Contacts of the helix formed by residues 200 - 214 (chain A) in PDB entry 6LU7
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 ILE 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A PRO 5.5 0.2 - - - -
109A GLY* 3.7 31.0 - - - +
129A ALA* 5.2 4.3 - - + -
130A MET 4.4 3.4 - - - +
131A ARG* 3.8 15.5 - - - +
132A PRO* 4.0 22.9 - - + -
199A THR* 1.3 69.4 - - - +
201A THR* 1.3 64.5 + - - +
202A VAL* 3.9 13.0 - - + -
203A ASN* 3.3 25.6 + - + +
204A VAL* 3.2 23.2 + - - +
240A GLU* 3.8 14.6 - - - +
289A ASP* 3.2 38.6 + - - +
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Residues in contact with THR 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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199A THR 3.1 1.8 + - - -
200A ILE* 1.3 72.5 - - - +
202A VAL* 1.3 64.1 + - - +
204A VAL* 3.1 5.2 + - - +
205A LEU* 3.1 22.6 + - + +
230A PHE* 3.6 37.2 - - + -
239A TYR* 3.3 24.7 - - + +
240A GLU* 2.6 42.5 + - - +
241A PRO 5.3 0.7 - - - -
242A LEU* 4.1 13.2 - - + -
246A HIS* 6.2 0.7 - - - -
268A LEU* 4.1 5.2 - - + -
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Residues in contact with VAL 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ILE* 3.9 11.7 - - + -
201A THR* 1.3 78.5 - - - +
203A ASN* 1.3 71.7 + - - +
205A LEU* 3.6 4.5 + - - +
206A ALA* 3.1 26.9 + - - +
240A GLU* 5.8 0.4 - - - +
242A LEU* 4.2 7.5 - - + +
246A HIS* 3.8 60.2 + - + +
249A ILE* 5.1 4.0 - - + -
250A LEU* 4.0 12.6 - - + +
293A PRO* 4.2 14.3 - - + +
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Residues in contact with ASN 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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109A GLY 3.0 26.4 + - - +
110A GLN* 5.5 0.7 - - - +
111A THR* 4.9 0.4 - - - +
129A ALA* 5.4 0.4 - - - +
200A ILE* 3.3 19.2 + - + +
201A THR 3.1 0.6 - - - -
202A VAL* 1.3 88.6 - - - +
204A VAL* 1.3 60.8 + - - +
206A ALA* 3.4 1.0 + - - -
207A TRP* 2.9 28.6 + - - +
288A GLU 4.1 2.4 - - - +
289A ASP 2.9 30.7 + - - +
290A GLU* 4.2 2.4 - - - +
291A PHE* 3.2 34.9 + - - +
292A THR* 3.6 12.1 - - - +
293A PRO* 3.9 2.9 - - - +
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Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A THR* 3.7 15.0 - - + -
200A ILE 3.2 12.8 + - - +
201A THR 3.1 8.2 + - - +
203A ASN* 1.3 78.0 - - - +
205A LEU* 1.3 56.5 + - - +
207A TRP* 3.2 4.5 + - + +
208A LEU* 2.8 35.1 + - + +
239A TYR* 4.1 10.1 - - + +
268A LEU* 3.8 31.4 - - + -
287A LEU* 4.1 18.8 - - + +
288A GLU 3.3 21.8 - - - +
289A ASP* 3.6 12.1 - - + -
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Residues in contact with LEU 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 THR* 3.1 19.0 + - + +
202A VAL* 3.9 1.3 - - - +
204A VAL* 1.3 76.4 - - - +
206A ALA* 1.3 56.9 + - - +
208A LEU* 3.1 8.1 + - + +
209A TYR* 2.9 35.3 + - + -
230A PHE* 4.9 0.2 - - + -
242A LEU* 3.7 27.6 - - + -
250A LEU* 3.7 25.6 - - + -
261A VAL* 4.7 0.9 - - + +
264A MET* 3.8 40.6 - - + +
265A CYS* 3.7 26.0 - - - +
268A LEU* 3.9 21.5 - - + -
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Residues in contact with ALA 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 VAL 3.1 18.7 + - - +
203A ASN 3.7 4.0 - - - +
205A LEU* 1.3 75.2 - - - +
207A TRP* 1.3 57.6 + - - +
209A TYR* 3.2 4.7 + - - +
210A ALA 3.0 22.3 + - - -
250A LEU* 3.8 14.9 - - + +
253A LEU* 4.0 7.0 - - + -
291A PHE 4.2 0.2 - - - +
292A THR 4.2 1.3 - - - -
293A PRO* 3.7 33.7 - - + -
296A VAL* 3.4 18.6 - - + +
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Residues in contact with TRP 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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3A PHE* 4.1 5.6 - + - -
203A ASN 2.9 17.9 + - - +
204A VAL* 3.2 6.5 + - + +
206A ALA* 1.3 75.0 - - - +
208A LEU* 1.3 84.8 + - + +
210A ALA* 3.2 7.7 + - - +
