Contacts of the helix formed by residues 169 - 183 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A ARG* 3.5 16.9 + - - -
357A TYR* 5.7 0.3 - - - -
168B TYR* 1.3 75.5 - - - +
170B PRO* 1.3 71.0 - - - +
171B GLU* 3.3 14.0 + - - +
172B GLU* 2.8 39.0 + - - +
173B PHE* 2.9 28.9 + - - +
199B TYR 3.5 6.7 - - - -
200B ASN* 3.6 2.0 - - - -
66G ARG* 3.6 12.2 + - - +
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Residues in contact with PRO 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ARG* 4.4 5.4 - - - +
169B SER* 1.3 88.7 - - - +
171B GLU* 1.3 63.4 + - - +
173B PHE* 3.2 10.7 + - + +
174B GLU 2.7 31.7 + - - -
199B TYR 3.4 12.3 - - - +
200B ASN* 4.0 22.2 - - - +
204B GLU* 3.6 33.9 - - + +
205B ARG* 4.4 5.6 - - - +
208B ILE* 3.3 27.7 - - + +
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Residues in contact with GLU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ARG* 3.1 40.5 + - - +
357A TYR* 5.5 2.0 - - + -
358A SER* 3.3 30.4 + - - +
169B SER* 3.3 9.3 + - - +
170B PRO* 1.3 81.8 - - - +
172B GLU* 1.3 64.5 + - + +
174B GLU* 3.2 29.9 + - - +
175B LYS* 3.4 6.8 + - - +
204B GLU* 4.7 3.6 - - - +
208B ILE* 4.6 2.9 - - + -
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Residues in contact with GLU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A LYS* 5.5 1.9 + - - -
168B TYR* 3.3 6.2 - - - -
169B SER* 2.8 35.5 + - - +
171B GLU* 1.3 77.0 - - + +
173B PHE* 1.3 62.0 + - - +
175B LYS* 3.3 8.7 + - - +
176B LEU 3.3 15.9 + - - -
61G TRP* 3.7 31.9 - - + +
62G TYR* 3.6 7.5 - - - +
63G GLU* 2.9 29.3 + - - +
66G ARG* 3.1 22.3 + - - -
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Residues in contact with PHE 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B PRO* 3.8 14.6 - - + -
168B TYR* 3.9 25.6 - + + -
169B SER 2.9 18.1 + - - +
170B PRO* 3.4 7.2 - - + +
172B GLU* 1.3 74.7 - - - +
174B GLU* 1.3 58.8 - - - +
176B LEU* 3.3 4.4 + - + -
177B ALA* 2.8 40.5 + - + +
188B MET* 3.8 34.5 - - + -
189B KCX 6.4 0.2 - - - -
190B ASP* 5.0 4.5 - - - -
200B ASN* 4.8 0.7 - - - +
205B ARG* 4.0 28.7 - - + -
208B ILE* 5.0 2.2 - - + -
209B MET* 3.3 43.3 - - + -
226B TRP* 4.4 8.5 - - - -
61G TRP* 3.9 8.4 - - - -
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Residues in contact with GLU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B PRO 2.7 15.0 + - - +
171B GLU* 3.3 17.8 - - - +
173B PHE* 1.3 73.5 - - - +
175B LYS* 1.3 62.6 + - - +
177B ALA* 3.6 4.1 - - - +
178B TYR* 3.1 24.3 + - - +
208B ILE* 3.3 44.7 - - + +
211B LYS* 5.8 2.6 - - - +
212B ILE* 3.7 19.2 - - + +
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Residues in contact with LYS 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B GLU 3.4 5.5 + - - +
172B GLU* 3.3 11.6 + - - +
173B PHE 3.2 0.6 - - - -
174B GLU* 1.3 76.7 - - - +
176B LEU* 1.3 68.7 + - - +
178B TYR* 3.1 19.8 + - + +
179B ASP* 2.9 41.9 + - - +
61G TRP* 6.5 1.3 - - + -
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Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B PRO* 4.2 14.8 - - + -
172B GLU 3.3 8.3 + - - +
173B PHE* 3.3 7.1 + - + +
175B LYS* 1.3 81.9 - - - +
177B ALA* 1.3 63.6 + - - +
179B ASP* 3.3 6.4 + - + +
180B LEU* 3.0 45.4 + - + +
