Contacts of the helix formed by residues 288 - 307 (chain A) in PDB entry 5J3V
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 288 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A MET* 3.6 39.3 - - + -
251A LEU* 3.8 24.7 - - + -
254A MET* 4.5 13.5 - - + -
283A LEU* 4.9 3.8 - - + -
286A GLN* 4.5 5.4 - - + -
287A PRO* 1.3 84.3 - - + +
289A CYS* 1.3 66.2 + - - +
290A LYS 3.4 0.9 - - - -
291A ASP* 3.3 12.3 + - + +
292A VAL* 3.2 33.2 + - + +
125B ASN* 4.7 14.1 - - - +
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Residues in contact with CYS 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 3.1 28.0 + - - +
284A ALA* 3.6 25.4 - - - +
286A GLN 3.1 12.4 + - - +
287A PRO 3.2 0.4 - - - -
288A ILE* 1.3 74.2 - - - +
290A LYS* 1.3 60.1 + - - +
291A ASP 3.0 9.7 + - - -
292A VAL* 3.3 1.4 + - - -
293A LEU* 3.2 46.1 + - - +
386A LEU* 4.2 9.4 - - - -
389A VAL* 4.4 14.8 - - + -
390A TYR* 3.3 6.5 + - - -
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Residues in contact with LYS 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A PRO 4.4 5.8 + - - +
288A ILE 3.4 0.8 - - - -
289A CYS* 1.3 78.1 - - - +
291A ASP* 1.3 56.6 + - - +
294A VAL* 3.2 20.2 - - - +
389A VAL* 3.7 33.2 - - + +
390A TYR* 3.5 29.9 - - + +
393A GLU* 2.7 41.4 + - - -
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Residues in contact with ASP 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A HIS* 5.4 1.6 + - - -
287A PRO 5.3 0.9 + - - +
288A ILE* 3.7 15.9 - - + +
289A CYS 3.0 1.0 - - - -
290A LYS* 1.3 81.0 - - - +
292A VAL* 1.3 64.3 + - + +
293A LEU 3.8 0.4 - - - -
294A VAL* 4.7 7.8 + - - +
295A ARG 5.4 0.5 + - - -
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Residues in contact with VAL 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A MET* 3.9 37.7 - - + -
255A HIS* 3.7 38.0 - - + +
258A VAL* 4.1 15.9 - - + -
283A LEU* 5.3 0.9 - - + -
288A ILE* 3.2 26.2 - - + +
289A CYS* 3.3 3.5 + - - +
291A ASP* 1.3 81.9 - - + +
293A LEU* 1.3 70.2 + - + +
294A VAL 3.3 3.1 + - - -
295A ARG* 3.7 8.3 + - - +
296A HIS* 3.8 5.9 - - + -
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Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A VAL* 4.2 13.7 - - + -
280A TRP* 3.9 23.8 - - + +
283A LEU* 3.7 31.6 - - + -
284A ALA 5.5 0.4 - - - +
289A CYS* 3.2 31.3 + - - +
292A VAL* 1.3 80.2 - - + +
294A VAL* 1.3 54.2 + - - +
295A ARG 3.2 0.4 - - - -
296A HIS* 2.9 6.6 + - + +
297A LEU* 2.6 41.1 + - + +
300A LEU* 4.4 16.8 - - + -
386A LEU* 3.9 19.1 - - + -
390A TYR* 3.3 15.7 - - + +
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Residues in contact with VAL 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A LYS* 3.2 28.5 - - + +
291A ASP* 4.8 7.0 - - - +
292A VAL 3.3 0.8 - - - -
293A LEU* 1.3 77.9 - - - +
295A ARG* 1.3 63.7 + - - +
297A LEU* 3.4 22.4 + - + +
298A PRO* 3.8 5.4 - - - +
390A TYR* 3.4 20.1 + - + -
393A GLU* 6.0 0.4 - - - +
397A HIS* 5.2 2.1 + - + -
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Residues in contact with ARG 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A HIS* 3.4 30.6 + - + -
259A GLU* 5.7 0.6 + - - -
291A ASP 5.4 0.4 + - - -
292A VAL 3.7 9.0 + - - +
293A LEU 3.2 0.2 - - - -
294A VAL* 1.3 80.9 - - - +
296A HIS* 1.3 89.5 + - + +
297A LEU 3.6 0.5 + - - -
298A PRO* 3.7 9.4 - - - +
299A LYS* 5.7 1.9 - - - +
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Residues in contact with HIS 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A HIS* 3.1 33.0 + - + +
258A VAL* 3.5 34.2 - - + +
259A GLU* 3.7 34.4 - - + +
262A LEU* 4.9 7.9 - - + +
292A VAL 3.8 11.9 - - - -
293A LEU* 2.9 12.1 + - + +
295A ARG* 1.3 93.6 - - - +
297A LEU* 1.3 59.1 + - - +
298A PRO* 3.5 2.2 - - - -
299A LYS* 3.2 26.5 + - - +
300A LEU* 2.8 31.6 + - + +
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Residues in contact with LEU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A LEU* 2.6 28.2 + - + +
294A VAL* 3.6 12.8 - - + +
296A HIS* 1.3 74.7 - - - +
298A PRO* 1.4 71.2 - - + +
300A LEU* 4.5 9.9 - - + -
301A ILE* 3.0 54.3 + - + +
386A LEU* 5.1 4.3 - - + -
390A TYR* 3.6 43.3 - - + -
393A GLU 5.2 2.7 - - - +
