Contacts of the helix formed by residues 167 - 179 (chain C) in PDB entry 1K82
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 GLY 167 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C GLU* 2.7 22.7 + - - +
56C LYS* 3.8 4.3 - - - +
158C MET* 4.0 7.6 - - - -
165C GLY 3.3 4.8 + - - -
166C VAL* 1.3 74.2 - - - +
168C ASN* 1.3 64.2 + - - -
171C ALA* 3.0 22.7 + - - +
428K G 3.2 22.9 - - - -
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Residues in contact with ASN 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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2C GLU* 3.3 1.4 + - - -
154C LYS* 2.7 30.5 + - - -
158C MET* 3.5 12.5 - - + +
167C GLY* 1.3 72.2 - - - +
169C ILE* 1.3 63.9 + - - +
171C ALA* 4.0 1.0 - - - +
172C SER* 3.6 19.6 + - - -
236C TYR* 3.9 8.1 - - - -
258C ARG* 3.5 24.8 - - - +
259C ALA* 2.8 29.7 + - - +
427K PED 2.7 34.3 + - - +
428K G 3.0 9.8 + - - +
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Residues in contact with ILE 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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2C GLU* 2.9 16.5 + - + +
5C GLU* 5.6 1.8 - - - +
168C ASN* 1.3 78.5 - - - +
170C TYR* 1.3 76.3 + - + +
172C SER* 3.3 5.4 + - - -
173C GLU* 3.0 27.3 + - + +
214C THR* 3.8 22.0 - - + +
216C LEU* 3.5 22.9 - - + -
233C LEU* 3.9 28.0 - - + -
236C TYR* 3.4 39.1 - - + +
427K PED 3.5 18.2 - - + +
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Residues in contact with TYR 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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2C GLU* 2.9 34.1 + - + +
4C PRO* 3.6 12.6 - - + -
5C GLU* 2.6 36.9 + - - -
166C VAL* 3.8 13.6 - - + +
167C GLY 5.0 0.2 - - - -
169C ILE* 1.3 86.9 - - + +
171C ALA* 1.3 61.3 + - - +
173C GLU* 3.9 5.2 - - + -
174C SER* 2.9 38.0 + - - +
204C VAL* 3.8 18.8 - - + -
205C LEU* 4.2 17.7 - - + -
208C SER* 2.6 30.8 + - - -
214C THR* 3.1 14.2 + - - -
229C PHE* 3.7 24.0 - + - -
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Residues in contact with ALA 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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154C LYS* 4.3 15.9 - - + +
157C LEU* 4.4 7.5 - - + +
158C MET* 3.6 27.8 - - + -
166C VAL* 3.5 13.3 - - + +
167C GLY 3.0 19.7 + - - +
168C ASN 4.0 2.0 - - - +
170C TYR* 1.3 77.5 - - - +
172C SER* 1.3 62.0 + - - +
174C SER* 3.8 2.1 - - - -
175C LEU* 3.2 31.7 + - - +
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Residues in contact with SER 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C LYS* 4.1 3.5 - - - +
168C ASN 3.6 10.4 + - - -
169C ILE 3.3 7.7 + - - -
171C ALA* 1.3 77.3 - - - +
173C GLU* 1.3 65.4 + - - +
175C LEU* 3.3 9.1 + - - +
176C PHE* 3.1 18.4 + - - +
182C PRO* 5.9 1.2 - - - +
235C VAL* 3.6 15.5 - - - +
236C TYR* 5.0 3.1 - - - -
259C ALA 4.7 0.2 + - - -
260C THR* 3.8 14.0 - - - -
261C PHE* 3.3 44.7 + - - +
267C GLN* 4.6 0.5 + - - -
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Residues in contact with GLU 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C ILE* 3.0 24.2 + - + +
170C TYR* 4.1 9.0 - - + +
172C SER* 1.3 75.4 - - - +
174C SER* 1.3 63.9 + - - +
176C PHE* 3.2 4.6 + - - +
177C ALA* 3.0 23.4 + - - +
