Contacts of the helix formed by residues 169 - 182 (chain C) in PDB entry 3KDO
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 SER 169 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134B ARG* 3.2 16.9 + - - -
357B TYR* 5.7 0.2 - - - -
168C TYR* 1.3 76.2 - - - +
170C PRO* 1.3 65.2 - - - +
171C GLU* 3.0 22.6 + - - +
172C GLU* 2.8 35.4 + - - +
173C PHE* 2.9 27.7 + - - +
199C TYR 3.6 5.8 - - - -
200C ASN* 3.6 1.6 - - - -
66F ARG* 3.6 13.5 + - - +
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Residues in contact with PRO 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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134B ARG* 4.0 5.6 - - - +
169C SER* 1.3 91.1 - - - +
171C GLU* 1.3 67.0 + - - +
173C PHE* 3.1 6.4 + - + +
174C GLU 2.8 24.3 + - - -
199C TYR 3.3 12.8 - - - +
200C ASN* 3.6 26.9 - - - +
201C ARG 4.6 0.2 - - - +
204C GLU* 3.6 33.4 - - + +
205C ARG* 4.6 4.5 - - + +
208C ILE* 3.2 28.7 - - + +
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Residues in contact with GLU 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ARG* 2.9 37.1 + - - -
357B TYR* 5.5 0.9 - - - -
358B SER* 3.2 32.8 + - - +
169C SER* 3.0 18.5 + - - +
170C PRO* 1.3 78.4 - - + +
172C GLU* 1.3 64.6 + - + +
174C GLU* 3.3 21.6 + - - +
175C LYS* 3.6 7.6 + - - +
204C GLU* 4.4 4.2 - - - +
208C ILE* 4.6 4.0 - - + -
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Residues in contact with GLU 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B LYS* 5.5 1.6 + - - -
168C TYR* 3.3 7.1 - - - +
169C SER* 2.8 37.9 + - - +
171C GLU* 1.3 78.5 - - + +
173C PHE* 1.3 61.3 + - - +
175C LYS* 3.7 5.4 + - - +
176C LEU 3.5 15.1 + - - -
61F TRP* 3.5 35.4 - - + +
62F TYR* 3.7 5.1 - - - +
63F GLU* 3.0 28.1 + - - +
66F ARG* 3.0 23.8 + - - -
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Residues in contact with PHE 173 (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 PRO* 3.5 29.8 - - + -
168C TYR* 3.6 26.2 - + + -
169C SER 2.9 15.7 + - - +
170C PRO* 3.3 11.7 - - + +
172C GLU* 1.3 76.5 - - - +
174C GLU* 1.3 63.0 + - - +
176C LEU* 3.4 2.0 + - + +
177C ALA* 2.8 30.4 + - + +
188C MET* 4.1 20.6 - - + -
189C KCX 6.0 0.4 - - - -
190C ASP* 4.7 6.3 - - - -
200C ASN* 4.6 0.9 - - - +
205C ARG* 4.1 25.8 - - + -
208C ILE* 4.6 4.3 - - + -
209C MET* 3.4 40.4 - - + -
226C TRP* 4.5 8.7 - - - -
61F TRP* 4.0 8.3 - + - -
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Residues in contact with GLU 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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170C PRO 2.8 10.1 + - - +
171C GLU* 3.6 12.3 - - - +
172C GLU 3.3 0.4 - - - -
173C PHE* 1.3 78.0 - - - +
175C LYS* 1.3 65.1 + - - +
177C ALA* 3.6 3.8 - - - +
178C TYR* 3.0 23.7 + - + +
208C ILE* 3.6 38.0 - - + +
212C ILE* 3.7 26.9 - - + +
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Residues in contact with LYS 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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171C GLU 3.6 8.1 + - - +
172C GLU* 4.1 7.4 - - - +
173C PHE 3.4 0.4 - - - -
174C GLU* 1.3 79.7 - - - +
176C LEU* 1.3 63.3 + - - +
178C TYR* 3.4 4.9 + - - +
179C ASP* 3.1 36.0 + - - +
