Contacts of the helix formed by residues 159 - 180 (chain Y) 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 SER 159 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160Y SER* 1.3 65.1 + - - +
161Y LEU* 3.4 10.6 + - - +
162Y ALA* 3.1 30.9 + - - +
163Y ILE* 3.0 36.0 + - - +
207Y LYS* 6.1 0.2 - - - -
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Residues in contact with SER 160 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160W SER* 3.2 39.4 + - - -
159Y SER* 1.3 72.5 + - - +
161Y LEU* 1.3 62.4 + - - +
163Y ILE* 4.0 9.3 + - - +
164Y GLN* 3.5 19.2 + - - +
207Y LYS* 4.6 14.5 + - - +
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Residues in contact with LEU 161 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168X ASN* 4.8 6.5 - - - +
218X ASP* 3.5 51.6 - - + +
219X HIS* 4.6 16.2 - - + +
159Y SER* 3.0 8.0 + - - +
160Y SER* 1.3 78.8 - - - +
162Y ALA* 1.3 71.3 + - - +
164Y GLN* 2.8 34.9 + - + +
165Y GLU* 3.1 17.7 + - + +
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Residues in contact with ALA 162 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159Y SER* 3.0 30.0 + - - +
161Y LEU* 1.3 77.2 - - - +
163Y ILE* 1.3 55.4 + - + +
165Y GLU* 2.7 31.5 + - - +
166Y ASN* 2.7 24.6 + - - +
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Residues in contact with ILE 163 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159Y SER 3.0 28.3 + - - +
160Y SER* 4.1 6.7 - - - +
162Y ALA* 1.3 77.1 - - + +
164Y GLN* 1.3 51.6 + - - +
166Y ASN* 3.4 11.0 + - + +
167Y ALA* 2.7 32.4 + - - +
189Y GLU* 5.0 4.5 - - - +
204Y VAL* 5.9 1.8 - - + -
207Y LYS* 4.6 24.0 - - + +
208Y VAL* 3.9 42.2 - - + +
211Y ALA* 3.4 25.6 - - + -
212Y VAL* 5.9 0.7 - - + -
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Residues in contact with GLN 164 (chain Y).
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* 3.1 23.7 - - - +
168X ASN* 5.7 1.9 + - - -
160Y SER 3.5 13.0 + - - +
161Y LEU* 2.8 30.0 + - + +
162Y ALA 2.8 4.6 + - - -
163Y ILE* 1.3 73.2 - - - +
165Y GLU* 1.3 64.3 + - - +
167Y ALA* 3.3 4.9 + - - +
168Y ASN* 2.4 46.1 + - - +
211Y ALA* 5.2 2.5 - - - -
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Residues in contact with GLU 165 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168X ASN* 3.5 30.6 + - - +
172X ARG* 2.7 46.9 + - - +
219X HIS* 4.1 9.1 - - + -
161Y LEU* 3.1 22.5 + - + +
162Y ALA* 2.7 14.4 + - - +
164Y GLN* 1.3 77.4 - - - +
166Y ASN* 1.3 57.7 + - - +
168Y ASN* 3.2 8.5 + - - +
169Y ALA* 2.8 31.5 + - - +
172Y ARG* 4.5 9.1 + - - +
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Residues in contact with ASN 166 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149Y PRO* 4.1 22.6 + - - +
162Y ALA* 2.7 37.1 + - - +
163Y ILE* 3.4 8.7 - - + +
165Y GLU* 1.3 78.2 - - - +
167Y ALA* 1.3 65.5 + - - +
169Y ALA* 3.2 4.8 + - - +
170Y LEU* 3.0 36.6 + - + +
189Y GLU* 2.8 42.1 + - - +
208Y VAL* 6.3 0.2 - - + -
212Y VAL* 6.2 0.7 - - + -
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Residues in contact with ALA 167 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163Y ILE 2.7 22.4 + - - +
164Y GLN* 3.5 7.6 - - - +
166Y ASN* 1.3 77.7 - - - +
168Y ASN* 1.3 61.2 + - - +
170Y LEU* 3.5 5.2 + - - +
171Y ALA* 3.2 14.6 + - - +
211Y ALA* 3.4 38.8 - - + +
212Y VAL* 3.8 16.4 - - + +
215Y ALA* 3.3 15.6 - - + +
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Residues in contact with ASN 168 (chain Y).
