Contacts of the helix formed by residues 169 - 183 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A ARG* 3.7 12.4 + - - +
134G ARG* 3.4 23.6 + - - -
357G TYR* 5.9 0.3 - - - -
168H TYR* 1.3 75.1 - - - +
170H PRO* 1.3 64.2 - - - +
171H GLU* 3.4 6.6 + - - +
172H GLU* 2.9 38.5 + - - +
173H PHE* 2.7 35.7 + - - +
199H TYR 3.6 5.6 - - - -
200H ASN* 3.8 3.1 - - - -
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Residues in contact with PRO 170 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134G ARG* 4.3 5.2 - - - +
169H SER* 1.3 90.5 - - - +
171H GLU* 1.3 68.1 + - - +
173H PHE* 3.5 10.6 - - + +
174H GLU 2.8 23.6 + - - -
199H TYR 3.4 13.2 - - - +
200H ASN* 3.6 21.1 - - - +
204H GLU* 3.6 34.8 - - + +
205H ARG* 4.4 4.3 - - - +
208H ILE* 3.0 30.4 - - + +
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Residues in contact with GLU 171 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134G ARG* 2.9 39.3 + - - -
357G TYR* 5.3 2.0 - - - +
358G SER* 3.5 34.0 + - - +
169H SER* 3.4 7.5 + - - +
170H PRO* 1.3 83.4 - - - +
172H GLU* 1.3 65.0 + - + +
174H GLU* 3.3 25.4 + - - +
175H LYS* 3.7 5.9 + - - +
204H GLU* 5.5 2.1 - - - +
208H ILE* 4.6 4.4 - - + +
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Residues in contact with GLU 172 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TRP* 3.4 37.0 - - + +
62A TYR* 3.5 16.8 - - - +
63A GLU* 3.1 19.4 + - - +
66A ARG* 3.1 24.3 + - - -
355G LYS* 5.5 1.6 + - - -
357G TYR* 5.7 0.5 - - - -
168H TYR* 3.3 6.1 - - - -
169H SER* 2.9 33.8 + - - +
171H GLU* 1.3 74.1 - - + +
173H PHE* 1.3 66.6 + - - +
174H GLU 3.3 0.7 + - - -
175H LYS* 3.5 12.2 + - - +
176H LEU 3.5 4.9 + - - -
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Residues in contact with PHE 173 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TRP* 3.7 10.3 - + - -
162H PRO* 3.9 23.8 - - + -
168H TYR* 3.6 28.3 - + + -
169H SER 2.7 21.3 + - - +
170H PRO* 3.5 9.0 - - + +
172H GLU* 1.3 74.9 - - - +
174H GLU* 1.3 67.5 + - - +
176H LEU* 3.5 2.1 + - + +
177H ALA* 2.9 25.1 + - + +
188H MET* 4.3 18.8 - - + -
189H KCX 5.9 0.2 - - - -
190H ASP* 4.9 7.2 - - - -
200H ASN* 4.8 0.7 - - - +
205H ARG* 4.1 25.4 - - + -
208H ILE* 4.4 4.7 - - + -
209H MET* 3.2 44.9 - - + -
226H TRP* 4.5 8.7 - - - -
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Residues in contact with GLU 174 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170H PRO 2.8 13.6 + - - +
171H GLU* 3.3 18.2 - - - +
172H GLU 3.1 0.4 - - - -
173H PHE* 1.3 78.0 - - - +
175H LYS* 1.3 64.4 + - - +
177H ALA 3.3 0.2 + - - -
178H TYR* 2.9 22.3 + - + +
208H ILE* 3.7 21.3 - - + +
211H LYS* 2.6 33.5 + - - -
212H ILE* 3.3 30.5 - - + +
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Residues in contact with LYS 175 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171H GLU 3.7 5.2 + - - +
172H GLU* 3.5 8.5 + - - +
173H PHE 3.4 0.4 - - - -
174H GLU* 1.3 77.6 - - - +
176H LEU* 1.3 68.3 + - - +
178H TYR* 3.0 8.3 + - + +
179H ASP* 2.8 44.5 + - - +
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Residues in contact with LEU 176 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A TRP* 3.3 57.2 - - + -
162H PRO* 4.0 19.7 - - + -
172H GLU 3.5 2.2 + - - -
173H PHE* 3.5 8.5 + - + +
174H GLU 3.4 0.2 - - - -