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Residues in contact with LEU 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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162C PRO* 4.0 18.2 - - + -
172C GLU 3.5 10.9 + - - +
173C PHE* 3.4 7.3 + - + +
174C GLU 3.3 0.6 - - - -
175C LYS* 1.3 78.7 - - - +
177C ALA* 1.3 64.4 + - - +
179C ASP* 3.2 6.5 + - + +
180C LEU* 2.9 45.5 + - + +
188C MET* 4.8 1.1 - - + -
395C LEU* 4.1 10.8 - - + -
401C PRO* 3.5 39.5 - - + -
61F TRP* 3.6 47.8 - - + -
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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 PHE* 2.8 27.5 + - + +
174C GLU* 3.6 5.6 - - - +
176C LEU* 1.3 74.2 - - - +
178C TYR* 1.3 62.5 + - - +
180C LEU* 3.8 0.3 - - - +
181C LEU* 3.0 29.9 + - - +
188C MET* 4.0 21.7 - - + +
209C MET* 3.8 28.5 - - + -
212C ILE* 4.4 8.7 - - + -
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Residues in contact with TYR 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 GLU* 3.0 17.3 + - + +
175C LYS* 3.7 6.3 - - - +
177C ALA* 1.3 77.1 - - - +
179C ASP* 1.3 70.2 + - - +
182C SER* 2.8 54.0 + - - -
212C ILE* 3.9 23.2 - - + +
215C LYS* 3.9 30.9 + - + -
216C VAL* 3.7 18.7 - - + +
219C GLU* 2.8 31.0 + - - -
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Residues in contact with ASP 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 LYS* 3.1 24.6 + - - +
176C LEU* 3.7 6.2 - - - +
178C TYR* 1.3 91.6 - - - +
180C LEU* 1.3 65.1 + - + +
182C SER* 3.8 2.4 - - - -
183C ASN* 2.8 37.9 + - - +
401C PRO* 5.4 3.4 - - + -
402C ALA* 4.6 15.9 - - + +
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Residues in contact with LEU 180 (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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160C VAL* 3.8 19.3 - - + -
176C LEU* 2.9 35.6 + - + +
177C ALA 3.8 2.7 - - - +
179C ASP* 1.3 74.4 - - - +
181C LEU* 1.3 61.5 + - - +
183C ASN* 2.9 18.9 + - - +
184C GLY 3.4 0.9 + - - -
185C ALA* 3.2 23.5 + - + +
188C MET* 3.4 36.8 - - + -
394C THR* 3.8 17.3 - - + -
395C LEU* 4.2 1.8 - - + -
401C PRO* 3.7 38.8 - - + +
405C ALA* 3.9 8.0 - - + +
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Residues in contact with LEU 181 (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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177C ALA 3.0 20.2 + - - +
180C LEU* 1.3 77.6 - - - +
182C SER* 1.3 61.1 + - - +
183C ASN 3.1 1.1 + - - -
184C GLY 3.6 3.6 + - - -
185C ALA* 3.3 23.1 - - + +
186C ASP 3.8 4.3 - - - +
187C TYR* 3.7 33.7 - - - +
188C MET* 4.1 7.0 - - + +
209C MET* 3.9 28.3 - - + -
212C ILE* 4.3 12.3 - - + -
213C ILE* 4.7 3.8 - - + -
216C VAL* 3.9 13.6 - - + +
220C THR* 5.3 0.9 - - - +
224C LYS* 3.2 48.4 + - + -
225C THR 4.6 1.1 - - - +
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Residues in contact with SER 182 (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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178C TYR* 2.8 42.9 + - - -
179C ASP* 3.8 6.7 - - - -
180C LEU 3.1 0.2 - - - -
181C LEU* 1.3 76.4 - - - +
183C ASN* 1.3 64.9 + - - +
184C GLY 3.6 0.6 + - - -
216C VAL* 3.6 22.4 - - - +
219C GLU* 4.7 2.4 + - - -
220C THR* 4.8 14.4 - - - +
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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