Contacts of the helix formed by residues 160 - 177 (chain B) in PDB entry 1SXG
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 ASP 160 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B ILE* 1.3 75.8 - - - +
161B TYR* 1.3 59.7 + - - +
162B GLU* 3.7 10.7 + - - +
163B GLN* 2.8 44.9 + - + +
164B ALA* 2.8 31.1 + - - +
320B GLN* 3.3 33.0 + - - +
321B LEU 4.2 2.6 + - - -
323B HIS* 3.9 9.4 + - + -
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Residues in contact with TYR 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B ALA* 3.1 40.2 + - - -
147B SER 4.9 0.9 - - - -
148B ILE* 3.9 28.7 - - + -
158B THR* 3.7 11.4 - - + -
159B ILE* 3.0 38.6 + - + +
160B ASP* 1.3 71.4 - - - +
162B GLU* 1.3 57.9 + - - +
164B ALA* 3.6 5.1 - - - +
165B ALA* 2.8 31.4 + - - +
191B ILE* 3.7 27.6 - - + -
195B LYS* 3.5 23.8 - - + +
196B LYS* 4.4 8.4 - - + +
274B PHE* 4.1 18.7 - + - -
292B GLN* 3.4 17.0 + - - -
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Residues in contact with GLU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ASP* 3.3 13.3 - - - +
161B TYR* 1.3 78.8 - - - +
163B GLN* 1.3 57.8 + - + +
165B ALA 3.3 0.9 + - - -
166B PHE* 2.7 35.3 + - - +
195B LYS* 3.4 32.6 - - + +
198B LYS* 2.7 33.7 + - - +
199B GLY* 3.1 17.9 - - - -
202B ARG* 2.8 41.4 + - - +
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Residues in contact with GLN 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B ASP* 2.8 29.7 + - + +
162B GLU* 1.3 77.4 - - + +
164B ALA* 1.3 59.3 + - - +
166B PHE* 3.5 14.6 - - - +
167B ASP* 2.7 70.9 + - - +
202B ARG* 3.2 21.5 + - - +
323B HIS* 3.9 11.2 - - + -
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Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B ILE* 3.9 11.0 - - + -
160B ASP 2.8 19.0 + - - +
161B TYR 3.6 4.9 - - - +
163B GLN* 1.3 76.0 - - - +
165B ALA* 1.3 59.0 + - - +
167B ASP* 4.0 1.7 - - - +
168B ALA* 3.0 29.5 + - - +
274B PHE* 3.7 25.1 - - + -
290B VAL* 3.7 18.8 - - + +
323B HIS* 3.7 14.5 - - + -
325B ILE* 4.6 1.1 - - - +
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Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B TYR 2.8 18.8 + - - +
162B GLU 3.5 4.7 - - - +
164B ALA* 1.3 75.1 - - - +
166B PHE* 1.3 65.6 + - - +
168B ALA* 3.6 0.5 - - - +
169B VAL* 2.9 30.4 + - - +
196B LYS* 3.5 34.8 - - + +
199B GLY 3.9 4.0 - - - -
244B PHE* 3.8 25.4 - - + -
274B PHE* 4.3 0.8 - - - -
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Residues in contact with PHE 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B GLU* 2.7 15.4 + - - +
163B GLN* 3.2 22.4 - - - +
165B ALA* 1.3 79.7 - - - +
167B ASP* 1.3 69.1 + - - +
169B VAL* 3.2 3.1 + - - +
170B GLN* 2.9 51.3 + - + +
199B GLY 3.2 10.9 + - - -
202B ARG* 3.0 59.5 - - + -
203B ALA* 4.0 8.2 - - - +
206B GLU* 3.0 40.2 - - + -
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Residues in contact with ASP 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B GLN* 2.7 45.4 + - - +
164B ALA 4.2 2.0 - - - +
166B PHE* 1.3 74.0 - - - +
168B ALA* 1.3 65.1 + - - +
170B GLN* 3.5 9.8 - - - +
171B SER* 3.0 22.5 + - - -
323B HIS* 3.0 21.8 + - + +
325B ILE* 4.7 17.5 - - + +
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Residues in contact with ALA 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B ALA 3.0 19.8 + - - +
165B ALA 3.6 2.2 - - - +
167B ASP* 1.3 77.5 - - - +
169B VAL* 1.3 65.3 - - - +
171B SER* 3.1 17.1 + - - -
172B LEU* 3.8 6.4 + - - +
244B PHE* 3.5 33.0 - - + -
272B ILE* 4.2 18.5 - - + +
290B VAL* 3.8 11.9 - - + -
325B ILE* 4.6 5.8 - - - +
