Contacts of the helix formed by residues 174 - 192 (chain D) in PDB entry 3G33
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 ARG 174 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59B MET* 5.9 2.2 - - - -
62B TYR* 3.6 26.9 - - + -
253B GLU 5.2 2.0 + - - -
254B SER 4.2 28.7 + - - -
170D LEU* 5.9 8.6 - - + +
171D PRO* 3.1 22.4 + - + +
173D ASP* 1.3 86.1 - - + +
175D GLN* 1.3 65.4 + - - +
176D ALA 3.1 4.8 + - - -
177D LEU* 3.7 9.0 + - - +
178D VAL* 3.8 16.1 + - + +
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Residues in contact with GLN 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLU* 4.4 6.6 - - - +
162D ALA* 6.1 0.2 - - - -
165D LEU* 3.8 50.9 + - + +
166D HIS* 4.5 12.4 - - - +
168D LEU* 6.0 0.2 - - - +
170D LEU* 4.2 21.3 + - + +
171D PRO 3.4 14.6 + - - +
172D ARG* 3.4 33.4 + - - +
174D ARG* 1.3 77.7 - - - +
176D ALA* 1.3 63.5 + - - +
177D LEU 3.4 0.2 - - - -
178D VAL* 4.0 7.7 - - - +
179D LYS* 3.0 30.7 + - + +
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Residues in contact with ALA 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B TYR* 3.6 31.9 - - + +
65B LEU* 3.3 30.3 - - + +
66B GLU* 4.1 17.3 - - + +
69B GLU* 5.3 4.5 - - + +
172D ARG 4.6 2.4 + - - -
174D ARG 3.1 1.2 - - - -
175D GLN* 1.3 80.2 - - - +
177D LEU* 1.3 62.6 + - - +
179D LYS* 3.8 4.7 - - - +
180D LYS* 3.2 20.4 + - - +
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Residues in contact with LEU 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B TYR* 3.5 30.9 - - + +
65B LEU* 3.9 18.2 - - + -
184B THR* 3.7 30.5 - - - +
187B ALA* 4.3 4.5 - - + -
188B LEU* 3.8 36.8 - - + +
191B THR* 3.8 8.7 - - + +
251B LEU* 5.4 4.7 - - + -
254B SER* 4.7 9.0 - - - +
174D ARG 3.7 2.7 + - - +
175D GLN 3.4 0.4 - - - -
176D ALA* 1.3 76.1 - - - +
178D VAL* 1.3 67.3 + - + +
180D LYS* 3.3 6.0 + - + +
181D HIS* 3.0 26.1 + - + +
215D LEU* 4.3 9.9 - - + -
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Residues in contact with VAL 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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254B SER* 5.9 2.9 - - - +
165D LEU* 4.3 17.0 - - + -
170D LEU* 4.4 18.8 - - + -
174D ARG* 3.8 17.0 - - + +
175D GLN* 3.5 7.6 + - - +
176D ALA 3.4 0.4 - - - -
177D LEU* 1.3 77.7 - - + +
179D LYS* 1.3 57.5 + - - +
181D HIS* 3.8 1.6 - - - +
182D ALA* 2.9 28.6 + - - +
208D ILE* 5.2 3.1 - - + -
211D ALA* 4.1 2.9 - - + +
212D VAL* 3.6 32.5 - - + +
215D LEU* 3.5 27.4 - - + -
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Residues in contact with LYS 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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69B GLU* 6.0 7.5 + - + +
70B GLU* 4.4 19.2 + - - -
158D HIS* 5.2 2.9 - - - -
161D LEU* 4.2 21.4 - - + +
162D ALA* 6.1 2.9 - - - +
165D LEU* 4.2 21.5 - - + +
175D GLN* 3.0 22.0 + - + +
176D ALA* 3.8 4.5 - - - +
178D VAL* 1.3 77.1 - - - +
180D LYS* 1.3 63.5 + - - +
182D ALA* 3.4 7.5 + - - +
183D GLN* 3.3 41.1 + - - +
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Residues in contact with LYS 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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65B LEU* 5.2 4.2 - - + +
69B GLU* 3.2 31.8 + - + +
75B GLU* 2.7 42.6 + - - -
