Contacts of the helix formed by residues 161 - 181 (chain X) in PDB entry 1XDM
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 LEU 161 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159X SER* 3.0 14.1 + - - +
160X SER* 1.3 78.5 + - - +
162X ALA* 1.3 62.9 + - - +
164X GLN* 3.4 22.3 + - - +
165X GLU* 3.1 43.8 + - + +
168Y ASN* 5.8 0.7 - - - +
218Y ASP* 3.3 46.4 - - + +
219Y HIS* 4.5 14.6 - - - +
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Residues in contact with ALA 162 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159X SER* 3.4 14.9 + - - +
161X LEU* 1.3 76.1 - - - +
163X ILE* 1.3 57.0 + - + +
164X GLN 2.8 14.4 + - - -
165X GLU* 2.9 16.2 + - - +
166X ASN* 2.9 31.8 + - - +
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Residues in contact with ILE 163 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159X SER 3.2 25.1 + - - +
160X SER* 4.5 7.6 - - - +
162X ALA* 1.3 75.8 - - + +
164X GLN* 1.3 59.9 + - - +
166X ASN* 4.7 5.1 - - - +
167X ALA* 3.3 23.5 + - - +
189X GLU* 5.6 3.4 - - - +
204X VAL* 5.6 4.3 - - + -
207X LYS* 4.4 19.3 - - + +
208X VAL* 3.7 41.1 - - + +
211X ALA* 3.2 26.4 - - + +
212X VAL* 5.6 0.3 - - - +
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Residues in contact with GLN 164 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160X SER 3.1 19.6 + - - +
161X LEU* 3.4 30.0 + - - +
162X ALA 2.8 1.6 + - - -
163X ILE* 1.3 77.8 - - - +
165X GLU* 1.3 67.3 + - - +
167X ALA* 3.4 4.5 + - - +
168X ASN* 2.6 42.4 + - - +
211X ALA* 5.3 2.0 - - - -
164Y GLN* 3.1 22.8 - - - +
168Y ASN* 4.7 11.2 + - - +
218Y ASP* 5.7 2.2 + - - -
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Residues in contact with GLU 165 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161X LEU* 3.1 26.4 - - + +
162X ALA* 2.9 11.3 + - - +
164X GLN* 1.3 79.2 - - - +
166X ASN* 1.3 72.3 + - - +
168X ASN* 2.8 20.8 + - - +
169X ALA* 2.8 14.1 + - - +
172X ARG* 5.3 0.5 + - - -
168Y ASN* 4.2 7.9 - - - +
172Y ARG* 2.8 39.4 + - - +
219Y HIS* 2.8 36.9 + - - -
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Residues in contact with ASN 166 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162X ALA* 2.9 30.4 + - - +
163X ILE* 4.7 3.3 + - - +
165X GLU* 1.3 77.1 - - - +
167X ALA* 1.3 65.0 + - - +
169X ALA* 3.4 7.5 - - - +
170X LEU* 2.9 37.2 + - + +
189X GLU* 3.1 31.5 - - + +
212X VAL* 6.3 0.7 - - + -
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Residues in contact with ALA 167 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163X ILE 3.3 20.3 + - - +
164X GLN* 3.4 6.7 + - - +
165X GLU 3.0 0.6 + - - -
166X ASN* 1.3 78.5 - - - +
168X ASN* 1.3 54.1 + - - +
170X LEU* 3.4 3.8 + - - +
171X ALA* 2.6 34.1 + - - +
211X ALA* 3.3 33.0 - - + +
212X VAL* 3.8 17.9 - - + +
215X ALA* 3.5 9.6 - - + +
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Residues in contact with ASN 168 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164X GLN* 2.6 38.4 + - - +
165X GLU* 2.8 12.5 + - - +
167X ALA* 1.3 70.3 - - - +