394A LEU* 4.1 10.1 - - + -
397A HIS* 4.0 27.6 - - + +
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Residues in contact with PRO 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A VAL 3.8 5.6 - - - +
295A ARG 3.7 12.3 - - - +
296A HIS 3.6 2.2 - - - -
297A LEU* 1.4 93.2 - - + +
299A LYS* 1.3 57.7 + - + +
301A ILE* 5.2 0.4 - - + -
302A PRO* 3.3 20.0 - - + +
397A HIS* 3.4 27.8 - - + +
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Residues in contact with LYS 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A GLU* 4.7 12.0 + - - +
262A LEU* 3.6 25.7 - - + +
266A GLN* 6.3 0.4 - - - +
295A ARG 5.7 0.9 - - - +
296A HIS* 3.2 31.6 + - - +
297A LEU 3.0 0.6 - - - -
298A PRO* 1.3 80.7 - - + +
300A LEU* 1.3 60.8 + - - +
302A PRO* 3.8 6.9 - - - +
303A VAL* 3.2 23.4 - - + +
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Residues in contact with LEU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LEU* 3.7 19.5 - - + -
280A TRP* 3.5 52.7 - - + +
293A LEU* 4.4 15.0 - - + -
296A HIS* 2.8 18.1 + - + +
297A LEU* 4.1 9.9 - - + +
299A LYS* 1.3 79.5 - - - +
301A ILE* 1.3 67.0 + - + +
302A PRO 3.4 0.4 - - - -
303A VAL* 3.0 16.6 + - + +
304A LEU* 3.0 29.0 + - + +
386A LEU* 4.1 24.0 - - + -
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Residues in contact with ILE 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LEU* 3.0 32.7 + - + +
298A PRO* 5.1 0.7 - - + +
300A LEU* 1.3 77.1 - - + +
302A PRO* 1.3 69.3 - - + +
304A LEU* 3.3 13.3 + - + +
305A VAL* 3.1 23.9 + - + +
383A LEU* 4.4 17.3 - - + -
386A LEU* 4.8 4.7 - - + -
394A LEU* 3.7 24.9 - - + -
397A HIS* 3.5 39.3 - - + +
398A ILE* 3.6 19.1 - - + -
401A LEU* 4.1 6.7 - - + -
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Residues in contact with PRO 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A PRO 3.3 25.6 - - - +
299A LYS* 3.8 9.2 - - - +
300A LEU 3.5 2.2 - - - -
301A ILE* 1.3 95.3 - - + +
303A VAL* 1.3 59.1 + - + +
305A VAL* 3.9 3.8 - - + +
306A ASN* 2.9 32.4 + - - +
401A LEU* 4.4 19.1 - - + -
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Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LEU* 4.0 11.4 - - + -
265A THR* 3.8 27.0 - - + +
266A GLN* 3.4 47.3 - - + +
299A LYS* 3.2 22.0 - - + +
300A LEU* 3.0 9.5 + - + +
302A PRO* 1.3 76.8 - - + +
304A LEU* 1.3 64.8 + - - +
306A ASN* 3.6 6.0 + - - +
307A GLY* 3.2 18.0 + - - -
379A SER* 5.3 0.3 + - - -
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Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A THR* 5.2 4.9 - - + -
277A CYS* 4.4 12.1 - - - -
280A TRP* 3.9 27.4 - - + +
300A LEU* 3.0 31.1 + - + +
301A ILE* 3.7 14.4 - - + +
303A VAL* 1.3 73.7 - - - +
305A VAL* 1.3 66.6 + - + +
307A GLY 3.1 9.2 + - - -
308A MET* 3.2 18.0 + - - +
379A SER* 3.4 17.2 - - - +
382A ALA* 4.1 20.9 - - + -
383A LEU* 4.6 13.0 - - + +
386A LEU* 3.7 30.3 - - + -
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Residues in contact with VAL 305 (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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301A ILE* 3.1 18.2 + - + +
302A PRO* 3.9 5.2 - - + +
304A LEU* 1.3 74.7 - - + +
306A ASN* 1.3 58.8 - - - +
308A MET* 3.0 30.8 + - - +
309A LYS* 3.9 9.1 + - - +
383A LEU* 4.2 14.1 - - + -
398A ILE* 4.4 8.1 - - + -
401A LEU* 4.2 18.4 - - + -
405A LEU* 3.7 26.7 - - + -
416A SER* 4.9 5.3 - - - +
420A VAL* 3.7 28.3 - - + -
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Residues in contact with ASN 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A PRO 2.9 20.3 + - - +
303A VAL* 3.9 5.8 + - - +
304A LEU 3.3 0.2 - - - -
305A VAL* 1.3 77.7 - - - +
307A GLY* 1.3 61.7 + - - +
308A MET 3.2 0.6 + - - -
309A LYS* 3.0 49.3 + - - +
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Residues in contact with GLY 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A VAL 3.2 10.6 + - - -
304A LEU 3.1 9.8 + - - -
306A ASN* 1.3 76.6 - - - +
308A MET* 1.3 60.1 + - - +
309A LYS 3.2 10.7 + - - +
375A LEU* 3.8 19.9 - - - +
376A ARG* 3.5 19.4 + - - -
379A SER* 4.2 9.9 - - - -
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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