211A ALA* 3.1 18.5 + - - +
276A MET* 4.6 0.9 - - + -
281A ILE* 3.2 47.8 - - + -
282A LEU* 3.6 22.2 - - + +
284A SER* 4.2 2.4 - - - -
286A LEU 3.4 18.2 - - - -
287A LEU* 3.6 23.8 - - + -
288A GLU* 3.5 49.6 - - + +
291A PHE* 3.8 32.4 - + + -
296A VAL* 4.2 4.4 - - - +
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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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204A VAL* 2.8 18.3 + - + +
205A LEU* 3.1 11.8 + - + +
207A TRP* 1.3 96.3 - - + +
209A TYR* 1.3 65.6 + - - +
211A ALA* 3.1 14.7 + - - +
212A VAL* 3.2 17.0 + - - +
219A PHE* 3.5 11.8 - - + -
264A MET* 3.8 31.2 - - + +
268A LEU* 4.1 31.9 - - + +
271A LEU* 4.1 17.0 - - + -
281A ILE* 4.0 21.5 - - + -
287A LEU* 4.4 0.9 - - + -
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Residues in contact with TYR 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 LEU* 2.9 29.7 + - + -
206A ALA* 3.2 10.3 + - - +
208A LEU* 1.3 77.3 - - - +
210A ALA* 1.3 56.6 + - - +
212A VAL* 3.1 4.5 + - + +
213A ILE* 2.9 35.3 + - - +
250A LEU* 4.3 24.7 - - + -
253A LEU* 3.6 34.5 - - + -
254A SER* 3.7 7.8 + - - -
257A THR* 3.2 32.7 - - + +
259A ILE* 2.8 23.7 + - + -
260A ALA 3.3 2.6 + - - -
261A VAL* 3.2 24.5 + - + +
264A MET* 3.6 32.8 - - + -
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Residues in contact with ALA 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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3A PHE* 4.0 26.7 - - + -
206A ALA 3.0 9.0 + - - +
207A TRP 3.2 10.3 + - - +
209A TYR* 1.3 75.7 - - - +
211A ALA* 1.3 60.7 + - - +
213A ILE* 3.5 2.1 + - - +
214A ASN* 2.5 32.8 + - - -
282A LEU* 4.0 9.0 - - + -
296A VAL* 3.7 25.9 - - + +
300A CYS* 4.0 7.4 - - - -
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Residues in contact with ALA 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 TRP 3.1 9.1 + - - +
208A LEU 3.1 10.0 + - - +
210A ALA* 1.3 74.6 - - - +
212A VAL* 1.3 56.9 + - - +
214A ASN* 3.1 2.6 + - - +
215A GLY 2.8 10.2 + - - -
216A ASP* 2.7 35.4 + - + +
219A PHE* 3.7 12.6 - - + -
281A ILE* 3.6 31.4 - - + -
282A LEU* 3.7 16.7 - - + +
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Residues in contact with VAL 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 13.2 + - - +
209A TYR* 3.1 9.3 + - - +
211A ALA* 1.3 72.6 - - - +
213A ILE* 1.3 66.3 + - - +
215A GLY* 3.0 13.2 + - - +
216A ASP 3.8 7.4 - - - +
217A ARG* 3.4 33.1 + - + +
219A PHE* 3.8 18.6 - - + -
220A LEU* 4.2 7.2 - - + -
257A THR* 4.3 14.1 - - + +
259A ILE* 3.6 19.3 - - + -
264A MET* 3.9 17.3 - - + -
304A THR 5.0 0.7 - - - +
305A PHE 4.6 8.0 - - - +
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Residues in contact with ILE 213 (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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209A TYR 2.9 18.9 + - - +
210A ALA* 3.8 5.4 - - - +
211A ALA 3.3 0.2 - - - -
212A VAL* 1.3 76.5 - - - +
214A ASN* 1.3 57.7 + - - +
253A LEU* 4.1 19.5 - - + -
256A GLN* 3.6 29.8 - - + +
257A THR* 3.6 20.0 - - + -
300A CYS* 3.2 44.0 - - + +
303A VAL* 3.5 24.4 - - + +
304A THR 4.2 7.3 - - - +
305A PHE* 3.5 19.9 - - - +
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Residues in contact with ASN 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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1A SER* 3.8 11.0 + - - -
2A GLY* 2.8 40.9 + - - +
3A PHE* 4.4 4.2 - - - +
210A ALA 2.5 29.2 + - - +
211A ALA 3.3 4.9 - - - +
212A VAL 3.1 0.2 - - - -
213A ILE* 1.3 82.5 - - - +
215A GLY* 1.3 58.5 + - - +
216A ASP* 3.5 2.0 + - + +
282A LEU* 3.9 19.7 - - + -
300A CYS* 3.7 23.4 - - - -
303A VAL* 5.5 2.7 - - - +
305A PHE* 3.7 12.9 - - - -
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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