Contacts of the helix formed by residues 195 - 214 (chain A) in PDB entry 1L8A
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 GLY 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A MET* 1.3 72.2 - - - +
196A LEU* 1.3 61.1 + - - +
197A GLY 3.4 1.8 - - - -
198A PRO* 3.2 13.4 - - - +
199A ILE* 3.6 4.7 - - - +
232A GLU* 2.8 16.2 + - - +
235A GLU* 3.8 4.7 - - - -
237A GLU* 3.4 32.5 - - - +
238A SER* 3.3 21.1 - - - -
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Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A TYR* 5.7 0.2 - - - -
190A PRO 5.0 7.9 - - - +
193A SER* 3.5 26.5 - - - +
194A MET 3.2 1.4 - - - -
195A GLY* 1.3 78.4 - - - +
197A GLY* 1.3 60.0 + - - +
199A ILE* 3.3 6.6 - - + +
200A GLY* 2.8 29.1 + - - -
237A GLU* 4.4 8.1 - - + +
572A LEU* 5.0 9.4 - - + -
576A CYS* 5.1 0.3 - - - -
609A ASP* 3.6 44.0 - - + +
610A LEU* 4.1 24.4 - - + +
613A ALA* 4.1 13.0 - - + -
606B ARG* 3.9 20.4 - - - +
639B GLN* 4.6 1.3 - - - +
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Residues in contact with GLY 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A TYR* 3.9 20.1 - - - -
190A PRO 5.2 1.3 - - - -
191A THR* 4.5 20.4 + - - +
193A SER 4.5 2.2 + - - -
195A GLY 4.4 1.0 - - - +
196A LEU* 1.3 78.8 - - - +
198A PRO* 1.3 68.3 - - - +
201A ALA* 2.9 27.8 + - - +
226A ALA* 5.0 1.1 - - - -
228A LEU* 4.6 4.7 - - - -
232A GLU* 4.8 1.2 + - - -
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Residues in contact with PRO 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A GLY 3.2 21.8 - - - +
197A GLY* 1.3 89.7 - - - +
199A ILE* 1.3 55.5 + - - +
201A ALA* 3.8 0.3 - - - +
202A ILE* 3.1 31.5 + - - +
226A ALA* 4.5 1.3 - - + -
228A LEU* 3.6 30.0 - - + -
232A GLU* 3.7 9.4 - - - +
238A SER* 3.5 35.9 - - - +
255A PHE* 3.4 29.0 - - + -
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Residues in contact with ILE 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A GLY 3.6 11.4 - - - +
196A LEU* 3.3 17.0 - - + +
198A PRO* 1.3 78.5 - - - +
200A GLY* 1.3 69.9 + - - +
202A ILE* 3.3 7.8 + - - -
203A TYR* 3.2 41.2 + - + -
237A GLU* 3.6 20.1 + - + +
241A ALA* 3.7 24.7 - - + -
572A LEU* 4.0 19.1 - - + -
573A GLY* 4.3 4.9 - - - +
576A CYS* 3.8 15.5 - - - -
610A LEU* 5.6 0.2 - - + -
236B PRO* 3.8 23.1 - - + -
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Residues in contact with GLY 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A TYR* 3.6 12.0 + - - -
196A LEU 2.8 19.2 + - - -
197A GLY 3.9 0.2 - - - -
199A ILE* 1.3 78.7 - - - +
201A ALA* 1.3 55.9 + - - +
203A TYR* 3.5 2.8 + - - +
204A GLN* 3.0 27.0 + - - +
576A CYS* 3.8 19.7 - - - +
579A LEU* 5.9 5.2 - - - -
580A ALA* 5.6 0.5 - - - +
610A LEU* 5.6 1.8 - - - -
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Residues in contact with ALA 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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138A TYR* 3.7 22.3 - - + -
197A GLY 2.9 18.9 + - - +
198A PRO 3.8 3.8 - - - +
200A GLY* 1.3 75.0 - - - +
202A ILE* 1.3 64.3 + - - +
204A GLN* 3.1 1.4 + - - +
205A ALA* 3.0 25.3 + - - +
224A VAL* 3.6 18.7 - - + +
226A ALA* 3.8 22.9 - - + -
253A LEU* 3.7 5.6 - - + +