180B LYS* 5.3 6.4 - - - +
183B GLN* 3.1 26.4 + - - -
184B THR* 4.0 23.1 - - + -
187B ALA* 3.8 15.5 - - + +
75D GLU* 6.0 0.9 - - - +
176D ALA 3.2 15.0 + - - +
177D LEU* 3.3 8.7 + - + +
179D LYS* 1.3 78.7 - - - +
181D HIS* 1.3 63.6 + - - +
183D GLN* 3.0 29.0 + - - +
184D THR* 3.6 8.1 + - + +
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Residues in contact with HIS 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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181B HIS* 3.3 36.6 + + - -
184B THR* 3.9 22.3 + - - +
251B LEU* 4.7 15.9 - - + +
177D LEU* 3.0 17.5 + - + +
178D VAL 3.8 2.7 - - - +
180D LYS* 1.3 77.0 - - - +
182D ALA* 1.3 62.9 + - - +
183D GLN 3.2 0.7 + - - -
184D THR* 3.2 21.8 + - - -
185D PHE* 3.2 42.8 - + - -
210D ALA 4.8 1.4 + - - -
211D ALA* 3.7 24.8 - - - -
214D GLY* 5.2 4.0 - - - -
215D LEU* 4.0 17.5 - - + -
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Residues in contact with ALA 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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161D LEU* 4.6 12.1 - - + -
178D VAL 2.9 18.6 + - - +
179D LYS* 3.6 8.7 - - - +
181D HIS* 1.3 76.2 - - - +
183D GLN* 1.3 57.7 + - - +
185D PHE* 3.4 9.2 + - - +
186D LEU* 3.1 28.9 + - + +
207D SER* 4.1 2.7 + - - -
208D ILE* 4.3 24.2 - - + -
211D ALA* 3.7 18.6 - - + +
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Residues in contact with GLN 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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69B GLU* 4.3 4.2 - - - +
72B ARG* 3.8 7.4 + - - +
180B LYS* 3.2 12.8 + - - +
75D GLU* 3.3 38.4 - - - +
158D HIS* 2.8 40.5 + - + -
161D LEU* 4.0 7.2 - - + +
179D LYS* 3.3 35.6 + - - +
180D LYS* 3.0 20.1 + - - +
182D ALA* 1.3 76.9 - - - +
184D THR* 1.3 59.0 + - - +
186D LEU* 3.4 8.4 + - + +
187D ALA* 2.9 22.9 + - - +
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Residues in contact with THR 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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177B LEU* 4.1 10.6 - - - +
180B LYS* 4.0 30.3 - - + +
181B HIS* 4.1 25.2 + - - +
184B THR* 4.0 21.8 - - + -
180D LYS* 3.7 15.0 - - + +
181D HIS* 3.2 10.5 + - - +
182D ALA 3.3 0.2 - - - -
183D GLN* 1.3 75.3 - - - +
185D PHE* 1.3 69.8 + - - +
187D ALA* 3.4 3.5 + - - +
188D LEU* 2.8 27.9 + - - +
251D LEU* 5.0 8.0 - - - +
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Residues in contact with PHE 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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181D HIS* 3.2 57.2 - + - -
182D ALA* 3.4 5.3 + - - +
184D THR* 1.3 83.2 + - - +
186D LEU* 1.3 57.7 + - - +
188D LEU* 3.2 6.2 + - + +
189D CYS* 2.9 33.1 + - - -
207D SER* 3.3 36.6 - - - -
210D ALA* 4.0 19.5 - - + -
211D ALA* 4.0 8.7 - - - -
247D ILE* 3.6 21.7 - - + +
248D GLU* 4.8 7.9 - - + -
251D LEU* 3.5 39.3 - - + -
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Residues in contact with LEU 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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79D PRO* 4.8 10.7 - - + +
157D ALA* 3.8 29.2 - - + -
158D HIS* 3.6 32.5 - - + +
161D LEU* 3.8 29.4 - - + -
182D ALA 3.1 19.3 + - - +
183D GLN* 3.5 11.2 - - - +
184D THR 3.2 0.2 - - - -
185D PHE* 1.3 77.2 - - - +
