Contacts of the helix formed by residues 160 - 180 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119G THR* 4.3 3.7 - - - +
122G GLU* 2.6 31.6 + - - -
157G ARG 4.9 5.8 - - - -
158G THR 2.2 16.7 + - - -
159G PRO* 1.3 69.4 - - - +
161G ALA* 1.3 69.4 + - - +
162G LEU* 3.9 8.3 + - - +
163G ALA* 2.7 23.9 + - - +
164G ILE* 2.8 14.4 + - - +
3H HIS* 6.2 3.6 - - - -
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Residues in contact with ALA 161 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161E ALA* 5.0 16.6 - - + -
159G PRO 4.1 0.8 + - - -
160G SER* 1.3 70.4 - - - +
162G LEU* 1.3 52.9 + - - +
164G ILE* 3.3 8.0 + - - +
165G LEU* 2.7 41.1 + - + +
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Residues in contact with LEU 162 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G LEU* 4.0 15.3 - - + -
117G ALA 4.5 4.7 - - - +
119G THR* 3.9 14.1 - - + -
160G SER* 2.9 9.2 + - - +
161G ALA* 1.3 78.9 - - - +
163G ALA* 1.3 55.7 + - - +
165G LEU* 3.1 13.0 + - + +
166G GLU* 2.7 38.7 + - + +
219H ASP* 3.5 27.8 - - - +
220H HIS* 3.7 41.3 - - + +
221H HIS* 3.7 28.0 - - + +
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Residues in contact with ALA 163 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G LEU* 3.8 17.7 - - + +
122G GLU* 2.9 34.1 - - + +
123G THR 4.7 0.7 - - - +
152G LEU* 3.8 12.3 - - + +
159G PRO 4.6 0.7 - - - -
160G SER* 2.7 18.4 + - - +
162G LEU* 1.3 75.7 - - - +
164G ILE* 1.3 52.4 + - - +
166G GLU 2.6 20.8 - - - +
167G ASN* 2.6 24.5 + - - +
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Residues in contact with ILE 164 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F HIS* 6.3 0.7 - - + -
152G LEU* 4.6 7.0 - - + -
159G PRO* 3.6 35.4 - - + +
160G SER 2.8 20.3 + - - +
161G ALA* 3.8 6.1 - - - +
163G ALA* 1.3 68.1 - - - +
165G LEU* 1.3 58.9 + - - +
166G GLU 2.5 18.5 - - - +
167G ASN* 5.0 0.4 - - - -
168G ALA* 3.0 20.9 + - + +
205G VAL* 6.0 0.7 - - + -
208G LYS* 4.7 11.2 - - + +
209G VAL* 4.4 28.7 - - + +
212G ALA* 3.5 28.9 - - + -
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Residues in contact with LEU 165 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161G ALA* 2.7 23.8 + - + +
162G LEU* 3.4 9.2 - - + +
164G ILE* 1.3 72.8 - - - +
166G GLU* 1.3 88.7 + - + +
168G ALA* 3.6 3.1 - - - +
169G ASN* 3.1 24.3 + - + +
212G ALA* 6.1 0.7 - - - -
169H ASN* 3.6 26.9 - - - +
219H ASP* 3.8 32.8 - - + +
220H HIS* 4.2 5.4 - - - +
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Residues in contact with GLU 166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G LEU* 4.4 11.2 - - + -
124G THR* 3.0 34.9 + - - +
125G THR 5.4 0.5 - - - +
162G LEU* 2.7 20.1 + - + +
163G ALA 2.6 13.7 - - - +
164G ILE 2.5 20.1 - - - +
165G LEU* 1.3 81.1 - - + +
167G ASN* 1.3 59.3 + - - +
169G ASN* 3.9 4.6 - - - +
170G VAL* 3.3 15.3 - - - +
128H LEU* 5.4 1.6 - - - +
169H ASN* 2.9 30.2 + - - -
173H ARG* 3.2 27.8 - - - +
220H HIS* 3.9 10.1 - - + -
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Residues in contact with ASN 167 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G LEU* 4.7 0.6 - - - +
123G THR 3.0 23.2 + - - +
124G THR* 3.5 18.3 - - - +
