Contacts of the helix formed by residues 168 - 187 (chain B) in PDB entry 1XAH
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 PRO 168 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B TYR* 4.7 7.6 - - - +
166B THR 3.4 9.6 - - - +
167B LEU* 1.3 88.0 - - - +
169B PHE* 1.3 65.4 + - - +
170B LYS* 4.1 13.2 - - + +
171B GLN* 3.1 21.0 + - + +
172B ILE* 3.1 14.9 + - - +
401B NAD 4.3 10.5 - - + +
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Residues in contact with PHE 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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167B LEU 3.6 0.4 + - - -
168B PRO* 1.3 73.1 - - - +
170B LYS* 1.3 53.5 + - - +
172B ILE* 4.0 11.4 - - + -
173B LEU* 2.8 69.2 + - + +
201B ARG* 3.3 43.7 - - + -
204B LEU* 3.9 13.2 - - + -
205B GLN* 3.5 56.5 - - + +
291B LEU 3.2 25.1 - - - -
292B GLY 4.4 0.4 - - - -
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Residues in contact with LYS 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B PRO* 4.1 9.8 - - + +
169B PHE* 1.3 78.8 - - - +
171B GLN* 1.3 71.5 + - + +
173B LEU* 4.7 4.0 - - - -
174B SER* 3.0 26.9 + - - -
255B PRO* 3.7 32.9 - - + +
258B HIS* 3.3 19.7 + - + +
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Residues in contact with GLN 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B THR* 5.4 4.0 - - + +
126B ILE* 4.8 4.3 + - - +
127B LEU 5.5 0.3 + - - -
167B LEU* 4.0 23.4 - - + +
168B PRO* 3.1 25.8 + - + +
170B LYS* 1.3 92.7 - - + +
172B ILE* 1.3 66.6 + - - +
174B SER* 3.8 12.7 + - - -
175B GLY* 2.9 19.9 + - - -
255B PRO* 5.3 4.5 - - - +
401B NAD 3.3 57.4 + - - +
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Residues in contact with ILE 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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126B ILE* 3.8 13.3 - - + +
167B LEU* 3.6 24.7 - - + +
168B PRO 3.1 11.6 + - - +
169B PHE* 3.0 17.4 + - + +
171B GLN* 1.3 76.7 - - - +
173B LEU* 1.3 51.7 + - - +
175B GLY* 3.0 2.9 + - - -
176B TYR* 2.7 36.1 + - - +
204B LEU* 3.3 34.3 - - + +
205B GLN* 3.8 24.5 - - + +
207B LEU* 3.6 35.9 - - + -
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Residues in contact with LEU 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 PHE* 2.8 47.9 + - + +
170B LYS* 4.8 2.2 - - - -
172B ILE* 1.3 72.7 - - - +
174B SER* 1.3 64.6 + - - +
176B TYR* 3.0 10.3 + - - -
177B ALA* 3.4 1.0 + - - +
204B LEU* 3.6 17.0 - - + -
258B HIS* 3.7 20.2 - - + +
291B LEU 3.4 23.6 - - - +
292B GLY 3.5 16.6 - - - +
293B TYR* 2.5 53.4 + - + -
294B PRO* 4.3 5.6 - - + -
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Residues in contact with SER 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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127B LEU* 3.5 16.4 - - - +
170B LYS 3.0 15.8 + - - -
171B GLN* 3.8 17.4 + - - -
173B LEU* 1.3 80.3 - - - +
175B GLY* 1.3 61.6 + - - +
177B ALA* 3.6 3.6 + - - +
178B GLU 4.5 0.3 + - - -
255B PRO* 3.7 21.3 - - - +
256B HIS 3.8 1.7 + - - -
257B GLY* 2.8 42.8 + - - -
258B HIS* 3.7 8.9 - - - +
401B NAD 4.4 0.7 + - - -
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Residues in contact with GLY 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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126B ILE* 3.7 13.9 - - - +
