Contacts of the helix formed by residues 160 - 180 (chain A) in PDB entry 1XFB
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 160 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A THR* 4.3 4.0 - - - +
122A GLU* 2.6 31.0 + - - -
157A ARG 4.9 5.8 - - - -
158A THR 2.2 17.9 + - - -
159A PRO* 1.3 67.8 - - - +
161A ALA* 1.3 69.2 + - - +
162A LEU* 3.9 8.1 + - - +
163A ALA* 2.7 23.6 + - - +
164A ILE* 2.8 13.9 + - - +
3B HIS* 6.2 4.3 - - - -
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Residues in contact with ALA 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A PRO 4.1 0.8 + - - -
160A SER* 1.3 70.7 - - - +
162A LEU* 1.3 53.0 + - - +
164A ILE* 3.3 8.0 + - - +
165A LEU* 2.7 41.5 + - + +
161C ALA* 5.8 9.2 - - + -
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Residues in contact with LEU 162 (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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116A LEU* 4.0 15.3 - - + -
117A ALA 4.5 4.3 - - - +
119A THR* 3.9 14.6 - - + -
160A SER* 2.9 8.5 + - - +
161A ALA* 1.3 79.5 - - - +
163A ALA* 1.3 55.4 + - - +
165A LEU* 3.1 13.7 + - + +
166A GLU* 2.7 38.5 + - + +
219B ASP* 3.5 28.3 - - - +
220B HIS* 3.6 42.8 - - + +
221B HIS* 3.7 28.7 - - + +
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Residues in contact with ALA 163 (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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116A LEU* 3.8 17.7 - - + +
122A GLU* 2.9 33.4 - - + +
123A THR 4.7 0.7 - - - +
152A LEU* 3.8 14.2 - - + +
159A PRO 4.6 0.9 - - - -
160A SER* 2.7 18.3 + - - +
162A LEU* 1.3 76.1 - - - +
164A ILE* 1.3 52.5 + - - +
166A GLU 2.6 21.7 - - - +
167A ASN* 2.6 24.1 + - - +
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Residues in contact with ILE 164 (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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152A LEU* 4.6 7.2 - - + -
159A PRO* 3.6 35.0 - - + +
160A SER 2.8 19.7 + - - +
161A ALA* 3.8 6.1 - - - +
163A ALA* 1.3 68.7 - - - +
165A LEU* 1.3 58.7 + - - +
166A GLU 2.5 19.2 - - - +
167A ASN* 4.2 0.4 - - - +
168A ALA* 3.0 20.2 + - + +
205A VAL* 6.0 0.2 - - + -
208A LYS* 4.7 9.6 - - + +
209A VAL* 4.4 29.8 - - + +
212A ALA* 3.5 28.9 - - + -
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Residues in contact with LEU 165 (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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161A ALA* 2.7 24.0 + - + +
162A LEU* 3.4 8.7 - - + +
164A ILE* 1.3 71.2 - - - +
166A GLU* 1.3 85.7 + - + +
168A ALA* 3.6 3.3 - - - +
169A ASN* 3.1 24.3 + - + +
212A ALA* 6.1 0.7 - - - -
169B ASN* 3.5 27.4 - - - +
219B ASP* 3.6 34.8 - - + +
220B HIS* 4.0 7.9 - - - +
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Residues in contact with GLU 166 (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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116A LEU* 4.4 10.5 - - + -
124A THR* 3.0 35.6 + - - +
125A THR 5.4 0.7 - - - +
162A LEU* 2.7 19.5 + - + +
163A ALA 2.6 13.2 - - - +
164A ILE 2.5 20.3 - - - +
165A LEU* 1.3 82.6 - - + +
167A ASN* 1.3 58.1 + - - +
169A ASN* 4.3 3.8 - - - +
170A VAL* 3.3 16.2 - - - +
128B LEU* 5.4 1.6 - - - +
169B ASN* 2.9 30.5 + - - -
173B ARG* 3.1 27.4 + - - +
220B HIS* 3.9 10.2 - - + -
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Residues in contact with ASN 167 (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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116A LEU* 4.7 0.4 - - - +
123A THR 3.0 22.8 + - - +
