Contacts of the helix formed by residues 231 - 250 (chain A) in PDB entry 6QVC
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 LYS 231 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A SER* 3.7 21.4 + - - -
135A MET* 4.6 16.6 - - - -
136A ASP* 3.9 21.4 + - - +
219A LEU* 4.6 17.4 - - + +
223A LEU* 4.6 28.5 - - + +
230A GLY* 1.3 75.4 - - - +
232A GLU* 1.3 68.9 + - + +
233A GLY 3.4 3.5 + - - -
234A PRO* 4.1 5.5 - - - +
235A PHE* 3.5 19.0 + - + +
278A CYS* 3.8 35.5 + - - -
279A PHE* 4.6 14.5 - - + -
316A PHE* 5.2 0.2 - - - -
421A ARG* 5.3 9.6 - - - +
482A GLY* 4.2 0.2 - - - -
485A MET* 4.5 19.2 - - + +
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Residues in contact with GLU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ILE* 4.3 7.3 - - - +
231A LYS* 1.3 77.6 - - - +
233A GLY* 1.3 71.8 + - - +
235A PHE* 3.1 2.9 + - - +
236A VAL* 2.6 43.1 + - + +
275A VAL* 5.1 9.6 - - + -
278A CYS* 3.6 24.6 - - + -
279A PHE* 5.0 7.4 - - + -
288A PHE* 4.2 24.0 - - + -
482A GLY* 4.0 0.8 - - - -
483A GLY 3.4 23.7 + - - -
484A PHE* 3.7 30.5 - - + +
578A TYR* 3.4 13.3 + - - -
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Residues in contact with GLY 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A GLY* 3.8 22.0 - - - -
191A ILE* 4.3 8.5 - - - -
232A GLU* 1.3 92.7 + - - +
234A PRO* 1.3 67.2 - - - +
236A VAL* 3.1 7.8 + - - +
237A HIS 3.0 21.0 + - - -
481A CYS 5.3 0.2 - - - -
482A GLY* 4.1 6.0 - - - -
578A TYR* 5.8 1.1 - - - -
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Residues in contact with PRO 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A SER* 3.6 23.8 - - - +
215A LYS* 4.0 21.3 - - + -
219A LEU* 4.5 15.0 - - + -
231A LYS 4.1 5.8 - - - +
233A GLY* 1.3 85.1 - - - +
235A PHE* 1.3 58.3 + - - +
237A HIS* 3.4 10.5 - - + +
238A ILE* 2.9 34.5 + - - +
480A PRO* 3.6 28.7 - - + +
482A GLY 4.0 15.5 - - - +
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Residues in contact with PHE 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A MET* 4.1 16.8 - - + -
131A VAL* 5.0 0.4 - - + -
132A SER* 3.6 30.5 - - - -
135A MET* 3.6 39.0 - - + -
219A LEU* 5.5 5.2 - - + +
231A LYS* 3.5 19.3 + - + +
232A GLU 3.1 9.0 + - - +
234A PRO* 1.3 76.1 - - - +
236A VAL* 1.3 59.7 + - - +
238A ILE* 3.3 18.3 - - + +
239A ALA* 2.9 29.5 + - - +
274A GLY* 3.1 33.7 - - - -
277A CYS* 3.7 20.4 - - + -
278A CYS* 3.5 14.1 - - - -
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Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ILE* 3.7 25.4 - - + -
194A MET* 4.4 13.5 - - + -
232A GLU* 2.6 27.0 + - - +
233A GLY 3.3 7.9 - - - +
235A PHE* 1.3 71.6 - - - +
237A HIS* 1.3 59.2 + - - +
239A ALA* 3.2 8.1 + - - +
240A SER* 2.9 27.5 + - - -
270A GLY 4.3 0.9 - - - +
271A CYS* 3.8 44.2 - - + +
274A GLY* 4.2 1.3 - - - -
275A VAL* 4.0 19.1 - - + +
288A PHE* 5.2 2.2 - - + -
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Residues in contact with HIS 237 (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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186A ALA* 5.3 3.2 - - - +
189A SER* 3.3 25.6 + - - +
190A GLY 4.3 12.2 + - - +
193A GLU* 5.0 1.4 - - - +
