Contacts of the helix formed by residues 170 - 187 (chain D) in PDB entry 1C2O
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 ASN 170 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D GLY 4.1 4.2 + - - -
158D PHE* 3.9 18.1 + - - +
169D GLY* 1.3 70.9 - - - +
171D VAL* 1.3 59.6 + - - +
172D GLY 3.1 3.1 - - - -
173D LEU* 2.7 30.4 + - + +
174D LEU* 3.0 13.0 + - + +
301D PRO* 3.0 14.5 - - - +
302D VAL* 2.7 48.4 + - - +
304D ASP* 2.5 32.7 + - - +
307D PHE* 4.0 18.6 - - + +
308D LEU* 5.1 1.5 - - - +
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Residues in contact with VAL 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D PHE* 3.6 15.5 - - - +
48D MET 3.6 3.4 - - - +
49D PRO* 3.5 32.8 - - + -
152D ARG* 3.5 25.4 - - - +
156D PHE 3.4 18.8 - - - +
157D GLY 3.2 15.3 + - - +
168D PRO* 4.4 6.5 - - + -
169D GLY* 3.0 13.2 - - - +
170D ASN* 1.3 78.3 - - - +
172D GLY* 1.3 56.3 + - - +
174D LEU* 3.2 9.9 + - + +
175D ASP* 2.8 34.4 + - - +
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Residues in contact with GLY 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D TYR* 3.2 15.9 - - - +
152D ARG 3.4 26.2 - - - -
157D GLY* 2.9 14.0 + - - -
158D PHE* 4.0 7.4 - - - -
170D ASN 3.1 0.6 - - - -
171D VAL* 1.3 78.9 - - - +
173D LEU* 1.3 60.6 + - - +
175D ASP* 3.3 9.0 - - - +
176D GLN* 3.2 21.5 + - - +
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Residues in contact with LEU 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D PHE* 4.5 11.0 - - + -
158D PHE* 4.0 12.5 - - + -
170D ASN* 2.7 15.4 + - + +
172D GLY* 1.3 75.8 - - - +
174D LEU* 1.3 56.2 + - - +
175D ASP 3.0 1.6 - - - -
176D GLN* 2.9 35.9 + - - +
177D ARG* 2.7 31.0 + - - +
208D SER* 3.8 21.1 - - - +
211D MET* 4.0 23.1 - - + -
212D HIS* 3.7 7.5 + - + +
301D PRO* 4.2 12.3 - - + -
307D PHE* 3.5 41.1 - - + -
308D LEU* 5.6 0.4 - - + -
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Residues in contact with LEU 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D PRO* 3.7 28.0 - - + -
50D PRO* 3.4 18.8 - - + +
168D PRO* 6.6 0.2 - - + -
169D GLY 5.2 2.9 - - - +
170D ASN* 3.0 15.1 + - + +
171D VAL* 3.5 9.0 - - + +
173D LEU* 1.3 74.9 - - - +
175D ASP* 1.3 66.4 + - - +
177D ARG* 3.7 21.2 - - - +
178D LEU* 2.8 25.8 + - - +
306D ASP* 6.1 0.7 - - - +
307D PHE* 3.3 33.4 - - + -
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Residues in contact with ASP 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D PHE* 3.3 13.2 - - + -
50D PRO* 3.2 14.4 - - - +
97D LEU* 3.3 16.7 - - + +
151D TYR* 3.7 12.1 - - + -
152D ARG* 2.9 67.3 + - - +
171D VAL 2.8 17.9 + - - +
172D GLY 3.3 8.5 - - - +
173D LEU 3.0 0.4 - - - -
174D LEU* 1.3 79.2 - - - +
176D GLN* 1.3 64.4 + - - +
178D LEU* 2.9 3.3 + - - +
179D ALA 2.9 18.0 + - - -
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Residues in contact with GLN 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D ILE* 3.1 29.4 - - + +
149D MET* 3.3 30.3 - - + +
151D TYR* 3.5 28.3 - - + +
172D GLY 3.2 12.1 - - - +
173D LEU* 2.9 32.0 + - - +
175D ASP* 1.3 75.0 - - - +
177D ARG* 1.3 64.8 + - - +
179D ALA* 3.0 4.6 + - - +
180D LEU* 2.8 24.0 + - - +
208D SER* 3.2 18.1 + - - -
212D HIS* 3.1 23.6 - - + -
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Residues in contact with ARG 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D LEU 2.7 16.5 + - - +
174D LEU* 3.2 21.1 + - - +
176D GLN* 1.3 72.5 - - - +
178D LEU* 1.3 59.7 + - - +
180D LEU* 2.9 15.7 + - - +
181D GLN* 2.8 45.7 + - - +
212D HIS* 3.9 3.5 + - - +
215D SER* 3.0 24.2 + - - -
217D PRO* 3.5 27.1 - - - +
218D SER* 2.6 45.8 + - - +
221D LEU* 4.1 11.4 - - + -
306D ASP* 5.9 1.0 + - - -
307D PHE* 3.4 25.0 - - + +
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Residues in contact with LEU 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D PHE* 3.2 45.1 - - + +
38D ALA* 3.5 15.7 - - + -
50D PRO* 4.3 15.7 - - + +
51D GLU 4.3 5.4 - - - +
52D PRO* 4.5 18.2 - - + -
174D LEU 2.8 13.4 + - - +
175D ASP 3.2 8.5 - - - +
177D ARG* 1.3 78.3 - - - +