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Residues in contact with ILE 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A PRO 3.1 22.0 + - - +
199A ILE* 3.5 11.4 - - - +
201A ALA* 1.3 78.0 - - - +
203A TYR* 1.3 74.4 + - + +
205A ALA* 3.4 0.7 + - - +
206A LYS* 3.1 21.5 + - + +
237A GLU 5.8 0.4 - - - +
238A SER 5.2 1.8 - - - +
241A ALA* 3.7 33.0 - - + +
242A ILE* 4.0 10.5 - - + +
244A ILE* 4.4 15.9 - - + -
245A ALA* 4.7 2.2 - - + +
250A LEU* 3.5 23.0 - - + +
253A LEU* 3.8 18.2 - - + -
255A PHE* 3.7 20.9 - - + -
287A TRP* 4.7 2.2 - - + -
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Residues in contact with TYR 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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199A ILE* 3.2 35.7 + - + +
200A GLY 4.1 0.7 - - - +
202A ILE* 1.3 85.3 - - + +
204A GLN* 1.3 60.1 + - - +
206A LYS* 3.6 19.5 - - + +
207A PHE* 2.8 28.8 + - - +
241A ALA* 4.4 3.8 - - + +
244A ILE* 3.6 22.9 - - + +
567A GLU* 3.5 24.3 + - - +
570A ASN* 2.8 25.1 + - - -
573A GLY* 3.3 27.4 - - - -
576A CYS* 3.6 31.4 - - + +
577A SER* 3.2 21.9 + - - +
580A ALA* 4.0 3.8 - - - +
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Residues in contact with GLN 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 3.4 31.4 - - + +
138A TYR* 3.2 30.5 + - + +
189A PHE* 3.7 15.4 - - - -
200A GLY 3.0 11.6 + - - +
201A ALA* 3.1 6.5 + - - +
203A TYR* 1.3 76.2 - - - +
205A ALA* 1.3 59.2 + - - +
207A PHE* 3.2 8.4 + - - +
208A LEU* 2.9 42.7 + - - +
224A VAL* 4.1 6.3 - - + -
580A ALA* 3.9 30.9 + - + +
583A THR* 4.8 3.3 + - - -
587A THR* 4.6 9.1 + - - +
588A ASN* 5.0 2.6 - - - +
617A GLN* 5.0 1.2 + - - -
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Residues in contact with ALA 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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201A ALA 3.0 12.4 + - - +
202A ILE 3.6 9.9 - - - +
204A GLN* 1.3 78.7 - - - +
206A LYS* 1.3 60.1 + - - +
208A LEU* 3.4 1.4 + - - -
209A LYS* 3.2 15.8 + - - +
224A VAL* 3.7 17.2 - - + +
250A LEU* 4.1 4.7 - - + -
252A ASN* 2.9 38.5 - - - +
253A LEU* 3.7 19.3 - - + -
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Residues in contact with LYS 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 ILE 3.1 14.8 + - - +
203A TYR* 3.6 26.2 - - + +
205A ALA* 1.3 78.3 - - - +
207A PHE* 1.3 58.0 + - - +
209A LYS* 3.2 6.0 + - + +
210A TYR* 3.0 25.5 + - + +
244A ILE* 4.3 10.5 - - + -
248A GLU* 3.7 39.5 + - + +
250A LEU* 3.7 14.8 - - + +
538A TYR* 4.3 9.4 + - + -
565A LEU* 4.1 18.8 - - - +
566A GLN 5.7 0.4 + - - -
567A GLU* 2.8 40.8 + - - -
577A SER* 4.0 3.2 + - - -
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Residues in contact with PHE 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 TYR 2.8 18.7 + - - +
204A GLN* 3.2 12.5 + - - +
206A LYS* 1.3 75.2 - - - +
208A LEU* 1.3 63.9 + - - +
210A TYR* 3.1 34.1 - + - +
211A LEU* 3.0 53.0 + - + +
516A VAL* 4.3 6.1 - - + -
565A LEU* 4.5 12.3 - - + -
577A SER* 4.5 4.5 - - - +
580A ALA* 3.7 21.3 - - + -
581A ALA* 3.5 40.2 - - + -
584A SER* 3.9 16.2 - - - -
588A ASN* 5.1 0.9 - - - -
592A MET* 3.9 12.6 - - + -
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Residues in contact with LEU 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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136A LEU* 3.8 13.2 - - + -
