Contacts of the helix formed by residues 298 - 320 (chain A) in PDB entry 4RA2
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 SER 298 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A GLU* 2.8 16.8 + - - -
296A LYS 3.3 4.9 + - - -
297A VAL* 1.3 74.3 - - - +
299A PRO* 1.3 70.7 - - - +
300A GLU* 3.3 9.9 + - - +
301A ALA* 3.1 27.8 + - - +
302A VAL* 2.9 26.8 + - - +
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Residues in contact with PRO 299 (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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297A VAL* 4.0 6.5 - - + +
298A SER* 1.3 84.7 - - - +
300A GLU* 1.3 58.3 + - - +
302A VAL* 3.3 8.6 + - + +
303A LYS* 3.0 32.5 + - - +
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Residues in contact with GLU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A SER* 3.2 7.6 + - - +
299A PRO* 1.3 76.5 - - - +
301A ALA* 1.3 61.9 + - - +
303A LYS* 3.3 9.3 + - + +
304A LYS* 2.9 64.4 + - + +
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Residues in contact with ALA 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A SER 5.6 0.2 - - - +
259A GLU* 3.5 39.9 - - + +
260A VAL* 3.7 8.4 - - + +
298A SER* 3.1 17.1 + - - +
300A GLU* 1.3 77.4 - - - +
302A VAL* 1.3 62.2 + - - +
304A LYS* 3.4 11.2 + - - +
305A GLU* 3.1 23.4 + - - +
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Residues in contact with VAL 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A VAL* 3.7 35.9 - - + +
297A VAL* 3.8 15.9 - - + -
298A SER 2.9 19.1 + - - +
299A PRO* 3.7 9.6 - - + +
301A ALA* 1.3 74.3 - - - +
303A LYS* 1.3 64.2 + - + +
305A GLU* 3.3 4.7 + - - +
306A ALA* 3.0 23.0 + - + +
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Residues in contact with LYS 303 (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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299A PRO* 3.0 17.2 + - - +
300A GLU* 3.6 12.8 - - + +
301A ALA 3.3 0.2 - - - -
302A VAL* 1.3 74.9 - - + +
304A LYS* 1.3 67.8 + - + +
306A ALA* 3.0 8.2 + - - +
307A GLU* 2.9 41.5 + - - +
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Residues in contact with LYS 304 (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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300A GLU* 2.9 50.7 + - + +
301A ALA* 3.7 8.3 - - - +
302A VAL 3.4 0.2 - - - -
303A LYS* 1.3 75.8 - - + +
305A GLU* 1.3 58.5 + - - +
307A GLU* 3.4 18.0 + - - +
308A LEU* 2.9 29.0 + - - +
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Residues in contact with GLU 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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257A ARG* 2.7 43.3 + - - -
260A VAL* 4.2 22.0 - - + +
270A GLU* 5.5 1.0 - - - +
301A ALA 3.1 13.7 + - - +
302A VAL* 3.5 8.7 - - - +
304A LYS* 1.3 75.6 - - - +
306A ALA* 1.3 64.1 + - - +
308A LEU* 3.2 12.4 + - - +
309A ASP* 2.9 33.6 + - - +
346A PRO* 4.6 1.4 - - - +
354A LYS* 3.2 22.5 + - - -
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Residues in contact with ALA 306 (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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302A VAL* 3.0 15.6 + - + +
303A LYS* 3.0 9.8 + - - +
305A GLU* 1.3 77.3 - - - +
307A GLU* 1.3 63.1 + - + +
309A ASP* 3.4 7.7 + - - +
310A LYS* 3.0 24.4 + - - +
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Residues in contact with GLU 307 (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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303A LYS* 2.9 39.1 + - - +
304A LYS* 3.6 21.3 - - - +
306A ALA* 1.3 77.7 - - + +
308A LEU* 1.3 57.2 + - - +
310A LYS* 3.3 6.0 + - - +
311A TYR* 2.9 29.7 + - - +
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Residues in contact with LEU 308 (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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304A LYS 2.9 18.0 + - - +
305A GLU* 3.7 11.7 - - - +
307A GLU* 1.3 75.6 - - - +
309A ASP* 1.3 58.7 + - - +
311A TYR* 3.3 8.5 + - + +
312A LEU* 2.9 46.2 + - + +
342A ILE* 4.4 13.9 - - + -
343A PRO 4.4 7.0 - - - +
344A SER* 3.7 22.9 - - - +
345A LEU* 4.2 13.7 - - + -
346A PRO* 4.2 7.4 - - + -
354A LYS* 3.9 34.1 - - + +
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Residues in contact with ASP 309 (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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305A GLU* 2.9 25.0 + - - +
306A ALA* 3.8 7.4 - - - +
307A GLU 3.3 0.2 - - - -
308A LEU* 1.3 77.9 - - - +
310A LYS* 1.3 56.9 + - - +
312A LEU* 3.3 4.0 + - - +
313A GLU* 2.9 40.1 + - - +
354A LYS* 2.6 36.4 + - - -
357A VAL* 3.6 27.1 - - + +
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Residues in contact with LYS 310 (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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306A ALA 3.0 16.2 + - - +
