - +
193C GLY 5.2 0.2 - - - +
194C PHE* 3.3 32.8 - - + -
214C LEU* 5.0 3.8 - - + -
215C HIS* 4.0 10.8 - - + +
216C ASN 3.2 27.6 - - - +
217C LEU* 3.8 19.7 - - + -
218C ASN* 4.0 7.2 + - - +
228C PRO* 4.0 20.2 - - + -
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Residues in contact with ASP 188 (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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184C ASN 2.9 22.4 + - - +
185C LYS* 3.6 7.0 - - - +
187C ILE* 1.3 77.5 - - - +
189C ILE* 1.3 64.4 + - + +
215C HIS* 3.3 29.6 + - - +
216C ASN 5.4 0.2 - - - +
218C ASN* 3.0 24.3 + - - +
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Residues in contact with ILE 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LEU* 5.0 7.2 - - + -
76C GLU* 5.3 0.2 - - - +
79C PHE* 4.4 6.5 - - + -
80C ARG* 3.1 64.6 + - + +
83C VAL* 3.9 29.1 - - + +
84C THR* 5.2 2.6 + - - -
185C LYS* 2.7 35.7 + - + +
186C LEU* 3.0 21.1 + - + +
188C ASP* 1.3 77.2 - - + +
190C GLY* 1.3 55.7 + - - +
191C VAL* 4.7 2.2 - - + +
218C ASN* 4.3 0.3 + - - -
221C TRP* 3.9 15.2 - - - -
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Residues in contact with GLY 190 (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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83C VAL* 3.9 11.2 - - - +
87C ASN* 3.8 11.3 + - - +
93C ILE 5.7 0.7 + - - -
186C LEU 3.1 0.2 + - - -
187C ILE 2.7 18.0 + - - -
188C ASP 4.1 1.3 - - - -
189C ILE* 1.3 74.7 - - - +
191C VAL* 1.3 68.7 + - - +
192C ALA 3.4 1.4 + - - -
218C ASN* 4.3 7.4 - - - -
221C TRP* 4.3 14.4 - - - -
222C PHE* 3.7 17.6 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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