Contacts of the helix formed by residues 168 - 187 (chain A) in PDB entry 1XAI
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A TYR* 4.5 11.7 - - + +
166A THR 3.5 8.7 - - - +
167A LEU* 1.3 91.2 - - + +
169A PHE* 1.3 66.1 + - - +
170A LYS* 4.4 8.5 - - + +
171A GLN* 3.1 32.7 + - + +
172A ILE* 3.1 10.3 + - - +
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Residues in contact with PHE 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A LEU 4.0 0.2 + - - -
168A PRO* 1.3 72.9 - - - +
170A LYS* 1.3 58.7 + - - +
172A ILE* 2.8 29.6 + - + +
173A LEU* 2.9 45.4 + - + +
201A ARG* 3.4 42.8 - - + +
204A LEU* 3.5 15.3 - - + -
205A GLN* 3.3 58.8 - - + +
291A LEU 3.1 28.3 - - - -
292A GLY* 4.4 0.7 - - - -
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Residues in contact with LYS 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PRO* 3.3 5.8 - - + +
169A PHE* 1.3 77.0 - - - +
171A GLN* 1.3 74.5 + - + +
173A LEU* 4.7 5.6 - - - -
174A SER* 3.3 5.4 + - - -
255A PRO* 3.8 24.7 - - + -
258A HIS* 2.9 44.1 - - + +
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Residues in contact with GLN 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A THR* 4.6 9.6 + - - +
126A ILE* 4.5 5.5 - - - +
167A LEU* 4.2 20.4 - - + -
168A PRO* 3.1 29.7 + - + +
169A PHE 3.0 0.8 - - - -
170A LYS* 1.3 99.5 + - + +
172A ILE* 1.3 59.4 + - - +
173A LEU 3.3 0.9 - - - -
174A SER* 3.5 15.3 + - - -
175A GLY* 2.6 31.0 + - - -
255A PRO* 5.1 5.1 - - - +
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Residues in contact with ILE 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ILE* 3.7 24.1 - - + +
167A LEU* 3.8 27.6 - - + +
168A PRO 3.1 14.5 + - - +
169A PHE* 2.8 21.9 + - + +
171A GLN* 1.3 73.8 - - - +
173A LEU* 1.3 56.2 + - - +
175A GLY* 3.3 0.5 + - - -
176A TYR* 2.6 38.9 + - - +
204A LEU* 3.3 38.1 - - + +
205A GLN* 5.2 3.8 - - - +
207A LEU* 3.5 32.3 - - + -
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Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A PHE* 2.9 34.7 + - + +
170A LYS* 4.7 4.3 - - - -
172A ILE* 1.3 80.9 - - - +
174A SER* 1.3 65.0 + - - +
176A TYR* 4.1 2.2 - - - -
177A ALA* 3.2 5.2 + - - +
204A LEU* 3.4 16.8 - - + -
258A HIS* 3.9 18.4 - - + +
291A LEU 3.2 26.0 - - - +
292A GLY 3.5 21.8 - - - +
293A TYR* 2.3 60.2 + - + +
294A PRO* 4.5 2.9 - - + -
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Residues in contact with SER 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LEU* 4.0 12.8 - - - +
170A LYS 3.3 18.8 + - - -
171A GLN* 3.5 19.0 + - - -
172A ILE 3.2 0.4 - - - -
173A LEU* 1.3 80.3 - - - +
175A GLY* 1.3 62.6 + - - +
177A ALA* 3.3 3.8 + - - +
178A GLU 4.3 0.9 + - - -
255A PRO* 3.5 11.5 - - - +
256A HIS 3.8 2.8 + - - -
257A GLY* 3.0 41.4 + - - -
258A HIS* 3.5 14.1 - - - -
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Residues in contact with GLY 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ILE* 3.6 17.2 - - - +