124A THR* 3.5 18.2 - - - +
150A CYS* 3.3 30.3 - - + +
151A VAL 4.2 3.1 + - - -
152A LEU* 3.5 23.5 - - + +
163A ALA* 2.6 25.8 + - - +
164A ILE* 4.2 0.9 - - - +
166A GLU* 1.3 80.3 + - - +
168A ALA* 1.3 56.9 + - - +
169A ASN 3.0 0.4 - - - -
170A VAL* 3.1 15.4 - - - +
171A LEU* 2.7 42.6 + - + +
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Residues in contact with ALA 168 (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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164A ILE* 3.0 19.0 + - + +
165A LEU* 3.6 4.0 - - - +
166A GLU 2.8 7.3 + - - -
167A ASN* 1.3 74.5 - - - +
169A ASN* 1.3 60.8 + - - +
171A LEU* 3.6 11.3 + - - +
172A ALA 3.2 17.0 + - - -
212A ALA* 4.1 11.7 - - + +
213A VAL* 4.0 33.0 - - + +
216A ALA* 3.4 16.0 - - + +
217A LEU* 5.8 0.2 - - - +
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Residues in contact with ASN 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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165A LEU* 3.1 19.8 + - + +
166A GLU* 4.3 7.6 + - - +
167A ASN 3.0 0.4 - - - -
168A ALA* 1.3 75.6 - - - +
170A VAL* 1.3 66.2 + - - +
172A ALA* 3.1 6.7 + - - +
173A ARG* 2.9 24.1 + - - +
216A ALA* 4.5 4.8 - - - +
220A HIS* 2.8 25.6 + - - -
165B LEU* 3.3 16.6 - - - +
166B GLU* 2.9 25.5 + - - -
169B ASN* 3.4 24.2 - - - +
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Residues in contact with VAL 170 (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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124A THR* 3.5 10.3 - - - +
125A THR 3.5 10.8 - - - +
128A LEU* 4.3 14.1 - - + -
148A TRP* 3.3 37.2 - - + +
150A CYS* 4.6 1.6 - - - -
166A GLU* 3.3 24.7 - - - +
167A ASN* 3.0 27.1 + - - +
169A ASN* 1.3 75.8 - - - +
171A LEU* 1.3 65.4 + - - +
173A ARG* 3.1 7.4 + - - +
174A TYR* 2.9 23.0 + - - +
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Residues in contact with LEU 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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148A TRP* 3.6 28.3 - - + +
150A CYS* 3.6 22.4 - - + -
167A ASN* 2.7 25.9 + - + +
168A ALA 3.7 3.8 - - - +
170A VAL* 1.3 74.2 - - - +
172A ALA* 1.3 53.1 + - - +
174A TYR* 3.2 8.5 + - + -
175A ALA* 2.8 37.3 + - - +
187A VAL* 3.5 37.2 - - + -
188A GLU 4.0 4.9 - - - +
189A PRO* 3.8 26.9 - - + -
213A VAL* 4.2 15.5 - - + -
217A LEU* 4.7 1.6 - - + -
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Residues in contact with ALA 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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168A ALA 3.2 10.6 + - - +
169A ASN 3.1 6.4 + - - +
171A LEU* 1.3 79.2 - - - +
173A ARG* 1.3 62.1 + - - +
176A SER* 2.9 26.0 + - - -
216A ALA* 3.8 17.9 - - + +
217A LEU* 3.7 17.4 - - - +
220A HIS* 3.4 34.4 - - + +
222A VAL* 3.6 4.2 - - - +
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Residues in contact with ARG 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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128A LEU* 3.7 28.1 - - + +
169A ASN* 2.9 17.6 + - - +
170A VAL* 3.4 8.1 - - - +
172A ALA* 1.3 74.8 - - - +
174A TYR* 1.3 64.9 + - - +
176A SER* 3.1 11.2 + - - -
177A ILE* 3.0 60.0 + - - +
220A HIS* 3.8 19.4 + - + -
114B VAL* 4.1 9.1 - - - +
115B PRO 3.5 22.0 + - - -
116B LEU* 3.6 21.2 - - - +
117B ALA 5.0 2.2 - - - +
124B THR* 3.2 20.2 - - - +
125B THR 5.8 0.4 + - - -
166B GLU* 3.0 31.6 + - - +
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Residues in contact with TYR 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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109A VAL* 3.6 17.3 - - + -
