Contacts of the helix formed by residues 164 - 180 (chain B) in PDB entry 5D9I
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 THR 164 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B THR* 1.4 82.6 + - - +
165B LYS* 1.3 59.7 + - - +
166B GLU* 3.8 11.0 + - - +
167B LYS* 3.2 29.8 + - - +
168B ALA* 2.8 28.6 + - - +
192B HIS* 4.0 15.7 - - + +
193B ASN 4.4 0.2 - - - -
219B SER* 4.0 23.9 - - - +
220B PHE* 3.8 18.3 - - + -
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Residues in contact with LYS 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B THR 3.9 0.8 + - - -
164B THR* 1.3 73.8 - - - +
166B GLU* 1.3 64.2 + - - +
169B ALA* 3.1 24.3 + - + +
186B ARG* 3.7 19.3 - - - +
188B ASN* 5.4 3.8 - - - +
191B ASN 4.3 13.6 + - - +
192B HIS* 4.4 2.6 + - - +
193B ASN* 3.7 34.2 - - - +
244B ILE* 4.0 19.4 - - - +
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Residues in contact with GLU 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B THR* 3.8 11.7 + - - +
165B LYS* 1.3 78.9 - - - +
167B LYS* 1.3 68.0 + - + +
169B ALA* 3.6 5.8 + - - +
170B LEU* 3.5 25.6 + - - +
216B CME 5.0 0.4 - - - -
218B PHE* 3.7 24.0 - - + -
219B SER* 5.1 1.9 + - - -
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Residues in contact with LYS 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B THR* 3.3 20.4 - - + +
164B THR* 3.2 20.9 + - - +
166B GLU* 1.3 75.4 - - - +
168B ALA* 1.3 60.1 + - - +
170B LEU* 3.2 2.9 + - - -
171B LEU* 2.9 29.9 + - - +
213B GLN* 5.4 1.2 + - - -
216B CME 3.4 39.2 + - - +
218B PHE* 2.6 50.7 + - + +
219B SER* 3.0 24.2 + - - -
220B PHE 3.1 11.1 + - - -
221B LEU* 3.9 7.2 - - - +
301B CA 3.6 13.4 - - - -
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Residues in contact with ALA 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B THR* 3.7 14.9 - - + +
164B THR 2.8 14.7 + - - +
167B LYS* 1.3 72.6 - - - +
169B ALA* 1.3 61.3 + - - +
171B LEU* 3.8 5.2 - - - +
172B TYR* 3.0 26.2 + - - +
186B ARG* 3.6 9.5 - - - -
193B ASN* 3.3 39.7 - - + +
195B LEU* 3.9 12.8 - - + +
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Residues in contact with ALA 169 (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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165B LYS* 3.1 18.1 + - + +
166B GLU* 3.9 7.2 - - - +
167B LYS 3.2 0.2 - - - -
168B ALA* 1.3 76.8 - - - +
170B LEU* 1.3 70.1 + - + +
172B TYR* 3.6 12.0 - - - +
173B LYS* 4.3 8.3 + - - +
186B ARG* 3.8 30.5 - - - +
245B GLU* 4.8 2.1 - - - +
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Residues in contact with LEU 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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166B GLU 3.5 12.7 + - - +
167B LYS 3.2 7.8 + - - +
169B ALA* 1.3 87.3 - - + +
171B LEU* 1.3 64.1 + - - +
172B TYR 3.3 0.9 + - - -
173B LYS* 3.4 7.4 + - - +
174B LYS* 3.4 32.1 + - + +
216B CME 3.9 22.7 - - + -
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Residues in contact with LEU 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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161B ILE* 4.0 18.6 - - + -
163B THR* 4.5 4.7 - - + -
167B LYS 2.9 17.1 + - - +
168B ALA* 3.3 1.3 + - - +
170B LEU* 1.3 71.2 - - - +
172B TYR* 1.3 57.7 + - - +
174B LYS* 4.2 4.0 - - + -
175B ILE* 2.8 54.2 + - + +
195B LEU* 3.6 17.0 - - + -
212B ALA* 4.4 11.2 - - + -
215B LEU* 3.6 30.3 - - + -
216B CME 3.6 17.7 - - - +
221B LEU* 3.8 29.2 - - + -
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Residues in contact with TYR 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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168B ALA 3.0 17.0 + - - +