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* 5.8 0.7 - - - +
164X GLN* 4.7 10.9 + - - +
165X GLU* 4.2 7.6 + - - +
164Y GLN* 2.4 51.5 + - - +
165Y GLU* 3.8 6.9 + - - +
167Y ALA* 1.3 74.6 - - - +
169Y ALA* 1.3 64.7 + - - +
171Y ALA* 3.1 3.5 + - - +
172Y ARG* 2.9 45.0 + - - +
215Y ALA* 3.8 13.0 - - - +
218Y ASP* 4.5 5.7 - - - +
219Y HIS* 3.3 24.6 + - - +
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Residues in contact with ALA 169 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147Y TRP* 4.5 23.6 - - + -
149Y PRO* 4.8 6.7 - - + -
165Y GLU 2.8 20.1 + - - +
166Y ASN* 3.7 5.6 - - - +
168Y ASN* 1.3 67.7 - - - +
170Y LEU* 1.3 55.2 + - - +
171Y ALA 2.7 15.4 + - - -
172Y ARG* 2.8 35.5 + - - +
173Y TYR* 3.0 15.7 + - - +
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Residues in contact with LEU 170 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147Y TRP* 3.6 19.5 - - + +
149Y PRO* 3.8 21.3 - - + +
166Y ASN* 3.0 26.5 + - + +
167Y ALA* 3.5 6.5 - - - +
169Y ALA* 1.3 78.7 - - - +
171Y ALA* 1.3 56.5 + - - +
173Y TYR* 3.7 17.8 - - + -
174Y ALA* 3.2 20.3 + - - +
186Y VAL* 3.9 21.6 - - + +
187Y GLU 3.3 45.5 - - - +
188Y PRO* 4.1 9.9 - - + -
189Y GLU* 5.5 1.1 - - - +
212Y VAL* 4.9 8.1 - - + -
216Y LEU* 4.2 4.4 - - - +
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Residues in contact with ALA 171 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167Y ALA 3.2 11.9 + - - +
168Y ASN 3.1 8.9 + - - +
169Y ALA 2.7 5.3 + - - -
170Y LEU* 1.3 76.0 - - - +
172Y ARG* 1.3 60.6 + - - +
173Y TYR 3.4 0.2 - - - -
174Y ALA* 3.3 7.9 - - - +
175Y SER* 2.8 24.9 + - - -
215Y ALA* 4.0 0.4 - - + -
216Y LEU* 3.9 24.7 - - + +
219Y HIS* 3.5 29.0 - - + +
221Y VAL* 3.9 4.2 - - - +
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Residues in contact with ARG 172 (chain Y).
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* 2.8 35.1 + - - +
168X ASN* 5.8 1.0 - - - +
172X ARG* 4.2 22.4 - - - +
147Y TRP* 6.3 0.2 - - + -
165Y GLU* 4.5 12.1 + - - +
168Y ASN* 2.9 31.8 + - - +
169Y ALA* 2.8 31.1 + - - +
171Y ALA* 1.3 74.1 - - - +
173Y TYR* 1.3 66.0 + - - +
175Y SER* 2.9 11.0 + - - -
176Y ILE* 2.9 33.3 + - + +
219Y HIS* 3.7 15.5 - - + +
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Residues in contact with TYR 173 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108Y LEU* 4.1 16.6 - - + -
130Y LEU* 4.4 3.4 - - + -
145Y GLY 3.3 10.4 + - - -
146Y LYS* 3.5 4.9 - - - -
147Y TRP* 3.2 67.2 - + + -
169Y ALA 3.0 4.3 + - - +
170Y LEU* 3.7 28.3 - - + -
172Y ARG* 1.3 78.6 - - - +
174Y ALA* 1.3 71.9 + - + +
176Y ILE* 3.1 15.6 + - - +
177Y CYS* 3.0 45.2 + - - -
184Y PRO* 4.2 3.8 - - + -
185Y ILE 3.1 35.8 + - - -
186Y VAL* 4.7 4.0 - - - -
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Residues in contact with ALA 174 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170Y LEU 3.2 19.8 + - - +
171Y ALA 3.3 9.2 + - - +
172Y ARG 3.0 0.4 - - - -
173Y TYR* 1.3 84.2 - - + +
