Contacts of the helix formed by residues 164 - 185 (chain D) in PDB entry 3HW4
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 164 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162D THR 4.2 0.4 + - - -
163D LEU* 1.3 78.1 - - - +
165D GLU* 1.3 63.0 + - - +
166D GLU* 3.3 12.0 + - - +
167D SER* 3.0 27.0 + - - -
168D ARG* 3.1 20.8 + - - +
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Residues in contact with GLU 165 (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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161D TYR* 5.4 2.3 - - - -
164D ASP* 1.3 76.1 - - - +
166D GLU* 1.3 57.2 + - - +
168D ARG* 3.1 38.3 + - - +
169D ALA* 2.9 30.7 + - - +
172D LYS* 4.8 7.4 + - - -
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Residues in contact with GLU 166 (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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164D ASP* 3.2 11.7 + - - +
165D GLU* 1.3 76.9 - - - +
167D SER* 1.3 61.9 + - - +
169D ALA* 3.5 6.9 + - - +
170D ARG* 3.3 46.4 + - - +
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Residues in contact with SER 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D MET 5.7 3.5 - - - +
163D LEU* 4.1 23.5 - - - +
164D ASP* 3.0 21.9 + - - -
166D GLU* 1.3 73.7 - - - +
168D ARG* 1.3 66.0 + - - +
170D ARG* 3.0 30.1 + - - +
171D ILE* 3.3 27.2 + - - +
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Residues in contact with ARG 168 (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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146D HIS* 3.6 19.3 - - + -
148D PHE* 4.4 6.3 - - + -
154D GLU* 2.8 51.4 + - - +
161D TYR* 3.4 28.9 - - - +
163D LEU* 3.0 41.4 + - + -
164D ASP* 3.1 8.7 + - - +
165D GLU* 3.1 52.7 + - - +
167D SER* 1.3 73.8 - - - +
169D ALA* 1.3 66.3 + - - +
171D ILE* 3.2 8.7 + - - +
172D LYS* 2.9 35.2 + - - +
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Residues in contact with ALA 169 (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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165D GLU 2.9 19.9 + - - +
166D GLU* 3.7 7.2 - - - +
168D ARG* 1.3 78.3 - - - +
170D ARG* 1.3 55.1 + - - +
172D LYS* 3.9 10.5 - - - +
173D THR* 2.7 40.5 + - - +
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Residues in contact with ARG 170 (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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47D MET* 4.0 13.3 - - - +
166D GLU* 3.3 39.9 + - - +
167D SER* 3.0 37.5 + - - +
168D ARG 3.3 0.4 - - - -
169D ALA* 1.3 77.1 - - + +
171D ILE* 1.3 63.8 + - + +
173D THR* 3.9 4.7 - - - -
174D ARG* 3.1 24.4 + - - +
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Residues in contact with ILE 171 (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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44D VAL* 4.2 15.5 - - + +
47D MET* 3.8 30.5 - - + +
48D TYR* 3.9 43.3 - - + +
148D PHE* 3.7 34.1 - - + -
163D LEU* 4.2 8.3 - - + -
167D SER* 3.3 13.6 + - - +
168D ARG* 3.2 8.2 + - - +
170D ARG* 1.3 81.1 - - - +
172D LYS* 1.3 63.0 + - - +
174D ARG* 3.4 3.5 + - - +
175D LEU* 3.0 34.6 + - + +
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Residues in contact with LYS 172 (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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148D PHE* 4.3 13.9 - - + -
149D SER 5.9 0.2 - - - +
152D GLY* 3.4 40.1 + - - +
153D GLU 5.0 0.2 - - - +
154D GLU* 3.0 46.3 + - - +
165D GLU* 4.8 6.5 + - - -
168D ARG* 2.9 32.9 + - - +
169D ALA* 4.0 7.6 - - - +
171D ILE* 1.3 73.7 - - - +
173D THR* 1.3 57.5 + - - +
175D LEU* 3.5 8.2 + - - +
176D PHE* 3.0 28.6 + - - +
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Residues in contact with THR 173 (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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169D ALA* 2.7 25.1 + - - +
170D ARG* 3.9 5.2 - - - -
172D LYS* 1.3 75.3 - - - +
174D ARG* 1.3 63.1 + - - +
176D PHE* 3.5 10.6 + - + +
177D THR* 2.8 36.3 + - - +
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Residues in contact with ARG 174 (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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8D CYS* 3.1 35.2 + - - -
9D PHE* 3.8 11.3 - - - +
43D GLU* 3.0 36.2 + - + +
44D VAL* 6.1 0.4 - - + -
47D MET* 3.7 28.0 - - + -
170D ARG 3.1 18.5 + - - +
171D ILE 3.7 4.9 - - - +
173D THR* 1.3 77.4 - - - +
175D LEU* 1.3 57.8 + - + +
177D THR* 3.3 20.3 + - - +
178D ILE* 3.0 53.6 + - + +
181D GLU* 5.0 5.3 + - - -
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Residues in contact with LEU 175 (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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40D THR* 3.3 34.1 - - + -