187D ALA* 1.3 61.4 + - - +
189D CYS* 3.5 7.4 + - - +
190D ALA* 3.3 19.9 + - - +
203D ILE* 4.1 7.6 - - + +
204D ALA* 4.1 6.1 - - - -
207D SER* 3.0 22.7 - - - +
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Residues in contact with ALA 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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177B LEU* 4.7 3.8 - - + -
180B LYS* 3.8 15.9 - - + +
65D LEU* 4.0 27.1 - - + -
75D GLU* 5.5 0.4 - - - +
78D PHE* 3.5 13.2 - - + -
79D PRO* 5.3 2.7 - - + +
183D GLN 2.9 17.6 + - - +
184D THR* 3.7 5.4 - - - +
185D PHE 3.3 0.2 - - - -
186D LEU* 1.3 73.8 - - - +
188D LEU* 1.3 67.0 + - - +
190D ALA* 3.2 6.6 + - - -
191D THR* 3.2 22.4 + - - +
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Residues in contact with LEU 188 (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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177B LEU* 4.4 18.1 - - + +
62D TYR* 5.5 0.2 - - - +
184D THR 2.8 15.6 + - - +
185D PHE* 3.2 11.0 + - + +
187D ALA* 1.3 77.2 - - - +
189D CYS* 1.3 64.3 + - - +
191D THR* 2.5 31.7 + - - +
192D ASP* 3.1 17.9 + - + +
195D PHE* 5.0 0.9 - - + -
247D ILE* 3.6 23.1 - - + +
250D ALA* 3.9 15.9 - - + +
251D LEU* 3.5 49.6 - - + +
254D SER* 5.0 5.2 - - - -
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Residues in contact with CYS 189 (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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57D ARG* 5.6 0.2 + - - -
185D PHE 2.9 19.7 + - - -
186D LEU 3.7 7.6 - - - +
187D ALA 3.3 0.2 - - - -
188D LEU* 1.3 76.1 - - - +
190D ALA* 1.3 60.4 + - - +
192D ASP 2.9 26.9 + - - +
195D PHE* 3.7 33.1 - - + +
196D ALA* 5.1 0.7 + - - -
203D ILE* 3.6 33.9 - - + -
207D SER* 4.9 0.4 - - - -
247D ILE* 3.9 33.0 - - - -
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Residues in contact with ALA 190 (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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57D ARG* 3.3 24.4 + - - +
78D PHE* 3.4 31.2 - - + -
79D PRO* 4.1 20.2 - - + -
82D MET* 3.7 17.6 - - + +
186D LEU 3.3 9.2 + - - +
187D ALA 3.2 2.8 + - - +
188D LEU 3.2 0.6 - - - -
189D CYS* 1.3 78.7 - - - +
191D THR* 1.3 56.7 - - - +
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Residues in contact with THR 191 (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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177B LEU* 4.3 1.8 - - + +
57D ARG* 3.3 11.9 + - - -
58D LYS* 3.3 23.9 - - - +
61D ALA* 3.8 17.7 - - + +
62D TYR* 4.0 29.6 + - + -
65D LEU* 4.5 13.5 - - + -
78D PHE* 3.6 21.5 - - + -
187D ALA 3.2 15.7 - - - +
188D LEU* 2.5 27.8 + - - +
190D ALA* 1.3 78.5 - - - +
192D ASP* 1.3 58.9 + - - +
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Residues in contact with ASP 192 (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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57D ARG* 3.7 2.8 + - - -
58D LYS* 4.3 13.0 + - - +
188D LEU* 3.1 14.1 + - + +
189D CYS 2.9 16.8 + - - +
191D THR* 1.3 79.3 + - - +
193D TYR* 1.3 67.8 + - - +
194D THR* 3.1 30.1 + - - +
195D PHE* 3.2 24.3 + - + +
196D ALA* 3.9 2.3 + - - -
250D ALA* 3.8 21.5 - - - +
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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