127A LEU* 3.5 32.8 - - - +
129A HIS* 4.4 0.2 - - - -
171A GLN 2.6 21.1 + - - -
172A ILE 3.7 0.2 - - - -
174A SER* 1.3 73.3 - - - +
176A TYR* 1.3 61.0 + - - +
178A GLU* 3.1 17.3 + - - +
179A VAL* 3.4 7.1 + - - +
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Residues in contact with TYR 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ILE* 4.0 2.8 - - - +
172A ILE 2.6 24.7 + - - +
173A LEU* 3.2 5.8 + - - +
175A GLY* 1.3 72.6 - - - +
177A ALA* 1.3 54.8 + - - +
179A VAL* 3.1 10.9 + - + -
180A TYR* 2.7 57.3 + + + +
194A ILE* 3.4 33.4 - - + +
198A PHE* 3.6 27.9 - + + +
204A LEU* 3.9 12.3 - - + -
210A MET* 3.8 19.1 - - + -
261A MET* 5.5 1.3 - - - -
287A TYR* 2.8 21.5 + - - -
291A LEU* 3.2 34.5 - - + -
293A TYR* 3.7 8.3 - + - +
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Residues in contact with ALA 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A LEU 3.2 6.8 + - - +
174A SER 3.5 0.4 - - - +
175A GLY 3.1 1.0 - - - -
176A TYR* 1.3 76.8 - - - +
178A GLU* 1.3 59.9 + - + +
181A LYS* 3.2 22.7 + - - +
257A GLY* 3.1 45.3 - - - +
260A VAL* 4.0 8.7 - - + +
261A MET* 3.1 34.8 - - + +
293A TYR* 3.5 1.1 + - - -
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Residues in contact with GLU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LEU* 4.1 21.3 - - + -
129A HIS* 3.3 21.5 - - + -
130A ASP* 3.3 20.6 - - + +
174A SER 4.9 1.3 - - - +
175A GLY 3.1 6.9 + - - +
177A ALA* 1.3 76.8 - - + +
179A VAL* 1.3 66.0 + - - +
180A TYR 3.1 1.3 - - - -
181A LYS* 3.0 34.6 + - - +
182A HIS* 3.1 30.2 + - + -
242A HIS* 3.6 3.1 + - - -
256A HIS* 3.3 11.3 - - - -
257A GLY* 5.7 0.2 - - - -
260A VAL* 4.0 5.9 - - - +
500A CRB 3.3 0.3 + - - -
600A ZN 2.2 32.7 - - - -
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Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ILE* 3.9 16.8 - - + -
129A HIS* 3.8 23.8 - - + +
175A GLY 3.8 9.6 - - - +
176A TYR* 3.1 17.6 + - + +
178A GLU* 1.3 77.6 - - - +
180A TYR* 1.3 61.8 + - - +
182A HIS* 3.8 5.2 + - - +
183A ALA* 3.5 17.3 + - - +
194A ILE* 3.7 21.2 - - + +
210A MET* 4.5 5.6 - - - -
213A TYR* 3.3 31.9 - - + +
214A ILE* 4.3 12.1 - - + -
217A GLY* 5.7 0.6 - - - -
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Residues in contact with TYR 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A TYR* 2.7 41.6 + + + +
177A ALA 4.0 3.6 - - - +
179A VAL* 1.3 77.2 - - - +
181A LYS* 1.3 57.8 + - - +
183A ALA* 3.0 8.0 - - - +
184A LEU* 3.0 51.5 + - + +
191A THR* 3.7 10.9 - - + +
194A ILE* 4.0 12.5 - - + +
195A GLU* 3.0 21.3 + - + -
261A MET* 3.6 28.0 - - + -
264A ILE* 4.9 4.7 - - + -
284A TYR* 2.9 37.3 - + - -
287A TYR* 3.7 24.2 - + - -
288A LEU* 5.7 1.6 - - + -
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Residues in contact with LYS 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ASP* 4.4 0.4 + - - -
177A ALA 3.2 20.3 + - - +
178A GLU* 3.0 25.2 + - - +
180A TYR* 1.3 74.5 - - - +