307A GLU* 3.8 5.8 - - - +
308A LEU 3.3 0.2 - - - -
309A ASP* 1.3 72.9 - - - +
311A TYR* 1.3 66.5 + - - +
313A GLU* 3.2 21.7 + - + +
314A CYS* 3.0 54.7 + - - -
317A GLU* 4.7 6.7 + - - -
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Residues in contact with TYR 311 (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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307A GLU 2.9 18.3 + - - +
308A LEU* 3.3 10.7 + - + +
310A LYS* 1.3 77.8 - - - +
312A LEU* 1.3 66.8 + - + +
314A CYS* 3.3 7.6 + - + +
315A ARG* 3.0 59.0 + - + +
340A GLU* 5.0 1.2 + - - -
342A ILE* 4.1 32.7 - - + +
343A PRO* 5.5 5.8 - - + +
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Residues in contact with LEU 312 (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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308A LEU* 2.9 33.8 + - + +
309A ASP* 3.6 4.7 - - - +
311A TYR* 1.3 78.3 - - + +
313A GLU* 1.3 63.3 + - - +
315A ARG* 3.2 4.2 + - - +
316A VAL* 3.0 29.8 + - - +
337A LEU* 4.7 4.9 - - + -
342A ILE* 3.8 30.3 - - + -
345A LEU* 5.0 1.1 - - + -
351A LEU* 4.9 4.9 - - + -
354A LYS* 3.6 46.0 - - + -
357A VAL* 4.5 10.5 - - + -
358A ILE* 4.1 27.4 - - + -
361A VAL* 5.4 0.4 - - - -
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Residues in contact with GLU 313 (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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309A ASP* 2.9 32.4 + - - +
310A LYS* 3.2 28.6 + - + +
312A LEU* 1.3 76.6 - - - +
314A CYS* 1.3 63.2 + - - +
316A VAL* 3.4 3.7 + - - +
317A GLU* 3.0 32.2 + - - +
357A VAL* 4.6 7.7 - - + +
361A VAL* 3.0 35.4 - - + +
364A ARG* 3.3 24.5 + - - +
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Residues in contact with CYS 314 (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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310A LYS* 3.0 47.1 + - - +
311A TYR* 3.7 8.3 - - + +
312A LEU 3.3 0.2 - - - -
313A GLU* 1.3 74.0 - - - +
315A ARG* 1.3 67.3 + - + +
317A GLU* 3.2 15.9 + - - +
318A GLU* 3.0 29.3 + - + +
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Residues in contact with ARG 315 (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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311A TYR* 3.0 52.8 + - + +
312A LEU* 3.6 7.6 - - - +
314A CYS* 1.3 75.5 - - + +
316A VAL* 1.3 58.6 + - - +
318A GLU* 3.2 37.7 + - - +
319A ILE* 2.8 47.7 + - - +
337A LEU* 3.7 19.7 - - + -
340A GLU* 2.8 47.6 + - - +
342A ILE* 4.7 0.7 - - + -
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Residues in contact with VAL 316 (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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312A LEU 3.0 22.7 + - - +
313A GLU 3.7 4.3 - - - +
314A CYS 3.2 0.2 - - - -
315A ARG* 1.3 76.1 - - - +
317A GLU* 1.3 61.9 + - - +
319A ILE* 3.9 6.6 - - - +
320A ILE* 2.9 27.1 + - + +
333A VAL* 4.2 15.4 - - + +
337A LEU* 4.3 7.2 - - + -
358A ILE* 3.9 33.9 - - + +
361A VAL* 4.2 7.4 - - + -
362A TYR* 4.1 26.9 - - + -
365A LEU* 4.0 17.3 - - + -
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Residues in contact with GLU 317 (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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310A LYS* 4.7 5.9 + - - -
313A GLU* 3.0 24.6 + - - +
314A CYS* 3.4 23.3 + - - +
316A VAL* 1.3 78.4 - - - +
318A GLU* 1.3 66.2 + - + +
320A ILE* 3.4 16.3 - - - +
321A LYS 3.5 10.6 + - - +
361A VAL* 4.9 3.1 - - + -
365A LEU* 3.9 27.8 - - + +
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Residues in contact with GLU 318 (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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314A CYS* 3.0 15.0 + - + +
315A ARG* 3.2 29.5 + - - +
317A GLU* 1.3 80.6 - - + +
319A ILE* 1.3 60.6 + - - +
321A LYS* 2.9 35.6 + - - +
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Residues in contact with ILE 319 (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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315A ARG* 2.8 37.4 + - - +
316A VAL* 3.9 4.3 - - - +
318A GLU* 1.3 67.4 - - - +
320A ILE* 1.3 59.3 + - - +
321A LYS* 2.9 26.2 + - - +
328A PRO* 4.1 12.2 - - + +
333A VAL* 4.3 24.0 - - + +
336A THR* 3.6 41.5 - - + +
337A LEU* 3.7 29.6 - - + -
340A GLU* 3.7 9.6 - - - +
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Residues in contact with ILE 320 (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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316A VAL* 2.9 15.8 + - + +
317A GLU 3.4 14.8 - - - +
318A GLU 3.2 0.4 - - - -
319A ILE* 1.3 75.8 - - - +
321A LYS* 1.3 72.2 + - - +
327A VAL* 4.6 18.1 - - + +
328A PRO* 4.2 21.1 - - + +
333A VAL* 5.0 2.4 - - + +
362A TYR* 4.0 35.2 - - + +
365A LEU* 3.8 38.6 - - + +
366A ASN* 4.3 11.9 - - + -
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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