Contacts of the helix formed by residues 287 - 308 (chain L) in PDB entry 6AH0
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 LEU 287 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283L LEU* 6.1 1.6 - - - -
284L PRO 2.9 9.8 + - - -
286L ASP* 1.3 75.5 - - - +
288L ARG* 1.3 64.3 + - - +
289L ARG 3.4 2.2 - - - -
290L LYS* 3.7 3.4 + - - +
291L ALA* 3.0 21.0 + - - -
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Residues in contact with ARG 288 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275L TYR* 5.9 1.2 - - - -
280L VAL* 4.8 14.2 - - - +
283L LEU* 5.9 1.8 - - - +
284L PRO 3.7 4.3 + - - -
285L PRO* 3.1 12.6 + - - -
287L LEU* 1.3 76.9 - - - +
289L ARG* 1.3 61.0 + - - +
291L ALA* 3.5 1.5 - - - +
292L ALA* 2.8 29.1 + - - -
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Residues in contact with ARG 289 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I G 5.6 3.7 - - - +
36I U 5.5 6.7 - - - -
39I A 5.4 12.9 - - - -
285L PRO 4.6 2.6 + - - -
286L ASP 4.8 2.4 + - - -
287L LEU 3.4 0.6 - - - -
288L ARG* 1.3 76.7 - - - +
290L LYS* 1.3 61.9 + - - +
292L ALA* 3.2 1.4 + - - +
293L ARG* 3.1 18.9 + - - -
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Residues in contact with LYS 290 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I G 5.3 18.6 - - - -
36I U 5.9 0.2 + - - -
286L ASP 5.7 0.4 + - - -
287L LEU* 3.7 4.5 + - - +
289L ARG* 1.3 76.6 - - - +
291L ALA* 1.3 57.5 + - - +
293L ARG* 3.5 2.2 + - - +
294L LEU* 3.0 23.9 + - - -
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Residues in contact with ALA 291 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280L VAL* 5.7 8.3 - - - +
287L LEU 3.0 17.2 + - - -
288L ARG* 3.5 4.0 - - - +
290L LYS* 1.3 74.9 - - - +
292L ALA* 1.3 58.5 + - - +
294L LEU* 3.4 1.5 + - - +
295L VAL* 2.9 26.0 + - - -
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Residues in contact with ALA 292 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250L MET* 5.7 3.1 - - - -
274L ILE* 5.1 6.9 - - - -
275L TYR* 5.1 16.8 - - - +
280L VAL* 5.8 3.5 - - - +
288L ARG 2.8 18.9 + - - -
289L ARG* 3.7 1.6 - - - +
291L ALA* 1.3 69.3 - - - +
293L ARG* 1.3 65.4 + - - +
295L VAL* 3.4 0.6 + - - +
296L ALA* 2.9 23.4 + - - -
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Residues in contact with ARG 293 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I A 6.0 0.9 - - - -
35I G 5.4 7.9 - - - -
41I C 5.8 4.0 - - - +
289L ARG 3.1 14.3 + - - -
290L LYS* 3.5 4.7 + - - +
292L ALA* 1.3 75.9 - - - +
294L LEU* 1.3 62.1 + - - +
296L ALA* 3.3 1.4 + - - +
297L ALA* 3.0 19.6 + - - -
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Residues in contact with LEU 294 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I A 5.5 6.2 + - - -
290L LYS 3.0 14.7 + - - -
291L ALA* 3.4 3.1 + - - +
292L ALA 3.2 0.4 - - - -
293L ARG* 1.3 75.1 - - - +
295L VAL* 1.3 61.2 + - - +
297L ALA* 3.2 2.6 + - - +
298L LYS* 3.2 18.4 + - - -
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Residues in contact with VAL 295 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291L ALA 2.9 16.0 + - - -
292L ALA* 3.9 1.1 - - - +
294L LEU* 1.3 70.6 - - - +
296L ALA* 1.3 66.8 + - - +
298L LYS* 3.3 1.8 + - - +
299L CYS* 2.9 21.8 + - - -
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Residues in contact with ALA 296 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246L ALA* 4.9 13.4 - - - -
249L ILE 5.6 1.8 - - - -
250L MET* 5.3 11.4 - - - +
274L ILE* 6.3 1.9 - - - +
292L ALA 2.9 15.0 + - - -
293L ARG* 3.7 4.0 - - - +
295L VAL* 1.3 75.3 - - - +
297L ALA* 1.3 63.7 + - - +
299L CYS* 3.1 1.9 + - - +
300L THR* 2.9 19.9 + - - -
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Residues in contact with ALA 297 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I G 4.7 19.0 + - - -
246L ALA* 5.1 9.7 - - - +
293L ARG 3.0 13.9 + - - -
294L LEU* 3.2 4.2 + - - +
296L ALA* 1.3 73.2 - - - +
298L LYS* 1.3 56.2 + - - +
300L THR* 3.0 17.8 + - - -
301L LEU* 3.3 8.8 + - - -
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Residues in contact with LYS 298 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I G 5.7 0.9 + - - -