179D ALA* 1.3 62.6 + - - +
181D GLN* 3.0 23.3 + - + +
182D TRP* 2.9 24.2 + - + +
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Residues in contact with ALA 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D PHE* 3.7 17.9 - - + -
99D LEU* 4.4 10.0 - - + +
147D VAL* 5.9 2.5 - - + +
149D MET* 3.7 41.1 - - + -
175D ASP 2.9 10.1 + - - +
176D GLN 3.0 7.6 + - - +
178D LEU* 1.3 76.4 - - - +
180D LEU* 1.3 60.8 + - + +
182D TRP* 3.1 4.7 + - - +
183D VAL* 2.9 28.8 + - - +
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Residues in contact with LEU 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D ILE* 3.5 24.7 - - + -
118D ILE* 5.4 0.9 - - + -
149D MET* 4.4 7.0 - - + -
176D GLN 2.8 16.2 + - - +
177D ARG* 2.9 20.3 + - - +
179D ALA* 1.3 77.8 - - - +
181D GLN* 1.3 60.1 + - - +
183D VAL* 3.0 11.2 + - - +
184D GLN* 2.9 21.7 + - - +
199D LEU* 3.4 37.0 - - + -
212D HIS* 4.1 26.2 - - + +
218D SER* 5.0 3.4 - - - +
221D LEU* 3.5 32.9 - - + +
222D PHE* 5.2 0.4 - - + -
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Residues in contact with GLN 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D ARG* 2.8 39.8 + - - +
178D LEU* 3.0 25.3 + - + +
180D LEU* 1.3 71.7 - - - +
182D TRP* 1.3 59.7 - - - +
184D GLN* 3.2 10.9 - - + +
185D GLU* 3.0 33.3 + - + +
221D LEU* 3.6 23.8 - - + +
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Residues in contact with TRP 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D VAL* 4.1 21.0 - - + +
35D ILE* 3.7 41.2 - - + +
36D PRO 4.4 8.9 + - - -
37D PHE* 4.3 19.7 - - + +
56D TRP* 5.8 0.8 - - - -
99D LEU* 3.5 29.4 - - + -
101D VAL* 4.3 9.6 - - + -
147D VAL* 5.4 0.4 - - + -
178D LEU* 2.9 15.6 + - + +
179D ALA* 3.5 10.1 - - - +
180D LEU 3.0 0.2 - - - -
181D GLN* 1.3 76.4 - - - +
183D VAL* 1.3 98.9 + - + +
185D GLU* 2.8 21.8 + - - -
186D ASN* 3.0 41.3 + - + +
187D ILE* 4.9 3.4 - - + -
190D PHE* 4.0 18.2 - + - -
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Residues in contact with VAL 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D VAL* 5.1 2.9 - - + -
116D ILE* 3.3 34.8 - - + -
147D VAL* 3.6 33.0 - - + -
179D ALA 2.9 12.5 + - - +
180D LEU 3.0 13.9 + - - +
182D TRP* 1.3 84.4 - - + +
184D GLN* 1.3 65.2 + - - +
187D ILE* 2.7 57.5 + - + +
197D VAL* 4.2 13.2 - - + -
221D LEU 4.9 1.1 - - - +
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Residues in contact with GLN 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D LEU 2.9 10.5 + - - +
181D GLN* 3.2 16.4 - - - +
182D TRP 2.9 0.2 + - - -
183D VAL* 1.3 81.8 - - - +
185D GLU* 1.3 61.0 + - + +
186D ASN 3.2 2.8 + - - -
187D ILE* 4.2 1.0 + - - +
188D ALA* 5.0 2.9 + - - +
194D PRO* 3.4 49.0 + - + +
195D MET* 4.9 7.1 - - - +
197D VAL* 4.0 6.9 - - - +
220D SER 3.6 22.3 + - - +
221D LEU* 3.9 24.1 - - + +
223D HIS* 4.9 3.4 + - - -
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Residues in contact with GLU 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ARG* 3.2 53.8 + - - +
181D GLN* 3.0 22.3 - - - +
182D TRP* 2.8 12.0 + - - +
184D GLN* 1.3 77.1 - - + +
186D ASN* 1.3 78.5 + - - +
188D ALA* 5.7 1.8 - - - -
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Residues in contact with ASN 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D VAL* 3.1 16.0 - - + +
13D ARG* 2.7 41.4 + - - +
182D TRP* 3.0 43.4 + - + +
184D GLN 3.2 1.8 + - - -
185D GLU* 1.3 106.3 + - - +
187D ILE* 1.3 69.8 + - - +
188D ALA* 3.0 6.1 + - - +
189D ALA* 3.3 11.9 + - - +
190D PHE* 3.2 17.9 - - - -
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Residues in contact with ILE 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D VAL* 4.2 8.1 - - + -
114D VAL* 3.5 25.8 - - + -
145D VAL* 3.5 23.6 - - + -
147D VAL* 3.7 19.3 - - + -
182D TRP* 4.9 2.2 - - + -
183D VAL* 2.7 43.0 + - + +
186D ASN* 1.3 79.8 - - - +
188D ALA* 1.3 57.6 + - - +
190D PHE* 2.7 39.7 + - + +
192D GLY* 3.0 23.5 + - - +
193D ASP 4.4 1.1 - - - -
194D PRO* 4.1 21.3 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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