150G CYS* 3.3 31.4 - - + +
151G VAL 4.2 3.1 + - - -
152G LEU* 3.5 21.6 - - + +
163G ALA* 2.6 24.9 + - - +
164G ILE* 4.2 1.1 - - - +
166G GLU* 1.3 81.3 + - - +
168G ALA* 1.3 55.2 + - - +
169G ASN 3.0 0.4 - - - -
170G VAL* 3.1 14.8 - - - +
171G LEU* 2.7 43.0 + - + +
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Residues in contact with ALA 168 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164G ILE* 3.0 19.5 + - + +
165G LEU* 3.6 3.6 - - - +
166G GLU 2.8 7.7 + - - -
167G ASN* 1.3 73.8 - - - +
169G ASN* 1.3 62.8 + - - +
171G LEU* 3.6 11.8 + - - +
172G ALA* 3.2 16.5 + - - +
212G ALA* 4.1 11.0 - - + +
213G VAL* 4.0 33.1 - - + +
216G ALA* 3.4 16.5 - - + +
217G LEU* 5.8 0.2 - - - +
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Residues in contact with ASN 169 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165G LEU* 3.1 19.8 + - + +
166G GLU* 4.3 8.2 + - - +
167G ASN 3.0 0.4 - - - -
168G ALA* 1.3 76.2 - - - +
170G VAL* 1.3 65.5 + - - +
172G ALA* 3.1 7.2 + - - +
173G ARG* 2.9 24.2 + - - +
216G ALA* 4.3 5.3 - - + +
220G HIS* 2.8 25.4 + - - -
165H LEU* 3.4 15.9 - - - +
166H GLU* 3.0 25.9 + - - -
169H ASN* 3.5 23.8 - - - +
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Residues in contact with VAL 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G THR* 3.5 9.9 - - - +
125G THR 3.5 10.1 - - - +
128G LEU* 4.3 14.6 - - + -
148G TRP* 3.3 37.9 - - + +
150G CYS* 4.6 1.1 - - - -
166G GLU* 3.3 24.2 - - - +
167G ASN* 3.0 28.5 + - - +
169G ASN* 1.3 76.3 - - - +
171G LEU* 1.3 64.5 + - - +
173G ARG* 3.1 7.6 + - - +
174G TYR* 2.9 23.4 + - - +
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Residues in contact with LEU 171 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148G TRP* 3.6 27.8 - - + +
150G CYS* 3.6 22.7 - - + -
167G ASN* 2.7 25.9 + - + +
168G ALA 3.7 3.8 - - - +
170G VAL* 1.3 75.0 - - - +
172G ALA* 1.3 52.9 + - - +
174G TYR* 3.2 9.1 + - + -
175G ALA* 2.8 36.8 + - - +
187G VAL* 3.5 36.8 - - + -
188G GLU 4.0 5.8 - - - +
189G PRO* 3.8 26.2 - - + -
213G VAL* 4.2 14.8 - - + -
217G LEU* 4.8 1.6 - - + -
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Residues in contact with ALA 172 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168G ALA 3.2 10.1 + - - +
169G ASN 3.1 6.6 + - - +
171G LEU* 1.3 79.9 - - - +
173G ARG* 1.3 62.0 + - - +
176G SER* 2.9 26.0 + - - -
216G ALA* 3.8 18.2 - - + +
217G LEU* 3.7 16.1 - - + +
220G HIS* 3.4 35.2 - - + +
222G VAL* 3.6 4.0 - - - +
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Residues in contact with ARG 173 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G LEU* 3.7 27.0 - - + +
169G ASN* 2.9 17.0 + - - +
170G VAL* 3.1 8.9 + - - +
172G ALA* 1.3 76.1 - - - +
174G TYR* 1.3 64.2 + - - +
176G SER* 3.1 11.0 + - - -
177G ILE* 3.0 59.3 + - - +
220G HIS* 3.8 19.6 + - + -
114H VAL* 4.2 8.1 - - - +
115H PRO 3.5 21.8 + - - -
116H LEU* 3.7 19.8 - - - +
117H ALA 5.0 2.8 - - - +
124H THR* 3.3 21.0 - - - +
166H GLU* 3.1 31.8 + - - +
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Residues in contact with TYR 174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109G VAL* 3.6 16.8 - - + -