175Y SER* 1.3 60.3 + - - +
177Y CYS* 3.2 11.1 + - - +
178Y GLN* 3.4 12.9 + - - -
184Y PRO* 3.6 27.2 - - + +
186Y VAL* 4.8 2.9 - - + -
216Y LEU* 3.6 22.4 - - + -
221Y VAL* 4.1 6.5 - - + -
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Residues in contact with SER 175 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Y LEU* 6.5 0.2 - - - -
171Y ALA 2.8 16.6 + - - -
172Y ARG* 3.0 10.0 + - - -
174Y ALA* 1.3 74.6 - - - +
176Y ILE* 1.3 59.7 + - - +
177Y CYS 3.3 0.2 - - - -
178Y GLN* 4.0 9.4 - - - +
179Y GLN* 2.7 42.5 + - - +
219Y HIS* 4.5 14.1 + - - +
220Y HIS 5.4 1.3 - - - -
221Y VAL* 4.3 14.5 - - - +
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Residues in contact with ILE 176 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129Y GLY 5.9 2.9 - - - +
130Y LEU* 3.3 33.4 - - + +
131Y SER* 3.4 30.1 - - - +
134Y CYS* 4.6 0.7 - - - -
147Y TRP* 6.0 0.4 - - + -
172Y ARG* 2.9 28.6 + - + +
173Y TYR* 3.1 18.4 + - + +
175Y SER* 1.3 77.8 - - - +
177Y CYS* 1.3 60.0 + - - +
179Y GLN* 3.2 7.0 - - + +
180Y ASN* 2.8 34.2 + - - +
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Residues in contact with CYS 177 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108Y LEU* 4.0 15.7 - - - -
130Y LEU* 5.3 0.2 - - - -
134Y CYS* 4.4 7.9 - - - -
145Y GLY 5.5 2.0 - - - -
173Y TYR* 3.0 55.4 + - - -
174Y ALA 3.2 6.0 + - - +
176Y ILE* 1.3 72.9 - - - +
178Y GLN* 1.3 55.4 + - - +
179Y GLN 2.9 4.5 - - - -
180Y ASN 2.6 34.7 + - - -
182Y LEU* 3.0 26.1 + - + -
184Y PRO* 3.8 18.6 - - + -
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Residues in contact with GLN 178 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Y LEU* 3.3 27.3 - - + +
11Y GLN* 4.2 4.3 + - - +
15Y LEU* 3.2 33.2 - - + +
174Y ALA 3.4 8.6 + - - +
175Y SER* 4.3 6.3 - - - +
176Y ILE 3.5 0.2 - - - -
177Y CYS* 1.3 79.6 - - - +
179Y GLN* 1.3 63.3 + - - +
181Y GLY* 3.4 8.9 + - - -
182Y LEU 3.7 9.4 - - - +
184Y PRO* 3.1 27.4 - - + +
221Y VAL* 3.2 26.6 - - - +
222Y TYR* 3.2 34.7 + - - +
225Y GLY 3.5 10.8 + - - +
226Y THR* 3.7 2.4 + - - -
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Residues in contact with GLN 179 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Y ALA* 3.7 30.3 + - - +
7Y LEU* 4.4 17.9 - - - +
11Y GLN* 4.2 14.0 + - - +
131Y SER* 5.7 0.9 - - - +
175Y SER* 2.7 36.2 + - - +
176Y ILE* 3.2 12.1 - - - +
177Y CYS 2.9 0.6 - - - -
178Y GLN* 1.3 81.8 - - - +
180Y ASN* 1.3 64.8 + - - +
181Y GLY 3.5 2.3 + - - -
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Residues in contact with ASN 180 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131Y SER* 3.0 45.2 + - - +
134Y CYS* 3.4 21.4 - - + +
135Y ALA* 3.5 21.2 - - - +
138Y LYS* 3.9 13.5 - - - +
176Y ILE 2.8 21.8 + - - -
177Y CYS 2.6 8.9 + - - +
179Y GLN* 1.3 83.4 - - - +
181Y GLY* 1.3 60.5 + - - +
182Y LEU* 3.2 12.0 + - - +
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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