204C VAL* 4.4 15.7 - - + +
229C PHE* 5.1 4.2 - - + -
232C GLU 4.2 1.2 - - - +
233C LEU* 3.5 28.0 - - + +
234C GLN* 2.7 31.8 + - - +
235C VAL* 2.6 38.9 + - + +
236C TYR* 2.8 8.9 + - + -
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Residues in contact with SER 174 (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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157C LEU* 4.9 2.7 - - - -
166C VAL* 5.1 1.0 - - - +
170C TYR* 2.9 23.5 + - - +
171C ALA* 3.8 5.2 - - - -
173C GLU* 1.3 76.4 - - - +
175C LEU* 1.3 62.8 + - - +
177C ALA* 3.5 3.3 + - - +
178C ALA* 3.1 23.7 + - - +
197C LEU* 4.1 4.4 - - - +
200C VAL* 3.7 4.8 - - - +
201C ILE* 3.4 44.6 - - - +
204C VAL* 4.0 19.5 - - - +
205C LEU* 5.8 0.5 - - - +
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Residues in contact with LEU 175 (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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153C ILE* 4.1 18.8 - - + -
154C LYS* 3.6 40.2 - - + -
157C LEU* 4.1 12.6 - - + -
171C ALA 3.2 19.5 + - - +
172C SER* 3.8 4.9 - - - +
173C GLU 3.2 0.4 - - - -
174C SER* 1.3 75.2 - - - +
176C PHE* 1.3 65.8 + - - +
178C ALA* 3.1 3.1 + - - -
179C GLY 2.9 18.4 + - - -
180C ILE* 3.0 38.8 + - + +
182C PRO* 4.0 11.2 - - + -
197C LEU* 4.1 20.0 - - + -
267C GLN* 3.6 7.2 - - - +
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Residues in contact with PHE 176 (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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172C SER 3.1 12.5 + - - +
173C GLU* 3.5 8.5 - - - +
175C LEU* 1.3 75.0 - - - +
177C ALA* 1.3 60.5 + - + +
179C GLY* 2.8 25.3 + - - -
234C GLN* 3.4 46.0 - - + -
235C VAL* 3.5 23.1 - - + -
243C CYS* 3.7 32.5 - - - -
244C ARG 5.3 0.4 - - - -
245C VAL* 4.4 12.1 - - + -
250C ILE* 5.1 0.9 - - + -
263C CYS* 3.8 12.8 - - + -
266C CYS* 4.1 13.7 - - + +
267C GLN* 3.4 32.1 - - + +
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Residues in contact with ALA 177 (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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173C GLU 3.0 16.6 + - - +
174C SER 3.7 5.2 - - - +
176C PHE* 1.3 84.6 - - + +
178C ALA* 1.3 58.2 + - - +
196C LEU* 5.4 1.4 - - - +
200C VAL* 4.1 18.4 - - + +
204C VAL* 4.2 19.3 - - + -
234C GLN* 6.5 0.2 - - + -
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Residues in contact with ALA 178 (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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174C SER 3.1 15.4 + - - +
175C LEU 3.1 4.2 + - - +
176C PHE 3.0 1.4 - - - -
177C ALA* 1.3 77.0 - - - +
179C GLY* 1.3 63.6 + - - +
180C ILE* 3.4 25.9 + - + +
196C LEU* 3.8 25.3 - - + +
197C LEU* 4.0 10.3 - - + -
200C VAL* 3.7 18.8 - - + -
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Residues in contact with GLY 179 (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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175C LEU 2.9 0.4 + - - -
176C PHE 2.8 14.5 + - - -
177C ALA 3.4 0.8 + - - -
178C ALA* 1.3 79.5 - - - +
180C ILE* 1.3 60.3 + - - +
266C CYS 3.5 18.1 - - - +
267C GLN* 3.7 3.0 - - - -
268C LYS* 2.9 27.4 + - - +
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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