169X ALA* 1.3 69.5 + - - +
171X ALA* 3.0 8.1 - - - +
172X ARG* 2.7 23.4 + - - +
215X ALA* 3.9 10.9 - - - +
218X ASP* 4.9 2.3 - - - +
219X HIS* 3.1 24.7 + - - +
161Y LEU* 4.8 7.1 - - - +
164Y GLN* 5.7 2.4 + - - -
165Y GLU* 3.5 31.3 + - - +
172Y ARG* 5.8 1.1 - - - +
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Residues in contact with ALA 169 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147X TRP* 5.3 15.5 - - + -
165X GLU 2.8 12.6 + - - +
166X ASN* 3.2 12.8 + - - +
168X ASN* 1.3 73.1 - - - +
170X LEU* 1.3 58.2 + - + +
172X ARG* 2.6 47.6 + - - +
173X TYR* 2.8 14.7 + - - -
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Residues in contact with LEU 170 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147X TRP* 4.4 20.5 - - + -
166X ASN* 2.9 25.6 + - + +
167X ALA 3.4 2.7 - - - +
169X ALA* 1.3 78.9 - - + +
171X ALA* 1.3 67.1 + - - +
173X TYR* 3.0 27.9 + - + +
174X ALA* 2.8 26.2 + - - +
186X VAL* 4.1 6.3 - - + -
187X GLU 3.6 43.7 - - - +
188X PRO* 4.4 4.9 - - + -
189X GLU* 6.0 0.9 - - + +
212X VAL* 4.5 24.5 - - + -
216X LEU* 4.9 1.8 - - + -
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Residues in contact with ALA 171 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167X ALA 2.6 19.3 + - - +
168X ASN* 3.0 17.0 - - - +
170X LEU* 1.3 74.1 - - - +
172X ARG* 1.3 57.0 + - - +
174X ALA* 3.1 14.9 - - - +
175X SER* 3.3 8.0 + - - -
215X ALA* 3.7 9.9 - - + -
216X LEU* 3.9 19.7 - - - +
219X HIS* 3.4 32.4 - - + +
221X VAL* 3.6 7.8 - - - +
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Residues in contact with ARG 172 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165X GLU 5.3 0.4 + - - -
168X ASN* 2.7 8.7 + - - +
169X ALA* 2.6 40.1 + - - +
171X ALA* 1.3 68.0 - - - +
173X TYR* 1.3 55.3 + - - +
174X ALA 2.6 15.5 + - - -
175X SER* 2.8 25.7 + - - +
176X ILE* 3.0 13.7 + - + +
219X HIS* 3.6 15.0 - - + +
165Y GLU* 2.7 35.4 + - - +
172Y ARG* 4.2 22.1 - - - +
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Residues in contact with TYR 173 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108X LEU* 4.4 8.3 - - + -
130X LEU* 4.3 20.9 - - + -
145X GLY 3.1 15.9 + - - -
146X LYS* 3.0 37.5 + - - -
147X TRP* 3.2 49.4 - + + -
169X ALA 2.8 13.3 + - - +
170X LEU* 3.6 27.6 - - + +
172X ARG* 1.3 73.3 - - - +
174X ALA* 1.3 65.3 + - + +
176X ILE* 3.6 5.1 - - - +
177X CYS* 3.1 32.5 + - - -
184X PRO* 3.8 13.1 - - + +
185X ILE 3.3 10.4 + - - -
186X VAL* 4.5 9.0 - - - -
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Residues in contact with ALA 174 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170X LEU 2.8 10.1 + - - +
171X ALA 3.1 13.2 - - - +
172X ARG 2.6 4.2 + - - -
173X TYR* 1.3 72.3 - - + +
175X SER* 1.3 55.4 - - - +
176X ILE 2.6 16.5 + - - -
177X CYS* 2.9 17.2 + - - +
178X GLN* 3.1 13.7 + - - +
184X PRO* 3.6 23.9 - - + +
186X VAL* 5.6 2.5 - - + -
216X LEU* 3.9 19.7 - - + -
221X VAL* 4.0 10.1 - - + -
