Contacts of the helix formed by residues 180 - 198 (chain D) in PDB entry 3G4C
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 GLN 180 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A ARG* 3.5 25.9 - - - +
144A GLU* 2.9 46.7 + - - +
145A VAL* 4.9 0.6 - - - +
147A ARG* 2.9 24.0 + - - -
148A ILE* 5.0 0.2 - - - +
303A UMP 4.6 1.4 + - - -
71D PHE* 3.6 17.8 - - - -
72D VAL* 6.2 0.2 - - + -
75D GLN* 3.2 21.6 + - - +
105D ARG* 4.2 0.6 - - - +
174D ARG* 5.6 0.2 - - - +
179D ALA* 1.3 72.9 - - - +
181D TRP* 1.3 67.8 + - - +
182D GLU* 3.0 31.1 + - + +
183D ILE* 2.9 18.7 + - + +
184D GLN* 2.9 10.1 + - - -
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Residues in contact with TRP 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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144A GLU* 4.5 3.3 + - - +
6D LEU* 3.6 26.7 - - + -
99D TYR* 3.9 10.5 - + - -
102D SER* 5.9 2.7 - - - -
105D ARG* 3.7 43.8 - - + +
179D ALA 3.4 3.8 + - - -
180D GLN* 1.3 73.0 - - - +
182D GLU* 1.3 79.7 + - - +
184D GLN* 3.0 33.4 + - - +
185D GLN* 3.0 54.9 + - + +
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Residues in contact with GLU 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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145A VAL* 4.7 3.1 - - - +
6D LEU* 3.9 14.7 - - + +
71D PHE* 4.0 9.2 - - + -
72D VAL* 3.8 17.7 - - + -
99D TYR* 2.5 47.5 + - + +
101D PRO* 5.3 0.3 - - - +
105D ARG* 2.7 27.8 + - - +
180D GLN* 3.0 31.4 + - + +
181D TRP* 1.3 83.7 - - + +
183D ILE* 1.3 61.5 + - - +
185D GLN* 3.2 12.3 + - - +
186D TYR* 3.3 18.8 - - - -
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Residues in contact with ILE 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D VAL* 3.8 25.2 - - + +
75D GLN* 3.5 29.2 - - + +
76D TRP* 3.8 43.3 - - + +
170D PHE* 4.5 3.8 - - + -
174D ARG* 4.0 29.8 - - + +
179D ALA* 4.0 19.1 - - + -
180D GLN* 2.9 16.4 + - - +
182D GLU* 1.3 71.9 - - - +
184D GLN* 1.3 69.3 + - - +
186D TYR* 3.1 4.3 + - + -
187D ALA* 2.8 22.0 + - - +
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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
----------------------------------------------------------
174D ARG 3.4 13.7 - - - +
176D ASP 3.4 20.4 - - - +
177D SER* 3.4 21.7 + - - +
179D ALA* 2.9 22.6 + - + +
180D GLN 2.9 15.3 + - - +
181D TRP* 3.0 29.8 + - - +
183D ILE* 1.3 77.5 - - - +
185D GLN* 1.3 62.6 + - - +
187D ALA* 3.2 2.8 + - - +
188D LEU* 2.9 32.9 + - - +
214D ILE* 3.7 25.9 - - + +
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Residues in contact with GLN 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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5D ILE* 3.5 29.9 - - + +
6D LEU* 4.4 3.4 - - + +
181D TRP* 3.0 80.6 + - + +
182D GLU 3.5 5.8 - - - +
183D ILE 3.1 0.4 - - - -
184D GLN* 1.3 83.7 + - - +
186D TYR* 1.3 62.9 + - - +
188D LEU* 3.5 21.8 + - - +
189D ALA 3.3 15.2 + - - -
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Residues in contact with TYR 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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5D ILE* 3.7 28.7 - - + -
6D LEU* 3.8 19.6 - - + +
9D GLY* 3.6 11.6 - - - -
10D PHE 3.8 11.7 - - - -
11D VAL* 3.6 18.5 - - + +
66D VAL* 3.9 5.8 - - + -
67D LYS 2.6 29.8 + - - -
68D ALA* 3.2 18.4 - - + -
69D PRO* 3.7 5.4 - - + +
72D VAL* 4.1 14.8 - - + -
76D TRP* 3.4 28.3 - + + -
155D TYR* 3.8 0.9 - - - -
182D GLU 3.3 19.1 - - - -
183D ILE* 3.1 8.2 + - + +
185D GLN* 1.3 76.9 - - - +
187D ALA* 1.3 64.5 + - - +
189D ALA* 3.1 6.6 + - - +
190D ILE* 3.0 24.9 + - - +
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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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170D PHE* 4.0 17.8 - - + -
171D LEU* 3.1 13.5 - - + +
174D ARG* 3.6 14.6 - - + -
175D ALA* 3.5 33.0 - - + +
183D ILE 2.8 12.5 + - - +
184D GLN 3.6 7.9 - - - +
186D TYR* 1.3 76.8 - - - +
188D LEU* 1.3 57.6 + - - +
190D ILE* 3.2 1.1 + - - -
191D ALA* 2.9 25.5 + - - +
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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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175D ALA* 5.0 0.6 - - + +
184D GLN 2.9 16.2 + - - +
185D GLN* 3.6 30.1 - - - +
186D TYR 3.2 0.2 - - - -
187D ALA* 1.3 75.3 - - - +
189D ALA* 1.3 54.7 + - - +
191D ALA* 3.4 6.3 + - - +
192D ARG* 3.1 26.7 + - - +
214D ILE* 3.7 28.0 - - + -
215D LEU* 3.5 26.0 - - + +
218D VAL* 4.3 34.3 - - + +
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Residues in contact with ALA 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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3D ILE* 3.5 33.5 - - + +