194A MET* 5.1 12.9 - - + +
197A ILE* 6.1 0.7 - - + -
206A TYR* 3.4 48.4 + + - -
207A LEU* 5.2 6.3 - - + -
211A ALA* 6.3 1.0 - - - +
215A LYS* 4.0 17.7 - - + -
233A GLY 3.0 10.7 + - - +
234A PRO* 3.4 7.9 - - + +
235A PHE 3.2 0.2 - - - -
236A VAL* 1.3 77.9 - - - +
238A ILE* 1.3 57.9 + - - +
240A SER* 3.3 7.8 + - - -
241A ILE* 3.0 60.6 + - + +
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Residues in contact with ILE 238 (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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128A MET* 4.4 12.3 - - - -
131A VAL* 5.0 9.0 - - + -
135A MET* 5.1 2.2 - - + -
212A PHE* 3.6 37.9 - - + +
215A LYS* 4.0 23.3 - - + -
216A VAL* 4.9 10.3 - - + -
234A PRO 2.9 20.2 + - - +
235A PHE* 3.3 42.4 - - + +
237A HIS* 1.3 73.3 - - - +
239A ALA* 1.3 60.2 + - - +
241A ILE* 3.3 13.9 + - + +
242A CYS* 2.9 33.0 + - - -
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Residues in contact with ALA 239 (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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124A LEU* 5.1 0.9 - - - +
128A MET* 3.6 27.4 - - + +
235A PHE* 2.9 18.8 + - + +
236A VAL 3.5 3.4 - - - +
238A ILE* 1.3 78.0 - - - +
240A SER* 1.3 57.6 + - - +
242A CYS* 3.3 3.3 + - - +
243A ALA* 2.9 27.0 + - - +
270A GLY* 3.3 25.3 - - - +
273A VAL* 4.8 1.1 - - + -
274A GLY* 3.7 15.5 - - - +
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Residues in contact with SER 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A MET* 4.4 18.1 - - - +
207A LEU* 4.5 9.7 - - - +
236A VAL 2.9 15.4 + - - -
237A HIS* 3.8 6.5 - - - -
239A ALA* 1.3 73.6 - - - +
241A ILE* 1.3 61.0 + - - +
243A ALA* 3.3 7.5 + - - +
244A ALA* 3.0 29.8 + - - +
266A ILE* 4.6 2.4 + - - +
267A LEU* 3.9 29.5 - - - +
270A GLY* 4.2 11.3 - - - -
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Residues in contact with ILE 241 (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 TYR 5.0 2.9 - - - +
207A LEU* 3.8 28.9 - - + +
208A THR 4.4 14.1 - - - +
209A MET* 4.7 3.6 - - + -
211A ALA* 5.6 2.7 - - + -
212A PHE* 4.0 35.9 - - + +
215A LYS* 5.9 0.7 - - - -
237A HIS* 3.0 46.8 + - + +
238A ILE* 3.4 18.4 - - + +
239A ALA 3.2 0.2 - - - -
240A SER* 1.3 76.5 - - - +
242A CYS* 1.3 58.0 + - - +
244A ALA* 3.2 3.5 + - - +
245A VAL* 3.0 44.0 + - + +
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Residues in contact with CYS 242 (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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124A LEU* 4.0 7.0 - - + +
127A LEU* 4.4 17.3 - - + -
128A MET* 3.8 27.6 - - + -
131A VAL* 6.2 0.4 - - - -
212A PHE* 3.6 32.1 - - - -
238A ILE* 2.9 20.7 + - - +
239A ALA 3.3 0.4 + - - +
241A ILE* 1.3 73.9 - - - +
243A ALA* 1.3 60.3 + - - +
245A VAL* 4.0 5.5 - - - +
246A LEU* 2.9 33.1 + - - +
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Residues in contact with ALA 243 (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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120A PHE* 4.4 6.2 - - + -
124A LEU* 4.0 21.0 - - + +
239A ALA 2.9 14.5 + - - +
240A SER* 3.4 11.2 - - - +
242A CYS* 1.3 76.6 - - - +
244A ALA* 1.3 57.8 + - - +