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Residues in contact with SER 175 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171X ALA 3.3 4.9 + - - -
172X ARG* 2.8 28.4 + - - +
174X ALA* 1.3 75.2 - - - +
176X ILE* 1.3 60.5 + - - +
178X GLN* 3.5 14.8 - - - +
179X GLN* 2.8 31.7 + - - +
219X HIS* 4.0 22.1 + - - +
220X HIS 5.5 0.7 - - - -
221X VAL* 4.5 6.2 - - - +
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Residues in contact with ILE 176 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130X LEU* 3.4 33.4 - - + -
131X SER* 3.7 25.1 - - - +
134X CYS* 4.2 4.7 - - - -
172X ARG* 3.0 15.2 + - + +
173X TYR* 3.6 10.8 - - - +
174X ALA 2.6 5.9 + - - -
175X SER* 1.3 70.7 - - - +
177X CYS* 1.3 59.2 + - - +
178X GLN 3.0 0.7 - - - -
179X GLN* 2.6 31.8 + - - +
180X ASN* 3.0 32.0 + - - +
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Residues in contact with CYS 177 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108X LEU* 4.4 2.2 - - - -
134X CYS* 4.3 16.6 - - - -
145X GLY* 5.7 2.5 - - - -
173X TYR* 3.1 41.5 - - - -
174X ALA 2.9 8.4 + - - +
176X ILE* 1.3 78.5 - - - +
178X GLN* 1.3 64.2 + - - +
180X ASN* 2.8 8.0 + - - +
181X GLY 2.8 21.0 + - - -
182X LEU* 2.8 37.5 + - + +
183X VAL 5.4 0.2 - - - -
184X PRO* 3.8 15.0 - - + -
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Residues in contact with GLN 178 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7X LEU* 3.3 18.8 - - + +
11X GLN* 2.8 27.7 + - - -
15X LEU* 3.2 25.0 - - + +
174X ALA 3.3 13.2 - - - +
175X SER* 3.5 19.5 - - - +
177X CYS* 1.3 78.9 - - - +
179X GLN* 1.3 50.9 + - - +
181X GLY 3.5 3.1 + - - -
182X LEU 3.7 3.1 + - - -
184X PRO* 2.8 37.8 - - - +
221X VAL* 4.4 5.8 - - + +
222X TYR* 2.8 43.2 + - - +
225X GLY 3.6 11.9 + - - -
226X THR* 4.8 0.6 + - - -
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Residues in contact with GLN 179 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X ALA* 2.6 43.3 + - - +
7X LEU* 4.1 8.2 - - - +
11X GLN* 2.9 20.0 + - - +
131X SER* 5.6 1.6 - - - +
175X SER* 2.8 27.3 + - - +
176X ILE* 2.6 19.7 + - - +
178X GLN* 1.3 74.3 - - - +
180X ASN* 1.3 59.2 + - - +
181X GLY 3.0 5.5 + - - -
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Residues in contact with ASN 180 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131X SER* 3.1 25.4 + - - -
134X CYS* 3.2 17.6 - - + +
135X ALA* 3.0 44.4 - - - +
138X LYS* 3.6 23.6 - - - +
176X ILE* 3.0 33.9 + - - +
177X CYS* 2.8 7.2 + - - +
179X GLN* 1.3 76.2 - - - +
181X GLY* 1.3 61.0 + - - +
182X LEU* 3.3 2.5 + - + +
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Residues in contact with GLY 181 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11X GLN* 4.4 8.3 - - - -
14X GLU* 3.4 15.7 - - - +
15X LEU* 3.8 12.0 - - - +
18X ILE* 4.1 1.4 - - - +
138X LYS* 3.3 27.0 + - - -
143X ASP 3.8 2.6 - - - +
177X CYS 2.8 2.8 + - - -
178X GLN 3.5 6.5 + - - -
179X GLN 3.0 7.4 + - - -
180X ASN* 1.3 80.0 - - - +
182X LEU* 1.3 59.7 + - - +
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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