Contacts of the helix formed by residues 169 - 183 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130C GLU* 4.3 0.7 - - - -
134C ARG* 3.3 23.5 + - - -
357C TYR* 5.8 0.3 - - - -
168D TYR* 1.3 75.3 - - - +
170D PRO* 1.3 69.8 - - - +
171D GLU* 3.2 7.9 + - - +
172D GLU* 2.9 35.5 + - - +
173D PHE* 2.9 29.1 + - - +
199D TYR 3.5 4.9 - - - -
200D ASN* 3.6 2.5 - - - -
66J ARG* 3.0 14.4 + - - +
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Residues in contact with PRO 170 (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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134C ARG* 4.3 7.9 - - - +
169D SER* 1.3 90.3 - - - +
171D GLU* 1.3 68.1 + - - +
173D PHE* 3.2 10.7 + - + +
174D GLU 2.9 23.9 + - - -
199D TYR 3.2 15.9 - - - +
200D ASN* 3.7 18.8 - - - +
204D GLU* 3.3 33.4 - - + +
205D ARG* 4.9 1.6 - - + +
208D ILE* 3.3 29.3 - - + +
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Residues in contact with GLU 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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134C ARG* 3.0 33.6 + - - -
357C TYR* 5.4 1.3 - - - -
358C SER* 2.8 41.7 + - - +
169D SER* 3.2 5.9 + - - +
170D PRO* 1.3 83.1 - - - +
172D GLU* 1.3 65.1 + - + +
174D GLU* 3.3 19.6 + - - +
175D LYS* 3.6 11.4 + - - +
208D ILE* 5.0 1.1 - - + -
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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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355C LYS* 5.6 1.2 + - - -
168D TYR* 3.3 8.5 - - - +
169D SER* 2.9 20.2 + - - +
171D GLU* 1.3 78.1 - - + +
173D PHE* 1.3 61.5 + - - +
175D LYS* 3.7 5.3 + - - +
176D LEU 3.3 16.3 + - - -
61J TRP* 3.5 36.4 - - + +
62J TYR* 3.6 5.9 - - - -
63J GLU* 2.9 26.5 + - - +
66J ARG* 2.3 38.5 + - - -
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Residues in contact with PHE 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D PRO* 3.8 24.5 - - + -
168D TYR* 3.8 26.9 - + + -
169D SER 2.9 14.8 + - - +
170D PRO* 3.3 12.3 - - + +
171D GLU 3.2 0.2 - - - -
172D GLU* 1.3 76.2 - - - +
174D GLU* 1.3 59.9 + - - +
176D LEU* 3.4 3.2 + - + +
177D ALA* 2.8 31.8 + - + +
188D MET* 3.9 17.9 - - + -
189D KCX 6.3 0.4 - - - -
190D ASP* 5.1 4.3 - - - -
200D ASN* 4.5 1.1 - - - +
205D ARG* 3.9 30.3 - - + -
208D ILE* 4.3 7.6 - - + -
209D MET* 3.5 42.6 - - + -
226D TRP* 4.4 12.1 - - - -
61J TRP* 4.1 7.2 - - - -
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Residues in contact with GLU 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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170D PRO 2.9 9.8 + - - +
171D GLU* 3.3 14.2 + - - +
173D PHE* 1.3 76.6 - - - +
175D LYS* 1.3 63.3 + - - +
177D ALA* 3.9 2.7 - - - +
178D TYR* 3.0 23.8 + - + +
208D ILE* 3.6 40.1 - - + +
211D LYS* 2.8 35.9 + - - -
212D ILE* 3.9 12.6 - - + +
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Residues in contact with LYS 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 GLU 3.6 8.8 + - - +
172D GLU* 4.0 7.2 - - - +
173D PHE 3.4 0.4 - - - -
174D GLU* 1.3 78.6 - - - +
176D LEU* 1.3 60.2 + - - +
178D TYR* 3.3 8.3 + - + +
179D ASP* 2.9 68.5 + - - +
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Residues in contact with LEU 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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162D PRO* 4.1 18.4 - - + -
172D GLU 3.3 15.1 + - - +
173D PHE* 3.8 4.0 - - + +
175D LYS* 1.3 81.8 - - - +
177D ALA* 1.3 58.5 + - - +
179D ASP* 3.4 5.1 + - + +
180D LEU* 2.9 49.6 + - + +
