Contacts of the helix formed by residues 190 - 211 (chain A) in PDB entry 4G1U
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 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A ASN 5.1 3.1 - - - -
54A ILE* 6.2 2.2 - - + -
57A PRO* 4.2 7.5 - - - +
188A GLN* 3.6 13.2 + - - +
189A ALA* 1.3 79.8 - - - +
191A TRP* 1.3 66.4 + - - +
192A SER* 3.4 15.9 + - - +
193A THR* 3.1 30.6 + - + +
194A LEU* 3.2 14.2 + - - +
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Residues in contact with TRP 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LEU* 3.0 32.4 + - + -
53A ASN* 3.4 30.3 + - + +
56A LEU* 3.7 27.8 - - + -
57A PRO* 3.6 18.9 - - + +
60A LEU* 4.5 11.4 - - + -
190A GLN* 1.3 73.8 - - - +
192A SER* 1.3 61.4 + - - +
194A LEU* 3.9 22.4 - - + +
195A LEU* 2.9 32.8 + - + +
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Residues in contact with SER 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 4.0 15.9 - - - +
190A GLN* 4.2 14.7 + - - +
191A TRP* 1.3 73.9 - - - +
193A THR* 1.3 69.0 + - - +
195A LEU* 3.2 6.9 + - - +
196A VAL* 3.0 29.8 + - - +
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Residues in contact with THR 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LEU* 5.1 0.9 - - - +
116A LEU* 3.7 33.7 - - + -
188A GLN 4.6 7.9 + - - +
189A ALA* 4.7 1.7 - - - -
190A GLN* 3.1 33.5 + - + +
192A SER* 1.3 81.8 + - - +
194A LEU* 1.3 70.9 + - - +
196A VAL* 3.1 2.3 + - - +
197A ALA* 2.9 26.7 + - - +
253A VAL* 4.3 25.8 - - + +
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Residues in contact with LEU 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PRO* 3.8 27.8 - - + +
60A LEU* 3.8 24.5 - - + +
61A LEU* 3.6 46.0 - - + +
64A VAL* 4.2 15.3 - - + -
189A ALA* 6.4 0.2 - - + -
190A GLN 3.2 14.3 + - - +
191A TRP* 4.0 21.3 - - + +
193A THR* 1.3 81.1 + - - +
195A LEU* 1.3 57.7 + - - +
197A ALA* 4.4 0.9 - - + -
198A SER* 2.9 36.0 + - - +
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Residues in contact with LEU 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A TRP* 2.9 23.8 + - + +
192A SER* 3.5 8.3 - - - +
193A THR 3.1 0.2 - - - -
194A LEU* 1.3 77.0 - - - +
196A VAL* 1.3 60.3 + - + +
198A SER* 3.1 10.1 + - - +
199A SER* 2.9 32.6 + - - -
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Residues in contact with VAL 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 4.6 16.2 - - + -
117A TYR* 4.2 32.1 - - + +
120A MET* 4.2 26.7 - - + -
192A SER* 3.0 18.8 + - - +
193A THR* 3.9 2.9 - - - +
195A LEU* 1.3 75.9 - - + +
197A ALA* 1.3 64.4 + - - +
199A SER* 2.5 26.6 + - - +
200A LEU* 2.9 15.7 + - + +
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Residues in contact with ALA 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LEU* 4.8 6.7 - - + -
64A VAL* 5.1 1.6 - - + -
65A VAL* 6.0 1.1 - - + -
120A MET* 5.0 3.3 - - - -
193A THR 2.9 18.2 + - - +
194A LEU* 3.9 5.8 - - - +
196A VAL* 1.3 77.0 - - - +
198A SER* 1.3 56.4 - - - +
200A LEU* 3.2 3.4 + - - +
201A ILE* 2.9 45.7 + - + +
249A ALA* 4.7 10.3 - - + +
250A ALA* 6.4 0.2 - - - -
253A VAL* 3.8 27.8 - - + +
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Residues in contact with SER 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A VAL* 4.1 23.1 - - - +
194A LEU* 2.9 24.0 + - - +
195A LEU* 3.1 16.1 + - - +
197A ALA* 1.3 76.3 - - - +
199A SER* 1.3 58.4 + - - +
201A ILE 4.3 0.4 - - - +
202A LEU* 2.9 47.9 + - - +
203A PRO* 3.8 0.2 - - - +
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Residues in contact with SER 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A TYR* 5.3 2.9 + - - -
195A LEU* 2.9 17.0 + - - -
196A VAL* 2.5 30.2 + - - +
198A SER* 1.3 78.2 + - - +
200A LEU* 1.3 61.7 + - - +
203A PRO* 3.2 21.2 - - - +
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Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A TYR* 5.6 10.8 - - + +
120A MET* 3.6 40.6 - - + -
196A VAL* 2.9 18.7 + - + +
197A ALA 3.8 6.1 - - - +
199A SER* 1.3 84.8 - - - +
201A ILE* 1.3 58.4 + - - +
202A LEU 3.8 0.2 - - - -
203A PRO* 3.7 4.5 - - - +
204A THR* 3.3 25.2 + - - +
245A ILE* 4.2 20.3 - - + +
249A ALA* 4.5 12.3 - - + +
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Residues in contact with ILE 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A VAL* 3.6 39.5 - - + +
65A VAL* 4.9 2.9 - - + -
67A CYS* 4.9 3.1 - - - -