294L LEU 3.2 13.1 + - - -
295L VAL* 3.8 2.2 - - - +
297L ALA* 1.3 71.9 - - - +
299L CYS* 1.3 59.4 + - - +
301L LEU* 3.2 4.1 + - - +
302L ALA* 2.9 25.3 + - - -
320L LEU* 6.5 1.8 - - - +
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Residues in contact with CYS 299 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219L LEU* 5.6 6.9 - - - +
295L VAL 2.9 18.9 + - - -
296L ALA* 3.6 3.8 - - - +
298L LYS* 1.3 70.2 - - - +
300L THR* 1.3 59.0 + - - +
302L ALA* 4.3 2.7 - - - +
303L ALA* 2.9 26.7 + - - -
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Residues in contact with THR 300 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242L SER* 5.5 4.2 - - - +
244L MET 5.7 4.7 - - - -
246L ALA* 5.4 9.4 - - - +
296L ALA 2.9 13.4 + - - -
297L ALA 3.0 5.3 + - - -
299L CYS* 1.3 77.2 - - - +
301L LEU* 1.3 60.4 + - - +
303L ALA* 3.4 1.6 + - - -
304L ARG* 3.2 18.4 + - - -
65M ILE* 5.4 4.7 - - - -
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Residues in contact with LEU 301 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297L ALA 3.3 7.6 + - - -
298L LYS* 3.2 7.0 + - - +
300L THR* 1.3 73.1 - - - +
302L ALA* 1.3 64.2 + - - +
304L ARG* 3.3 3.3 + - - +
305L VAL* 3.1 19.6 + - - -
62M PRO* 6.1 1.4 - - - +
65M ILE* 5.7 7.1 + - - +
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Residues in contact with ALA 302 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218L ASN* 4.9 7.3 - - - +
219L LEU* 4.4 20.4 + - - +
298L LYS 2.9 15.7 + - - -
299L CYS* 3.4 3.6 + - - +
301L LEU* 1.3 75.0 - - - +
303L ALA* 1.3 61.5 + - - +
305L VAL* 3.7 1.6 + - - +
306L ASP* 3.1 18.4 + - - -
316L VAL 6.5 0.2 - - - -
317L GLY* 6.1 3.8 - - - +
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Residues in contact with ALA 303 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219L LEU* 5.3 3.6 - - - +
238L LEU 5.0 4.8 - - - +
241L LEU 6.3 0.4 - - - -
242L SER* 5.1 7.8 - - - +
299L CYS 2.9 16.7 + - - -
300L THR 3.9 1.3 - - - -
301L LEU 3.2 0.4 - - - -
302L ALA* 1.3 77.2 - - - +
304L ARG* 1.3 57.7 + - - +
306L ASP* 3.1 4.1 + - - +
307L SER* 2.8 26.3 + - - -
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Residues in contact with ARG 304 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242L SER* 4.9 12.1 - - - +
300L THR 3.2 13.0 + - - -
301L LEU 3.3 3.5 + - - -
303L ALA* 1.3 72.7 - - - +
305L VAL* 1.3 66.0 + - - +
307L SER* 3.0 11.9 + - - +
308L PHE* 3.5 6.1 + - - -
64M GLU* 4.5 30.3 - - - +
65M ILE* 4.9 2.2 - - - +
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Residues in contact with VAL 305 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301L LEU 3.1 14.0 + - - -
302L ALA* 4.1 1.8 - - - +
304L ARG* 1.3 72.8 - - - +
306L ASP* 1.3 56.9 + - - +
308L PHE* 3.0 19.9 + - - -
309L HIS 3.3 6.9 + - - -
310L GLU* 3.5 16.1 + - - +
62M PRO* 6.4 0.2 - - - +
64M GLU 5.7 0.4 - - - +
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Residues in contact with ASP 306 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215L ILE 4.7 9.4 - - - +
216L ALA* 5.4 12.1 - - - +
217L PRO 6.0 0.2 - - - -
218L ASN 6.0 2.9 - - - +
302L ALA 3.1 15.0 + - - -
303L ALA 3.1 6.0 + - - -
305L VAL* 1.3 75.1 - - - +
307L SER* 1.3 59.9 + - - +
308L PHE 3.1 0.4 + - - -
309L HIS* 3.3 14.3 + - - +
310L GLU 4.8 5.1 + - - +
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Residues in contact with SER 307 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238L LEU* 5.1 13.7 - - - +
239L THR* 5.7 2.7 - - - +
303L ALA 2.8 16.0 + - - -
304L ARG* 3.0 7.3 + - - +
306L ASP* 1.3 73.4 - - - +
308L PHE* 1.3 56.0 + - - +
309L HIS 3.4 0.9 - - - -
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Residues in contact with PHE 308 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304L ARG 3.5 4.3 + - - -
305L VAL 3.0 7.3 + - - -
307L SER* 1.3 77.6 - - - +
309L HIS* 1.3 65.9 + - - +
310L GLU* 3.3 3.9 + - - -
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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
------------------------------------------------------------
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