175H LYS* 1.3 78.7 - - - +
177H ALA* 1.3 64.4 + - - +
179H ASP* 3.0 8.7 + - + +
180H LEU* 2.9 39.5 + - + +
188H MET* 4.8 0.9 - - + -
395H LEU* 3.6 30.5 - - + -
401H PRO* 3.8 22.2 - - + -
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Residues in contact with ALA 177 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173H PHE* 2.9 23.2 + - + +
174H GLU 3.4 4.5 - - - +
176H LEU* 1.3 76.8 - - - +
178H TYR* 1.3 63.6 + - - +
180H LEU* 4.0 0.2 - - - +
181H LEU* 3.1 32.0 + - - +
188H MET* 4.0 21.7 - - + +
209H MET* 3.8 21.1 - - + -
212H ILE* 3.7 16.2 - - + -
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Residues in contact with TYR 178 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174H GLU* 2.9 15.5 + - + +
175H LYS* 3.6 9.6 - - + +
177H ALA* 1.3 76.6 - - - +
179H ASP* 1.3 70.6 + - - +
182H SER* 2.3 54.4 + - - -
212H ILE* 3.9 17.0 - - + +
215H LYS* 2.9 43.7 + - + -
216H VAL* 3.9 14.0 - - + +
219H GLU* 2.7 25.3 + - - -
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Residues in contact with ASP 179 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175H LYS* 2.8 43.6 + - - +
176H LEU* 3.5 12.2 - - + +
178H TYR* 1.3 86.2 - - - +
180H LEU* 1.3 67.4 + - + +
182H SER* 3.2 4.5 + - - -
183H ASN* 3.0 32.0 + - - +
401H PRO* 5.7 1.2 - - + +
402H ALA* 4.5 21.8 - - + +
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Residues in contact with LEU 180 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160H VAL* 3.8 20.2 - - + -
176H LEU* 2.9 33.9 + - + +
179H ASP* 1.3 71.5 - - - +
181H LEU* 1.3 56.4 + - - +
182H SER 2.9 3.8 - - - -
183H ASN* 2.5 35.7 + - - -
185H ALA* 3.5 17.2 + - + -
188H MET* 3.6 34.8 - - + -
394H THR* 3.8 25.8 - - + -
395H LEU* 4.4 2.5 - - + -
401H PRO* 4.0 24.0 - - + -
405H ALA* 4.0 13.7 - - + -
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Residues in contact with LEU 181 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177H ALA 3.1 16.7 + - - +
180H LEU* 1.3 78.6 - - - +
182H SER* 1.3 61.0 + - - +
183H ASN 3.4 0.2 + - - -
184H GLY 4.1 0.9 + - - -
185H ALA* 3.6 14.1 - - + +
186H ASP 4.0 3.4 - - - +
187H TYR* 3.7 42.4 - - - +
188H MET* 3.8 8.3 - - + -
209H MET* 3.8 28.7 - - + -
212H ILE* 4.3 11.9 - - + -
213H ILE* 4.6 4.7 - - + -
216H VAL* 3.8 14.7 - - + +
220H THR* 4.8 1.0 - - - +
224H LYS* 3.0 48.9 + - + -
225H THR 4.5 2.2 - - - +
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Residues in contact with SER 182 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178H TYR* 2.3 51.5 + - - -
179H ASP* 3.3 8.5 - - - -
180H LEU 2.8 0.8 + - - -
181H LEU* 1.3 77.5 - - - +
183H ASN* 1.3 67.7 + - - +
184H GLY 3.7 1.3 + - - -
216H VAL* 3.9 12.0 - - - +
219H GLU* 5.3 0.5 + - - -
220H THR* 4.6 14.3 - - - +
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Residues in contact with ASN 183 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179H ASP* 3.0 23.8 + - - +
180H LEU 2.5 19.5 + - - +
182H SER* 1.3 82.4 - - - +
184H GLY* 1.3 55.6 + - - +
402H ALA* 3.7 33.3 - - - +
405H ALA* 2.9 23.7 - - + +
406H ARG* 3.3 35.5 + - + +
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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
------------------------------------------------------------
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