188D MET* 4.4 2.9 - - + -
395D LEU* 3.2 31.4 - - + -
401D PRO* 3.7 22.4 - - + -
61J TRP* 3.5 44.0 - - + -
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Residues in contact with ALA 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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173D PHE* 2.8 28.1 + - + +
174D GLU* 3.9 4.0 - - - +
176D LEU* 1.3 72.8 - - - +
178D TYR* 1.3 64.7 + - - +
180D LEU* 4.0 0.2 - - - +
181D LEU* 3.0 32.2 + - - +
188D MET* 3.9 29.2 - - + -
209D MET* 3.9 21.3 - - + -
212D ILE* 4.3 6.3 - - + -
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Residues in contact with TYR 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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174D GLU* 3.0 18.4 + - + +
175D LYS* 3.6 9.4 - - + +
177D ALA* 1.3 77.7 - - - +
179D ASP* 1.3 74.4 + - - +
181D LEU 4.1 0.2 - - - -
182D SER* 2.7 47.6 + - - -
212D ILE* 4.0 20.1 - - + +
215D LYS* 3.0 43.6 - - + -
216D VAL* 3.7 16.6 - - + +
219D GLU* 2.7 27.0 + - - -
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Residues in contact with ASP 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 LYS* 2.9 53.6 + - - +
176D LEU* 3.8 5.9 - - + +
178D TYR* 1.3 93.6 - - - +
180D LEU* 1.3 63.1 + - + +
182D SER* 3.4 2.0 + - - -
183D ASN* 2.7 34.1 + - - +
401D PRO* 5.8 2.5 - - + -
402D ALA* 4.5 20.1 - - + +
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Residues in contact with LEU 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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160D VAL* 3.9 19.7 - - + -
176D LEU* 2.9 44.0 + - + +
179D ASP* 1.3 77.0 - - + +
181D LEU* 1.3 62.5 + - - +
183D ASN* 3.1 12.5 + - - +
184D GLY 3.5 0.9 + - - -
185D ALA* 3.2 25.4 + - + +
188D MET* 3.5 34.5 - - + -
394D THR* 4.0 17.0 - - + -
395D LEU* 4.8 1.6 - - + -
401D PRO* 3.9 37.2 - - + +
402D ALA 4.5 0.2 - - - +
405D ALA* 4.1 8.3 - - + +
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Residues in contact with LEU 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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177D ALA 3.0 22.2 + - - +
180D LEU* 1.3 75.4 - - - +
182D SER* 1.3 62.0 + - - +
183D ASN 3.4 0.7 + - - -
184D GLY 3.7 2.3 + - - -
185D ALA* 3.3 24.5 - - + +
186D ASP 4.1 2.5 - - - +
187D TYR* 3.8 31.9 - - - +
188D MET* 4.0 7.6 - - + -
209D MET* 4.0 26.0 - - + -
212D ILE* 4.2 13.2 - - + -
213D ILE* 4.5 4.7 - - + -
216D VAL* 3.8 18.9 - - + +
220D THR* 5.1 1.0 - - - +
224D LYS* 3.0 46.5 + - + -
225D THR 4.9 1.1 - - - +
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Residues in contact with SER 182 (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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178D TYR* 2.7 44.5 + - - -
179D ASP* 3.7 6.1 - - - -
180D LEU 3.2 0.2 - - - -
181D LEU* 1.3 77.4 - - - +
183D ASN* 1.3 66.8 + - - +
184D GLY 3.5 0.9 + - - -
216D VAL* 3.9 15.0 - - - +
219D GLU* 4.8 2.8 + - - -
220D THR* 4.6 15.3 - - - +
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Residues in contact with ASN 183 (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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179D ASP* 2.7 27.4 + - - +
180D LEU 3.1 8.3 + - - +
182D SER* 1.3 86.8 - - - +
184D GLY* 1.3 54.9 + - - +
185D ALA 3.7 0.2 - - - -
402D ALA* 3.6 30.3 - - - +
405D ALA* 3.5 14.4 - - + +
406D ARG* 2.7 51.1 + - + +
409D ARG* 4.4 0.9 - - - +
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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