246A LEU* 3.9 1.0 - - - +
247A SER* 2.9 30.5 + - - -
266A ILE* 3.8 29.7 - - + +
269A VAL* 6.2 0.9 - - + -
270A GLY* 4.4 6.7 - - - +
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Residues in contact with ALA 244 (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 LYS* 6.1 3.6 - - - +
207A LEU* 4.6 17.5 - - + +
240A SER* 3.0 16.9 + - - +
241A ILE 3.8 3.8 - - - +
243A ALA* 1.3 75.7 - - - +
245A VAL* 1.3 60.8 + - + +
247A SER* 3.3 5.4 + - - -
248A LYS* 2.9 26.9 + - - +
266A ILE* 4.0 20.8 - - + +
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Residues in contact with VAL 245 (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 5.3 6.1 - - - +
209A MET* 4.5 24.7 - - + +
241A ILE* 3.0 31.4 + - + +
242A CYS* 4.1 5.2 - - - +
244A ALA* 1.3 77.7 - - + +
246A LEU* 1.3 59.9 + - - +
248A LYS* 3.1 12.3 + - + +
249A PHE* 2.9 27.5 + - + +
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Residues in contact with LEU 246 (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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120A PHE* 3.6 28.5 - - + +
123A LEU* 3.7 41.3 - - + -
124A LEU* 3.9 24.0 - - + -
242A CYS 2.9 18.6 + - - +
243A ALA 4.0 0.9 - - - +
245A VAL* 1.3 74.5 - - - +
247A SER* 1.3 58.2 + - - +
249A PHE* 4.1 21.3 - - + +
250A MET* 2.6 37.6 + - + +
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Residues in contact with SER 247 (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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120A PHE* 3.9 15.3 - - - -
243A ALA 2.9 19.2 + - - -
244A ALA* 3.5 8.7 - - - -
246A LEU* 1.3 77.2 - - - +
248A LYS* 1.3 57.1 + - - +
250A MET 2.9 17.2 - - - +
251A SER* 3.4 10.5 + - - -
252A VAL* 5.5 0.9 - - - +
266A ILE* 4.5 18.4 - - - +
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Residues in contact with LYS 248 (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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244A ALA 2.9 13.3 + - - +
245A VAL* 3.1 14.5 + - + +
247A SER* 1.3 76.7 - - - +
249A PHE* 1.3 63.5 + - + +
250A MET 3.9 0.2 - - - +
252A VAL* 3.5 23.3 - - - +
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Residues in contact with PHE 249 (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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245A VAL* 2.9 17.1 + - + +
246A LEU* 3.1 21.1 + - + +
248A LYS* 1.3 81.8 - - + +
250A MET* 1.3 68.0 + - + +
252A VAL* 3.4 16.4 - - - +
253A PHE* 4.0 23.9 - + + +
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Residues in contact with MET 250 (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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116A GLU 5.9 2.7 - - - +
120A PHE* 4.0 33.4 - - + -
123A LEU* 5.3 8.5 - - + -
246A LEU* 2.6 24.8 + - + +
247A SER* 2.9 13.4 - - - +
248A LYS 3.9 2.4 - - - +
249A PHE* 1.3 79.1 - - + +
251A SER* 1.3 83.8 + - - +
252A VAL* 3.1 7.4 + - - +
253A PHE* 3.8 38.1 - - + +
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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
------------------------------------------------------------
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