169B ALA 3.6 9.0 - - - +
170B LEU 3.2 0.2 - - - -
171B LEU* 1.3 77.4 - - - +
173B LYS* 1.3 87.2 + - + +
176B MET* 3.2 40.5 + - + +
184B ILE* 3.7 47.5 - - + +
186B ARG* 4.0 16.8 - - + -
195B LEU* 4.1 5.8 - - + +
245B GLU* 3.7 41.0 - - + +
246B GLU* 3.1 31.0 + - - -
247B SER* 3.2 7.8 + - - -
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Residues in contact with LYS 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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169B ALA 4.6 7.9 - - - +
170B LEU* 3.4 7.6 + - - +
171B LEU 3.3 0.6 - - - -
172B TYR* 1.3 103.8 - - + +
174B LYS* 1.3 62.9 + - + +
176B MET* 3.4 16.4 + - + +
177B GLU* 3.0 41.1 + - + +
245B GLU* 3.9 10.1 + - - -
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Residues in contact with LYS 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU* 3.4 24.0 + - + +
171B LEU* 3.2 7.5 + - + +
173B LYS* 1.3 76.9 - - - +
175B ILE* 1.3 57.4 + - - +
177B GLU* 3.4 19.1 + - - +
178B LYS* 2.8 36.6 + - - +
211B TYR* 3.4 21.4 + - - +
215B LEU* 4.1 27.1 - - + -
216B CME 5.8 2.0 - - + -
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Residues in contact with ILE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ILE* 5.5 2.0 - - + -
171B LEU* 2.8 41.6 + - + +
174B LYS* 1.3 71.7 - - - +
176B MET* 1.3 66.5 + - - +
178B LYS* 4.5 2.7 - - - -
179B TYR* 2.9 36.9 + - + +
181B VAL* 3.9 6.4 - - + +
184B ILE* 3.9 11.9 - - + -
195B LEU* 4.6 4.9 - - + -
197B PHE* 3.7 52.3 - - + -
208B ILE* 4.8 5.2 - - + -
211B TYR* 4.0 25.1 - - + -
212B ALA* 5.0 5.4 - - + -
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Residues in contact with MET 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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172B TYR* 3.2 44.6 + - + +
173B LYS* 3.5 17.7 - - + +
175B ILE* 1.3 77.4 - - - +
177B GLU* 1.4 59.7 + - + +
180B SER* 3.0 28.9 + - - -
181B VAL* 3.4 26.3 + - + +
184B ILE* 3.5 22.7 - - + -
247B SER* 4.2 10.1 - - - -
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Residues in contact with GLU 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 LYS* 3.0 27.6 + - - +
174B LYS* 3.8 24.3 + - - +
176B MET* 1.4 76.0 - - + +
178B LYS* 1.3 66.8 + - - +
179B TYR 3.4 0.3 + - - -
180B SER* 3.6 13.0 + - - +
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Residues in contact with LYS 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 LYS 2.8 21.2 + - - +
177B GLU* 1.3 76.2 - - - +
179B TYR* 1.3 98.5 + - + +
180B SER* 3.9 1.2 + - - -
211B TYR* 3.7 44.3 - - + +
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Residues in contact with TYR 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 ILE* 2.9 33.3 + - + +
176B MET 4.0 0.2 - - - -
178B LYS* 1.3 109.6 - - + +
180B SER* 1.3 71.6 + - - +
181B VAL* 3.0 6.9 + - + -
197B PHE* 5.0 2.2 - + - -
199B THR* 4.0 17.6 - - + +
200B PRO* 3.4 16.3 - - - +
201B HIS* 5.6 2.7 + - - -
203B HIS* 3.6 32.3 + + - -
207B ALA* 3.5 15.7 + - + +
208B ILE* 3.4 29.7 - - + +
211B TYR* 3.5 32.6 - + + +
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Residues in contact with SER 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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176B MET 3.0 13.5 + - - -
177B GLU* 3.6 9.7 + - - +
178B LYS 3.5 1.8 + - - -
179B TYR* 1.3 79.0 - - - +
181B VAL* 1.3 68.6 + - - +
182B THR* 4.5 0.3 - - - +
200B PRO* 3.1 20.3 - - - +
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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