128A LEU* 3.7 9.5 - - + +
131A LEU* 4.0 7.4 - - + +
146A ALA* 3.0 25.7 + - + -
147A LYS* 3.3 1.6 - - - -
148A TRP* 3.3 58.8 - + + -
170A VAL 2.9 11.7 + - - +
171A LEU* 3.4 16.4 - - + +
173A ARG* 1.3 76.6 - - - +
175A ALA* 1.3 70.6 + - + +
177A ILE* 3.2 4.0 + - - +
178A CYS* 3.0 45.0 + - - -
185A PRO* 3.5 15.3 - - + +
186A ILE 2.9 31.0 + - - -
187A VAL* 4.4 6.7 - - + -
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Residues in contact with ALA 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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171A LEU 2.8 20.1 + - - +
172A ALA 3.7 0.2 - - - +
174A TYR* 1.3 73.9 - - + +
176A SER* 1.3 64.2 + - - +
178A CYS* 3.2 3.3 + - - +
179A GLN* 3.1 27.6 + - - +
185A PRO* 3.8 27.6 - - + -
187A VAL* 4.5 6.3 - - + -
217A LEU* 3.9 11.7 - - + -
222A VAL* 3.6 23.3 - - + -
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Residues in contact with SER 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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172A ALA 2.9 18.1 + - - -
173A ARG* 3.4 12.7 + - - -
175A ALA* 1.3 76.9 - - - +
177A ILE* 1.3 64.2 + - - +
179A GLN* 3.5 5.7 + - - +
180A GLN* 3.3 22.6 + - - +
220A HIS* 3.7 24.2 + - - -
221A HIS 5.5 0.9 + - - -
222A VAL* 3.7 9.3 - - - +
117B ALA* 3.3 27.3 + - - +
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Residues in contact with ILE 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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128A LEU* 3.9 28.7 - - + +
131A LEU* 4.0 19.3 - - + +
132A SER* 3.5 42.2 - - - +
135A CYS* 4.8 0.4 - - - -
173A ARG* 3.0 44.3 + - - +
174A TYR 3.6 4.9 - - - +
176A SER* 1.3 73.0 - - - +
178A CYS* 1.3 67.4 + - - +
180A GLN* 3.1 28.4 - - - +
181A ASN* 3.1 9.4 + - - +
114B VAL* 6.4 0.2 - - + -
115B PRO 5.8 0.4 - - - +
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Residues in contact with CYS 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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109A VAL* 5.1 0.2 - - - -
131A LEU* 4.8 1.3 - - - -
135A CYS* 4.0 24.5 - - - -
146A ALA* 4.1 13.0 - - - -
174A TYR* 3.0 46.8 + - - -
175A ALA 3.2 7.2 + - - +
177A ILE* 1.3 75.9 - - - +
179A GLN* 1.3 58.2 + - - +
181A ASN* 2.8 21.1 + - - +
183A ILE* 3.1 35.1 + - + +
185A PRO* 3.8 10.5 - - + -
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Residues in contact with GLN 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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8A LEU* 3.5 21.9 - - + +
12A GLN* 5.4 1.7 + - - +
16A LEU* 3.8 19.9 - - + +
175A ALA 3.1 14.6 + - - +
176A SER* 3.9 4.9 - - - +
177A ILE 3.3 0.2 - - - -
178A CYS* 1.3 72.2 - - - +
180A GLN* 1.3 58.8 + - - +
181A ASN 2.9 9.6 + - - -
182A GLY* 3.1 12.0 + - - -
183A ILE 3.8 4.9 - - - +
185A PRO* 3.8 12.6 - - + -
221A HIS 4.8 0.7 - - - +
222A VAL* 3.7 12.6 - - - +
223A TYR* 2.8 59.6 + - - +
226A GLY* 3.0 23.4 + - - -
227A THR* 3.5 4.4 - - - +
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Residues in contact with GLN 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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7A ALA 5.3 3.8 - - - +
8A LEU* 4.1 12.1 - - + +
12A GLN* 4.8 9.7 + - - +
132A SER* 3.5 17.5 + - - -
176A SER 3.3 10.2 + - - +
177A ILE* 3.1 26.6 - - - +
179A GLN* 1.3 77.4 - - - +
181A ASN* 1.3 62.6 + - - +
182A GLY 3.5 0.6 + - - -
115B PRO* 4.8 18.3 - - - +
117B ALA* 3.3 34.4 - - + +
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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