204A GLN* 2.9 30.2 + - - +
205A ALA 3.7 6.5 - - - +
206A LYS 3.2 0.2 - - - -
207A PHE* 1.3 77.6 - - + +
209A LYS* 1.3 62.1 + - - +
211A LEU* 3.3 5.4 + - + +
212A GLU 3.2 10.6 + - - -
219A THR* 2.5 35.9 + - + +
222A GLN* 4.0 34.8 - - + +
224A VAL* 3.7 27.4 - - + -
252A ASN* 4.0 8.7 - - - +
588A ASN* 3.8 28.0 - - - +
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Residues in contact with LYS 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 ALA 3.2 15.8 + - - +
206A LYS* 3.4 8.1 - - + +
208A LEU* 1.3 77.1 - - - +
210A TYR* 1.3 53.4 + - - +
212A GLU* 3.1 17.8 + - - +
213A HIS* 2.8 51.9 + - + +
219A THR* 4.6 0.2 - - - -
248A GLU 4.9 2.9 - - - +
249A LYS 3.8 14.1 + - - -
250A LEU* 4.0 12.3 - - + +
251A ASP* 2.6 29.6 + - - -
252A ASN* 3.6 28.0 - - + +
538A TYR* 3.5 10.8 - - - +
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Residues in contact with TYR 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 LYS* 3.0 13.3 + - + +
207A PHE* 3.1 43.5 - + - +
209A LYS* 1.3 76.4 - - - +
211A LEU* 1.3 60.9 + - + +
213A HIS* 3.2 1.2 + - - +
214A ARG* 2.8 78.3 + - + +
515A LEU 4.1 2.4 + - - -
516A VAL* 4.0 14.4 - - + +
538A TYR* 3.3 34.9 + + + -
562A GLY 3.9 5.6 - - - -
563A GLN* 2.6 30.3 + - - +
565A LEU* 3.7 17.3 - - + -
592A MET* 4.1 12.8 - - + -
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Residues in contact with LEU 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 PHE* 3.0 43.4 + - + +
208A LEU* 3.7 8.5 - - + +
209A LYS 3.3 0.2 - - - -
210A TYR* 1.3 78.5 - - + +
212A GLU* 1.3 60.4 + - - +
214A ARG* 3.6 1.1 + - - -
215A GLY 3.2 2.3 + - - -
216A LEU* 2.9 54.0 + - + +
217A LYS* 3.2 16.3 + - + +
219A THR* 4.1 15.3 - - + -
584A SER* 4.0 3.8 - - - +
588A ASN* 3.8 27.1 - - - +
590A LEU* 3.9 20.6 - - + -
592A MET* 3.9 8.3 - - + -
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Residues in contact with GLU 212 (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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208A LEU 3.2 2.9 + - - +
209A LYS* 3.1 22.4 + - - +
211A LEU* 1.3 80.2 - - - +
213A HIS* 1.3 70.6 + - + +
215A GLY* 3.2 13.3 + - - -
217A LYS 3.1 16.5 + - - +
218A ASP* 3.8 12.3 - - - +
219A THR* 3.7 11.5 + - - +
220A SER* 3.5 32.2 - - - -
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Residues in contact with HIS 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LYS* 2.8 32.5 + - + +
212A GLU* 1.3 79.1 + - + +
214A ARG* 1.3 60.2 + - - +
215A GLY 3.1 5.8 + - - -
538A TYR* 2.6 32.7 + - + -
540A PRO* 3.5 19.8 - - + +
560A GLU* 3.1 44.5 - - + +
561A LYS* 3.8 17.5 - - - +
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Residues in contact with ARG 214 (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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210A TYR* 2.8 68.5 + - + +
211A LEU 4.1 0.4 - - - +
213A HIS* 1.3 75.8 - - - +
215A GLY* 1.3 62.1 + - - +
216A LEU* 3.5 20.9 + - + +
513A ASP* 3.4 49.6 + - - +
515A LEU 4.3 1.0 + - - -
560A GLU 4.6 2.5 - - - +
561A LYS* 3.6 23.4 + - - +
562A GLY 3.4 24.2 - - - -
563A GLN* 3.6 25.2 + - - +
592A MET* 4.8 0.4 - - - +
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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