44D VAL* 3.7 18.2 - - + -
122D VAL* 4.1 7.6 - - + -
148D PHE* 3.4 34.5 - - + -
149D SER 3.5 22.2 - - - +
150D PHE* 3.6 16.6 - - + -
171D ILE* 3.0 30.6 + - + +
172D LYS* 3.9 5.2 - - - +
174D ARG* 1.3 74.0 - - + +
176D PHE* 1.3 68.0 + - - +
178D ILE* 3.2 9.2 + - + -
179D ARG* 3.0 23.6 + - - +
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Residues in contact with PHE 176 (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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150D PHE 3.6 14.0 + - - +
151D THR* 5.3 7.4 - - - -
152D GLY* 5.4 3.6 - - - +
172D LYS 3.0 18.9 + - - +
173D THR* 3.7 11.4 - - + +
175D LEU* 1.3 77.0 - - - +
177D THR* 1.3 65.3 + - - +
179D ARG* 3.3 26.0 + - - +
180D GLN* 2.8 50.6 + - + +
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Residues in contact with THR 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 THR* 2.8 26.1 + - - +
174D ARG* 3.5 17.4 - - - +
175D LEU 3.2 0.2 - - - -
176D PHE* 1.3 77.4 - - - +
178D ILE* 1.3 66.1 + - - +
180D GLN* 3.2 22.0 + - - +
181D GLU* 2.9 50.2 + - - +
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Residues in contact with ILE 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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4D PHE* 4.1 0.5 - - - -
8D CYS* 4.2 12.1 - - - -
9D PHE* 3.8 30.1 - - + -
40D THR* 4.1 21.5 - - + +
43D GLU* 4.4 2.9 - - + +
44D VAL* 6.3 0.2 - - + -
150D PHE* 3.8 17.5 - - + -
174D ARG* 3.0 51.2 + - + +
175D LEU* 3.2 13.7 + - + +
177D THR* 1.3 75.3 - - - +
179D ARG* 1.3 63.3 + - - +
181D GLU* 3.3 5.6 + - - +
182D MET* 3.1 43.7 + - + +
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Residues in contact with ARG 179 (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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150D PHE* 3.3 34.8 + - + +
151D THR* 4.5 11.2 - - - +
175D LEU 3.0 12.7 + - - +
176D PHE* 3.4 30.6 + - - +
178D ILE* 1.3 78.6 - - - +
180D GLN* 1.3 61.8 + - - +
182D MET* 3.4 1.9 + - - +
183D ALA* 2.9 32.3 + - - +
188D TRP* 3.6 53.6 - - + +
192D ARG* 4.7 6.7 - - - +
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Residues in contact with GLN 180 (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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176D PHE* 2.8 36.4 + - + +
177D THR* 3.2 28.4 + - - +
179D ARG* 1.3 82.4 - - - +
181D GLU* 1.3 64.4 + - + +
183D ALA* 3.4 4.5 + - - +
184D SER* 3.1 31.0 + - - +
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Residues in contact with GLU 181 (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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4D PHE* 3.5 18.2 - - + -
7D GLN* 4.1 11.4 + - - +
8D CYS* 4.0 20.7 - - - +
174D ARG* 5.0 6.0 + - - -
177D THR* 2.9 39.8 + - + +
178D ILE* 4.4 0.4 - - - +
180D GLN* 1.3 77.1 - - + +
182D MET* 1.3 63.6 + - - +
184D SER* 2.9 19.2 + - - -
185D ARG* 3.2 25.0 + - - +
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Residues in contact with MET 182 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D MET* 4.0 10.5 - - + -
4D PHE* 3.5 30.9 - - + -
9D PHE* 5.7 1.6 - - + -
36D ALA* 3.9 22.7 - - + -
40D THR* 5.3 1.8 - - - +
178D ILE* 3.1 29.7 + - + +
179D ARG 3.6 7.2 - - - +
181D GLU* 1.3 76.8 - - - +
183D ALA* 1.3 61.5 + - - +
185D ARG 3.1 3.5 + - - -
186D GLY 3.0 4.5 + - - -
187D LEU* 2.8 33.8 + - + +
188D TRP* 3.8 23.1 - - + +
191D PHE* 3.3 47.3 - - + -
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Residues in contact with ALA 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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179D ARG* 2.9 27.3 + - + +
180D GLN* 4.1 4.9 - - - +
182D MET* 1.3 72.9 - - - +
184D SER* 1.3 62.6 + - - +
186D GLY* 3.1 13.6 + - - -
188D TRP* 3.5 28.5 - - + +
189D ASP* 5.7 0.9 - - - +
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Residues in contact with SER 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 GLN* 3.1 15.6 + - - +
181D GLU* 2.9 21.5 + - - -
183D ALA* 1.3 78.4 - - - +
185D ARG* 1.3 60.3 + - - +
186D GLY 3.4 1.2 + - - -
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Residues in contact with ARG 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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-2D LEU* 3.4 22.9 - - - +
-1D GLY* 5.1 9.5 + - - +
0D SER 5.6 0.2 + - - -
3D ASP* 5.1 1.2 + - - +
4D PHE* 3.3 40.9 - - - +
7D GLN* 3.2 36.7 + - - +
181D GLU* 3.2 21.1 + - - +
182D MET 3.1 2.0 + - - +
184D SER* 1.3 80.9 + - - +
186D GLY* 1.3 56.8 + - - +
187D LEU* 3.2 24.7 + - + +
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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