182A HIS* 1.3 89.2 + - - +
184A LEU* 3.3 13.4 + - - +
185A LEU* 3.1 24.5 + - + +
238A LEU* 2.6 39.6 + - - +
240A LEU* 3.6 31.2 - - + +
242A HIS* 3.6 16.1 - - + -
260A VAL* 5.0 0.9 - - + -
264A ILE* 4.3 7.6 - - + -
500A CRB 3.4 15.0 + - - +
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Residues in contact with HIS 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A HIS* 3.2 36.1 + + - -
130A ASP* 4.0 22.1 + - + -
178A GLU 3.1 11.3 + - - +
179A VAL* 4.0 5.1 - - - +
181A LYS* 1.3 96.9 + - - +
183A ALA* 1.3 51.7 + - - +
185A LEU* 3.3 15.6 + - + +
186A ASN* 2.8 32.7 + - - +
217A GLY* 3.4 31.3 + - - -
220A THR* 4.0 20.2 - - + +
221A LYS* 4.3 14.0 - - + +
238A LEU* 4.6 9.7 - - + +
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Residues in contact with ALA 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A VAL 3.5 11.2 + - - +
180A TYR* 3.0 15.0 - - + +
181A LYS 3.0 0.2 - - - -
182A HIS* 1.3 76.1 - - - +
184A LEU* 1.3 56.0 + - - +
185A LEU 2.9 1.6 - - - -
186A ASN* 2.7 28.0 + - - +
187A GLY 3.3 10.6 + - - +
190A ALA* 4.0 11.4 - - + +
191A THR* 3.3 10.2 + - - -
194A ILE* 3.9 29.6 - - + -
216A LYS* 6.0 1.8 - - - +
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Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A TYR* 3.0 47.2 + - + +
181A LYS* 3.3 9.8 + - - +
183A ALA* 1.3 75.1 - - - +
185A LEU* 1.3 60.2 + - - +
187A GLY* 3.7 2.8 + - - -
191A THR* 3.2 14.7 + - + +
240A LEU* 4.2 20.9 - - + -
264A ILE* 3.6 35.0 - - + -
268A PHE* 3.7 24.0 - - + -
284A TYR* 4.2 1.6 - - + -
326A MET* 2.9 27.6 - - + +
329A PHE* 3.6 26.0 - - + -
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Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A LYS* 3.1 29.3 + - + +
182A HIS* 3.3 16.6 - - + +
183A ALA 2.9 0.6 - - - -
184A LEU* 1.3 79.1 - - - +
186A ASN* 1.3 59.1 + - - +
187A GLY 3.2 3.8 + - - -
220A THR* 5.1 7.9 - - + -
224A ILE* 6.1 2.9 - - + -
237A PHE* 3.4 32.3 - - + +
238A LEU* 4.5 11.7 - - + -
240A LEU* 2.9 37.0 - - + -
326A MET* 4.7 1.8 - - + -
330A GLY* 5.5 4.0 + - - -
332A ILE* 4.5 25.4 - - + +
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Residues in contact with ASN 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A HIS 2.8 11.9 + - - +
183A ALA* 2.7 14.0 + - - +
185A LEU* 1.3 78.9 - - - +
187A GLY* 1.3 55.8 + - - -
189A SER* 5.7 1.2 - - - -
190A ALA* 3.6 22.0 + - + +
216A LYS* 3.6 25.3 + - - +
220A THR* 3.6 24.5 + - + +
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Residues in contact with GLY 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A ALA 3.3 1.3 + - - +
184A LEU 3.7 2.5 + - - -
185A LEU 3.2 5.4 + - - -
186A ASN* 1.3 80.3 - - - +
188A GLU* 1.3 64.9 + - - -
189A SER* 3.1 5.0 + - - -
190A ALA 3.5 1.0 + - - -
191A THR* 3.1 26.0 + - - -
329A PHE* 3.5 20.2 - - - -
330A GLY* 5.1 1.6 - - - -
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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