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Residues in contact with VAL 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ALA 2.9 17.0 + - - +
166B PHE 3.5 0.9 - - - +
168B ALA* 1.3 75.4 - - - +
170B GLN* 1.3 53.1 + - - +
172B LEU* 2.8 40.6 + - - +
173B ILE* 3.3 8.7 + - + +
180B ILE* 4.4 7.4 - - + -
200B TYR* 3.5 46.7 - - + +
203B ALA* 3.2 24.5 - - + -
204B LEU* 4.3 16.6 - - + +
244B PHE* 4.0 14.1 - - + -
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Residues in contact with GLN 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B PHE* 2.9 41.1 + - + +
167B ASP* 3.5 12.1 - - - +
169B VAL* 1.3 76.7 - - - +
171B SER* 1.3 60.6 + - - +
173B ILE* 3.1 28.3 + - - +
174B ASP* 2.6 53.9 + - - +
203B ALA* 4.3 6.2 - - + +
206B GLU* 5.3 2.6 - - - +
207B SER* 3.9 14.8 + - - -
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Residues in contact with SER 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ASP 3.0 12.4 + - - -
168B ALA* 3.1 16.8 - - - -
170B GLN* 1.3 76.4 - - - +
172B LEU* 1.3 57.5 + - - +
174B ASP* 3.9 7.9 + - - +
175B SER* 2.5 32.1 + - - -
272B ILE* 4.6 8.0 - - - +
325B ILE* 5.5 1.3 - - - -
327B PHE* 3.5 34.2 - - - -
331B THR* 5.6 2.8 + - - +
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Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B ALA 4.1 9.6 - - - +
169B VAL* 2.8 14.7 + - - +
171B SER* 1.3 83.0 - - - +
173B ILE* 1.3 67.0 + - - +
175B SER* 2.9 16.0 + - - +
176B GLY 3.1 7.4 + - - -
177B HIS* 3.3 14.7 - - + +
180B ILE* 3.6 35.7 - - + -
242B ALA* 3.9 21.3 - - + -
243B ILE 4.8 5.2 - - - +
244B PHE* 4.9 2.0 - - + -
270B GLU* 3.6 28.3 - - + +
272B ILE* 4.2 20.9 - - + +
331B THR* 4.5 11.0 - - + -
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Residues in contact with ILE 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B VAL* 3.5 10.8 - - + +
170B GLN* 3.3 35.4 - - - +
172B LEU* 1.3 75.7 - - - +
174B ASP* 1.3 58.6 + - - +
176B GLY* 2.6 30.5 + - - -
177B HIS 3.4 11.9 + - - +
180B ILE* 3.7 20.4 - - + -
203B ALA 4.7 3.6 - - - +
204B LEU* 4.4 11.4 - - + +
207B SER* 3.7 26.2 - - - +
209B LEU* 3.7 21.3 - - + -
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Residues in contact with ASP 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B GLN* 2.6 44.9 + - - +
171B SER* 4.0 7.0 - - - +
173B ILE* 1.3 73.8 - - - +
175B SER* 1.3 59.1 + - - +
176B GLY* 3.2 0.4 - - - -
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Residues in contact with SER 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B SER* 2.5 24.8 + - - -
172B LEU* 2.9 14.1 + - - +
173B ILE 2.9 0.2 + - - -
174B ASP* 1.3 77.7 - - - +
176B GLY* 1.3 59.0 + - - +
177B HIS* 3.8 17.0 + - - -
270B GLU* 4.4 5.7 + - - -
332B LYS* 3.6 22.4 + - - -
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Residues in contact with GLY 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B LEU 3.1 0.4 + - - -
173B ILE 2.6 17.7 + - - -
174B ASP 3.2 0.8 - - - -
175B SER* 1.3 72.7 - - - +
177B HIS* 1.3 71.9 + - - +
241B THR* 4.9 0.7 + - - -
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Residues in contact with HIS 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B LEU* 3.3 20.4 + - + +
173B ILE* 3.4 12.2 + - - +
175B SER* 3.8 12.7 - - - -
176B GLY* 1.3 94.9 + - - +
178B LYS* 1.3 60.0 + - - +
179B ASN* 4.9 0.2 - - - +
180B ILE* 3.7 27.5 - - + +
209B LEU* 3.7 8.8 - - - +
241B THR* 2.8 44.0 + - - +
242B ALA* 3.3 24.1 - - + +
268B ASP 5.5 1.0 + - - -
270B GLU* 4.0 25.0 - - - +
332B LYS* 5.9 0.9 - - - -
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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