68A ALA* 3.6 28.5 - - + +
197A ALA* 2.9 25.0 + - + +
198A SER* 4.3 0.2 - - - -
200A LEU* 1.3 77.3 - - - +
202A LEU* 1.3 70.8 + - + +
204A THR* 3.0 8.3 - - + +
205A CYS* 2.9 39.6 + - - +
246A LEU* 4.1 6.1 - - + +
249A ALA* 3.8 24.0 - - + -
250A ALA* 4.4 7.0 - - - +
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Residues in contact with LEU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A VAL* 4.3 20.2 - - + -
67A CYS* 6.3 3.4 - - - -
198A SER* 2.9 44.1 + - - +
201A ILE* 1.3 75.9 - - + +
203A PRO* 1.3 62.7 - - + +
205A CYS* 3.6 6.1 + - + +
206A ILE* 3.3 27.7 + - - +
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Residues in contact with PRO 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A SER 3.8 2.0 - - - +
199A SER* 3.2 28.5 - - - +
200A LEU* 3.7 6.5 - - - +
201A ILE 3.5 1.8 - - - -
202A LEU* 1.3 94.1 - - + +
204A THR* 1.3 57.6 + - - +
206A ILE* 3.3 9.5 + - + +
207A LEU* 2.9 35.6 + - + +
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Residues in contact with THR 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A LEU 3.3 16.2 - - - +
201A ILE* 3.0 22.4 + - - +
203A PRO* 1.3 80.2 - - - +
205A CYS* 1.3 58.6 + - - +
207A LEU* 3.2 7.5 + - - -
208A GLY 2.9 22.5 + - - -
242A LEU* 3.1 44.1 + - - +
245A ILE* 4.4 18.8 - - + +
246A LEU* 3.6 28.9 - - + +
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Residues in contact with CYS 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A CYS* 3.4 32.8 - - - -
71A VAL* 3.7 27.2 - - + +
201A ILE* 2.9 23.1 + - - +
202A LEU* 4.0 6.7 - - + +
203A PRO 3.3 0.2 - - - -
204A THR* 1.3 75.4 - - - +
206A ILE* 1.3 67.5 + - + +
208A GLY* 3.6 1.7 + - - +
209A LEU* 3.3 19.6 + - - +
246A LEU* 3.8 21.3 - - - -
280A LEU* 5.7 1.6 - - - +
284A ALA* 5.7 1.1 - - + -
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Residues in contact with ILE 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A LEU 3.3 16.0 + - - +
203A PRO* 3.6 10.3 - - + +
204A THR 3.2 0.4 - - - -
205A CYS* 1.3 80.3 - - + +
207A LEU* 1.3 64.3 + - + +
208A GLY 3.2 0.2 - - - -
209A LEU* 3.0 29.3 + - + +
210A LEU* 3.1 27.5 + - + +
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Residues in contact with LEU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A PRO* 2.9 22.6 + - + +
204A THR* 3.2 8.0 + - - +
206A ILE* 1.3 77.2 - - + +
208A GLY* 1.3 61.6 + - - +
210A LEU* 3.6 28.4 + - + +
211A GLN* 3.1 32.0 + - - +
242A LEU* 4.1 19.9 - - + +
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Residues in contact with GLY 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A VAL* 5.3 0.7 - - - -
75A ILE* 4.5 11.9 - - - -
204A THR 2.9 11.7 + - - -
205A CYS* 3.6 3.8 + - - -
206A ILE 3.2 0.2 - - - -
207A LEU* 1.3 76.7 - - - +
209A LEU* 1.3 60.7 + - - +
211A GLN* 3.4 13.7 + - - +
212A ALA* 3.5 4.0 + - - -
215A LEU* 4.9 2.1 - - - +
239A LEU* 5.7 0.7 - - - -
242A LEU* 3.6 19.3 - - - +
280A LEU* 3.1 24.4 - - - +
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Residues in contact with LEU 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A CYS 3.3 13.0 + - - +
206A ILE* 3.0 23.8 + - + +
208A GLY* 1.3 74.9 - - - +
210A LEU* 1.3 66.7 + - + +
211A GLN 3.2 1.6 - - - -
212A ALA* 3.5 14.0 + - - +
276A HIS 4.7 0.2 - - - +
277A ARG* 4.2 9.0 - - - +
280A LEU* 3.6 16.4 - - + +
281A PRO* 3.6 40.8 - - + -
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Residues in contact with LEU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ILE* 3.1 20.4 + - + +
207A LEU* 3.6 32.1 + - + +
208A GLY 3.4 0.2 - - - -
209A LEU* 1.3 80.1 - - + +
211A GLN* 1.3 69.6 + - - +
212A ALA 3.5 0.5 + - - -
213A ARG* 4.5 8.5 + - - +
214A GLN* 4.2 9.5 + - - -
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Residues in contact with GLN 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A LEU* 3.1 21.8 + - - +
208A GLY* 3.4 7.3 + - - +
209A LEU 3.2 0.6 - - - -
210A LEU* 1.3 85.8 + - - +
212A ALA* 1.3 55.1 + - - +
213A ARG 2.9 11.8 + - - -
214A GLN* 3.1 39.0 + - + +
215A LEU* 3.1 12.3 + - + +
235A ALA* 4.7 6.1 - - - -
238A ARG* 3.9 44.1 + - + +
239A LEU* 3.9 26.2 - - + +
242A LEU* 5.4 4.5 - - + -
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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
------------------------------------------------------------
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