5D ILE* 3.4 30.3 - - + -
11D VAL* 4.2 10.5 - - + -
185D GLN 3.3 2.2 + - - -
186D TYR 3.1 9.2 + - - +
188D LEU* 1.3 76.7 - - - +
190D ILE* 1.3 65.7 + - - +
192D ARG* 3.2 3.0 + - - -
193D ILE* 3.1 22.2 + - - +
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Residues in contact with ILE 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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11D VAL* 3.6 24.5 - - + -
64D PHE* 3.9 24.2 - - + -
76D TRP* 4.1 14.1 - - + -
160D TRP* 4.0 13.0 - - + -
167D LEU* 2.9 42.2 - - + -
170D PHE* 4.0 15.9 - - + -
171D LEU* 4.0 8.7 - - + -
186D TYR 3.0 18.1 + - - +
187D ALA 3.4 7.2 - - - +
189D ALA* 1.3 74.7 - - - +
191D ALA* 1.3 58.3 + - - +
193D ILE* 3.4 2.9 + - - +
194D PHE* 2.8 27.9 + - - +
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Residues in contact with ALA 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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171D LEU* 3.9 24.0 - - + +
187D ALA 2.9 13.2 + - - +
188D LEU 3.4 9.9 - - - +
189D ALA 3.2 0.2 - - - -
190D ILE* 1.3 78.1 - - - +
192D ARG* 1.3 51.8 + - - +
194D PHE* 3.4 3.1 + - - +
195D LYS* 2.7 35.7 + - - +
202D PHE* 3.7 11.7 - - + -
215D LEU* 3.6 29.4 - - + -
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Residues in contact with ARG 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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1D MET* 4.8 6.8 - - - -
3D ILE* 4.3 15.3 - - + -
188D LEU 3.1 12.9 + - - +
189D ALA* 3.2 9.2 + - - +
191D ALA* 1.3 74.5 - - - +
193D ILE* 1.3 60.0 + - - +
195D LYS* 3.4 19.1 + - - +
196D GLU* 2.7 67.0 + - - +
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Residues in contact with ILE 193 (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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1D MET* 3.8 30.7 - - + +
3D ILE* 3.8 13.9 - - + -
11D VAL* 3.6 36.3 - - + +
13D LEU* 3.5 48.5 - - + +
62D PHE* 4.7 3.6 - - + -
64D PHE* 3.6 16.4 - - + -
189D ALA 3.1 12.0 + - - +
190D ILE 3.8 5.6 - - - +
192D ARG* 1.3 72.8 - - - +
194D PHE* 1.3 65.7 + - - +
196D GLU* 3.3 3.3 + - - +
197D LYS* 3.1 22.6 + - + +
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Residues in contact with PHE 194 (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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62D PHE* 3.4 31.2 - + - -
64D PHE* 5.3 0.2 - - - -
164D ALA* 4.1 15.7 - - + -
167D LEU* 4.0 14.4 - - + -
168D MET* 3.8 28.5 - - + -
171D LEU* 4.2 13.5 - - + -
190D ILE 2.8 21.9 + - - +
191D ALA* 3.5 5.6 - - - +
193D ILE* 1.3 72.9 - - - +
195D LYS* 1.3 61.1 + - - +
197D LYS* 3.2 1.6 + - - -
198D CYS* 2.9 46.3 + - + +
201D THR* 3.7 25.6 - - + -
202D PHE* 3.7 30.1 - + - -
205D PHE* 4.7 2.9 - + - -
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Residues in contact with LYS 195 (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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191D ALA 2.7 21.4 + - - +
192D ARG* 3.6 22.9 - - - +
194D PHE* 1.3 73.8 - - - +
196D GLU* 1.3 68.3 + - - +
199D PRO* 3.2 29.4 - - + +
202D PHE* 3.5 45.4 - - + -
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Residues in contact with GLU 196 (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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1D MET* 3.7 27.5 - - + +
192D ARG* 2.7 53.4 + - - +
193D ILE 3.3 8.3 + - - +
195D LYS* 1.3 79.9 - - - +
197D LYS* 1.3 64.0 + - + +
199D PRO* 4.0 6.6 - - - +
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Residues in contact with LYS 197 (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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1D MET* 4.5 11.6 - - + +
13D LEU* 3.3 29.3 - - + +
16D VAL* 3.9 26.2 - - + -
18D GLY 5.0 0.9 - - - +
19D ASN* 4.0 17.7 - - - +
20D ASP 4.6 0.2 + - - -
62D PHE* 3.8 18.8 - - + -
193D ILE* 3.1 18.7 + - + +
194D PHE 4.1 0.2 - - - +
196D GLU* 1.3 80.6 - - + +
198D CYS* 1.3 67.3 + - - +
199D PRO* 3.6 5.0 - - - +
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Residues in contact with CYS 198 (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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16D VAL* 5.5 0.2 - - - -
18D GLY 5.3 0.7 - - - -
19D ASN* 4.2 13.9 - - - -
20D ASP* 3.2 22.0 - - - +
60D ILE* 3.7 33.4 - - - -
62D PHE* 3.9 15.3 - - - -
194D PHE* 2.9 23.0 + - + +
195D LYS 3.6 2.5 - - - -
197D LYS* 1.3 83.7 - - - +
199D PRO* 1.3 60.6 - - - +
201D THR* 4.1 3.4 - - - -
202D PHE* 3.0 27.0 + - - +
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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