128G LEU* 3.7 8.9 - - + +
131G LEU* 4.0 7.2 - - + -
146G ALA* 3.0 24.9 + - + -
147G LYS* 3.3 1.2 - - - -
148G TRP* 3.3 60.1 - + + -
170G VAL 2.9 12.0 + - - +
171G LEU* 3.4 16.2 - - + +
173G ARG* 1.3 76.2 - - - +
175G ALA* 1.3 69.8 + - + +
177G ILE* 3.2 4.0 + - - +
178G CYS* 3.0 46.3 + - - -
185G PRO* 3.5 15.2 - - + +
186G ILE 2.9 31.4 + - - -
187G VAL* 4.4 7.6 - - + -
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Residues in contact with ALA 175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171G LEU 2.8 19.5 + - - +
172G ALA 3.7 0.2 - - - +
174G TYR* 1.3 75.3 - - + +
176G SER* 1.3 64.1 + - - +
178G CYS* 3.2 4.0 + - - +
179G GLN* 3.1 27.8 + - - +
185G PRO* 3.8 27.4 - - + -
187G VAL* 4.5 5.6 - - + -
217G LEU* 3.9 11.4 - - + -
222G VAL* 3.6 23.3 - - + -
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Residues in contact with SER 176 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172G ALA 2.9 18.1 + - - -
173G ARG* 3.1 12.1 + - - -
175G ALA* 1.3 75.1 - - - +
177G ILE* 1.3 64.7 + - - +
179G GLN* 3.5 6.9 + - - +
180G GLN* 3.3 23.0 + - - +
220G HIS* 3.7 24.7 + - - -
221G HIS 5.5 0.7 + - - -
222G VAL* 3.7 8.7 - - - +
117H ALA* 3.4 26.2 + - - +
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Residues in contact with ILE 177 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128G LEU* 3.9 28.9 - - + +
131G LEU* 4.0 21.1 - - + +
132G SER* 3.5 42.0 - - - +
135G CYS* 4.8 0.2 - - - -
173G ARG* 3.0 44.1 + - - +
174G TYR 3.6 5.2 - - - +
176G SER* 1.3 71.9 - - - +
178G CYS* 1.3 67.2 + - - +
180G GLN* 3.1 27.5 - - - +
181G ASN* 3.1 9.3 + - - +
114H VAL* 6.4 0.2 - - + -
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Residues in contact with CYS 178 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G VAL* 5.1 0.7 - - - -
131G LEU* 4.8 1.3 - - - -
135G CYS* 4.0 25.1 - - - -
146G ALA* 4.1 13.0 - - - -
174G TYR* 3.0 47.8 + - - -
175G ALA 3.6 7.0 - - - +
177G ILE* 1.3 77.6 - - - +
179G GLN* 1.3 57.8 + - - +
181G ASN* 2.8 21.0 + - - +
183G ILE* 3.1 34.0 + - + +
185G PRO* 3.8 11.0 - - + -
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Residues in contact with GLN 179 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G LEU* 3.5 20.9 - - + +
12G GLN* 5.4 1.4 + - - +
16G LEU* 3.8 20.3 - - + +
175G ALA 3.1 14.7 + - - +
176G SER* 3.9 5.3 - - - +
178G CYS* 1.3 72.3 - - - +
180G GLN* 1.3 58.9 + - - +
181G ASN 2.9 9.9 + - - -
182G GLY* 3.1 11.4 + - - -
183G ILE 3.8 4.9 - - - +
185G PRO* 3.8 12.6 - - + -
221G HIS 4.8 1.0 - - - +
222G VAL* 3.7 12.0 - - - +
223G TYR* 2.8 59.3 + - - +
226G GLY* 3.0 23.8 + - - -
227G THR* 3.5 4.6 - - - +
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Residues in contact with GLN 180 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G ALA 5.3 4.0 - - - +
8G LEU* 4.1 12.5 - - + +
12G GLN* 4.8 10.0 + - - +
132G SER* 3.5 18.1 + - - -
176G SER 3.3 9.3 + - - +
177G ILE* 3.1 27.1 - - - +
179G GLN* 1.3 77.3 - - - +
181G ASN* 1.3 62.4 + - - +
182G GLY 3.5 1.1 + - - -
115H PRO* 4.9 17.2 - - - +
117H ALA* 3.3 33.7 - - + +
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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