127B LEU* 3.6 31.7 - - - +
171B GLN 2.9 16.0 + - - -
172B ILE 3.5 3.1 - - - -
174B SER* 1.3 72.3 - - - +
176B TYR* 1.3 67.1 + - - +
177B ALA 3.1 3.3 + - - -
178B GLU* 3.1 15.4 + - - +
179B VAL* 3.6 6.8 + - - +
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Residues in contact with TYR 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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126B ILE* 4.1 2.4 - - - +
172B ILE 2.7 20.7 + - - +
173B LEU* 3.0 7.4 + - - +
175B GLY* 1.3 72.5 - - - +
177B ALA* 1.3 55.9 + - - +
179B VAL* 3.1 12.6 + - + +
180B TYR* 2.8 43.9 + + + +
194B ILE* 3.4 37.1 - - + +
198B PHE* 3.5 29.7 - + + +
204B LEU* 4.0 16.4 - - + -
210B MET* 3.9 19.5 - - + -
261B MET* 3.9 8.1 - - + -
287B TYR* 2.8 21.2 + - - -
291B LEU* 3.7 25.8 - - + -
293B TYR* 3.6 11.7 - - - +
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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 LEU 3.4 3.4 + - - -
174B SER 3.7 0.4 - - - +
175B GLY 3.1 1.2 + - - -
176B TYR* 1.3 78.4 - - - +
178B GLU* 1.3 58.0 + - + +
180B TYR* 3.8 1.7 - - - +
181B LYS* 2.9 26.0 + - - +
257B GLY* 3.1 41.7 - - - +
260B VAL* 4.1 10.1 - - + +
261B MET* 3.5 28.5 - - + -
264B ILE* 4.1 6.6 - - - +
293B TYR* 3.6 1.9 + - - +
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Residues in contact with GLU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU* 3.8 29.2 - - + -
129B HIS* 3.7 20.0 - - + -
130B ASP* 3.3 8.0 - - + +
174B SER 4.8 2.5 - - - +
175B GLY 3.1 5.2 + - - +
177B ALA* 1.3 74.6 - - + +
179B VAL* 1.3 66.9 + - - +
180B TYR 3.1 1.1 - - - -
181B LYS* 3.0 35.0 + - - +
182B HIS* 3.0 30.2 + - + -
242B HIS* 3.1 8.2 + - - -
256B HIS* 3.4 12.1 + - - -
257B GLY* 5.5 0.2 - - - -
260B VAL* 3.5 8.5 - - - +
601B ZN 2.4 30.1 - - - -
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Residues in contact with VAL 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ILE* 3.7 30.1 - - + -
129B HIS* 3.8 23.1 - - + +
175B GLY 3.6 2.4 + - - +
176B TYR* 3.5 15.3 - - + +
178B GLU* 1.3 77.3 - - - +
180B TYR* 1.3 57.6 + - - +
182B HIS* 3.6 4.7 + - - +
183B ALA* 3.1 23.9 + - - +
194B ILE* 3.5 22.4 - - + -
210B MET* 4.5 5.8 - - - -
213B TYR* 3.9 27.6 - - + +
214B ILE* 4.4 11.4 - - + -
217B GLY* 5.4 0.7 - - - -
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Residues in contact with TYR 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B TYR* 2.8 33.0 + - + +
177B ALA 3.8 2.7 - - - +
179B VAL* 1.3 76.5 - - - +
181B LYS* 1.3 60.0 + - - +
183B ALA* 3.1 5.0 + - + +
184B LEU* 2.8 54.3 + - + +
191B THR* 4.0 7.2 - - + +
194B ILE* 3.8 22.4 - - + +
195B GLU* 2.9 31.5 + - + -
261B MET* 3.9 28.9 - - + -
264B ILE* 4.2 7.2 - - + -
284B TYR* 3.1 26.4 - + - -
287B TYR* 3.5 25.4 - + - -
288B LEU* 6.2 0.7 - - + -
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Residues in contact with LYS 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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130B ASP* 3.7 10.3 + - - -
177B ALA 2.9 19.5 + - - +
178B GLU* 3.0 27.4 + - - +
180B TYR* 1.3 74.6 - - - +
182B HIS* 1.3 81.8 + - - +