188B MET* 4.7 1.3 - - + -
395B LEU* 4.1 15.3 - - + -
401B PRO* 3.7 37.5 - - + -
61G TRP* 3.7 50.7 - - + -
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Residues in contact with ALA 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B PHE* 2.8 31.1 + - + +
174B GLU* 3.6 6.1 - - - +
176B LEU* 1.3 75.2 - - - +
178B TYR* 1.3 64.3 + - - +
180B LEU* 3.8 0.5 - - - +
181B LEU* 3.0 28.3 + - - +
188B MET* 4.3 17.7 - - + +
209B MET* 3.9 27.8 - - + -
212B ILE* 4.4 8.5 - - + -
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Residues in contact with TYR 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B GLU 3.1 11.0 + - - +
175B LYS* 3.1 12.8 + - + +
177B ALA* 1.3 77.9 - - - +
179B ASP* 1.3 68.4 + - - +
181B LEU* 4.0 1.2 - - - +
182B SER* 2.4 51.5 + - - -
212B ILE* 3.8 26.1 - - + +
215B LYS* 3.9 25.2 + - + -
216B VAL* 3.7 23.6 - - + -
219B GLU* 2.6 33.1 + - - -
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Residues in contact with ASP 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B LYS* 2.9 48.3 + - - +
176B LEU* 3.7 10.5 - - + +
178B TYR* 1.3 89.8 - - - +
180B LEU* 1.3 59.0 + - + +
182B SER* 3.2 7.2 + - - -
183B ASN* 3.0 34.9 + - - +
401B PRO* 5.7 1.1 - - + -
402B ALA* 4.8 18.2 - - + +
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Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B VAL* 3.9 19.7 - - + -
176B LEU* 3.0 37.6 + - + +
177B ALA 3.9 2.0 - - - +
179B ASP* 1.3 76.4 - - - +
181B LEU* 1.3 62.9 + - - +
183B ASN 3.0 12.8 + - - -
184B GLY 3.5 0.2 + - - -
185B ALA* 3.2 25.2 + - + +
188B MET* 3.6 37.0 - - + -
394B THR* 3.7 18.4 - - + -
395B LEU* 4.3 2.0 - - + -
401B PRO* 3.6 37.0 - - + +
405B ALA* 3.8 8.4 - - + +
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Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B ALA 3.0 18.7 + - - +
178B TYR 4.2 1.6 - - - +
180B LEU* 1.3 77.4 - - - +
182B SER* 1.3 61.6 + - - +
183B ASN 3.5 0.3 + - - -
184B GLY 3.7 1.0 + - - -
185B ALA* 3.4 20.0 - - + +
186B ASP 4.1 2.5 - - - +
187B TYR* 3.8 32.5 - - - +
188B MET* 3.9 8.5 - - + -
209B MET* 4.0 27.4 - - + -
212B ILE* 4.2 13.7 - - + -
213B ILE* 4.3 11.4 - - + -
216B VAL* 3.8 17.8 - - + +
220B THR* 5.2 0.9 - - - +
224B LYS* 2.7 40.2 + - + -
225B THR 4.5 2.2 - - - +
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Residues in contact with SER 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B TYR* 2.4 51.1 + - - -
179B ASP* 3.4 7.9 - - - -
180B LEU 3.1 0.2 - - - -
181B LEU* 1.3 78.2 - - - +
183B ASN* 1.3 65.3 + - - +
184B GLY 3.3 3.6 + - - -
216B VAL* 4.1 10.7 - - - +
219B GLU* 5.3 0.5 + - - -
220B THR* 4.6 14.8 - - - +
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Residues in contact with ASN 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B ASP* 3.0 18.3 + - - +
180B LEU 3.0 1.2 + - - -
182B SER* 1.3 84.5 - - - +
184B GLY* 1.3 54.3 + - - +
402B ALA* 2.6 54.7 + - - +
405B ALA* 3.0 23.8 - - + +
406B ARG* 3.1 42.9 + - + +
409B ARG* 4.2 0.5 - - - +
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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
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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