184B LEU* 3.0 8.4 + - - +
185B LEU* 2.7 41.4 + - + +
238B LEU* 2.9 36.8 + - - +
240B LEU* 3.8 28.3 - - + +
242B HIS* 3.7 15.6 - - + -
260B VAL* 5.0 0.9 - - + -
264B ILE* 4.2 14.4 - - + -
601B ZN 4.5 1.6 - - - -
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Residues in contact with HIS 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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129B HIS* 3.1 31.1 + + - -
130B ASP* 3.8 25.0 + - + -
178B GLU 3.0 13.7 + - - +
179B VAL 3.8 4.7 - - - +
181B LYS* 1.3 99.7 + - - +
183B ALA* 1.3 56.7 + - - +
185B LEU* 3.6 7.8 - - + +
186B ASN* 2.6 37.2 + - - +
217B GLY* 3.4 30.7 + - - +
220B THR* 3.9 13.9 - - + +
221B LYS* 3.9 14.3 - - + +
238B LEU* 4.0 16.5 - - + +
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Residues in contact with ALA 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 VAL 3.1 13.9 + - - +
180B TYR* 3.1 12.0 + - + +
182B HIS* 1.3 76.0 - - - +
184B LEU* 1.3 63.6 + - - +
186B ASN* 3.1 16.1 + - - +
187B GLY 3.2 10.4 + - - +
190B ALA* 3.9 15.4 - - + +
191B THR* 3.1 12.4 + - - +
194B ILE* 4.0 30.5 - - + -
213B TYR* 6.2 0.2 - - + -
216B LYS* 6.3 2.2 - - - -
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Residues in contact with LEU 184 (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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180B TYR* 2.8 37.2 + - + +
181B LYS* 3.1 8.3 - - - +
183B ALA* 1.3 75.6 - - - +
185B LEU* 1.3 62.6 + - - +
187B GLY* 3.2 9.7 + - - -
191B THR* 3.3 28.7 - - + +
240B LEU* 4.1 15.5 - - + -
264B ILE* 3.5 41.1 - - + -
268B PHE* 4.2 16.8 - - + -
284B TYR* 4.5 1.3 - - + -
326B MET* 3.1 21.5 - - + +
329B PHE* 3.8 20.1 - - + -
330B GLY 5.6 0.3 + - - -
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Residues in contact with LEU 185 (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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181B LYS* 2.7 33.9 + - + +
182B HIS* 3.7 7.9 - - + +
184B LEU* 1.3 74.6 - - - +
186B ASN* 1.3 61.9 + - - +
187B GLY* 3.1 1.6 + - - -
220B THR* 4.7 8.5 - - + -
224B ILE* 6.3 0.4 - - + -
237B PHE* 3.4 37.9 - - + +
238B LEU* 3.9 27.1 - - + -
240B LEU* 4.1 17.7 - - + -
326B MET* 4.6 1.1 - - + -
330B GLY* 5.6 3.1 + - - -
332B ILE* 4.1 33.5 - - + +
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Residues in contact with ASN 186 (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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182B HIS 2.6 22.4 + - - +
183B ALA* 3.1 8.0 + - - +
185B LEU* 1.3 73.4 - - - +
187B GLY* 1.3 56.0 + - - +
190B ALA* 4.0 15.1 - - + +
216B LYS* 2.9 36.8 + - + +
220B THR* 2.5 32.0 + - - +
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Residues in contact with GLY 187 (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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183B ALA 3.2 4.9 + - - +
184B LEU 3.2 4.3 + - - -
185B LEU 3.1 6.4 - - - -
186B ASN* 1.3 79.6 - - - +
188B GLU* 1.3 64.4 + - - -
189B SER 3.4 3.1 - - - -
190B ALA 3.5 1.8 + - - -
191B THR* 3.0 25.6 + - - -
329B PHE* 3.6 12.6 - - - -
330B GLY* 5.2 6.5 - - - -
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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