Contacts of the helix formed by residues 349 - 367 (chain A) in PDB entry 2XLR
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 349 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A PRO* 1.3 78.0 - - - +
350A LYS* 1.3 66.5 + - - +
351A GLU* 3.8 11.7 + - - +
352A GLU* 2.9 33.5 + - - +
353A MET* 3.0 19.5 + - - +
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Residues in contact with LYS 350 (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 GLU 3.8 14.4 - - - +
311A ASP* 3.3 31.8 + - - +
349A SER* 1.3 72.9 - - - +
351A GLU* 1.3 62.5 + - - +
353A MET* 3.3 23.3 + - + +
354A LYS* 3.0 47.4 + - + +
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Residues in contact with GLU 351 (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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349A SER* 4.0 11.1 + - - +
350A LYS* 1.3 77.8 + - - +
352A GLU* 1.3 65.0 + - + +
354A LYS* 3.3 8.3 + - - +
355A ALA* 3.0 22.5 + - - +
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Residues in contact with GLU 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A TYR* 5.2 0.4 - - - -
348A PRO* 3.8 19.1 - - + +
349A SER* 2.9 37.9 + - - +
351A GLU* 1.3 78.3 - - + +
353A MET* 1.4 62.5 + - - +
355A ALA* 3.3 7.0 + - - +
356A ASP* 3.0 24.9 + - - +
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Residues in contact with MET 353 (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 TYR* 3.7 46.0 - - + -
308A VAL* 5.1 4.7 - - - -
310A GLU* 3.7 36.6 - - + +
313A PRO* 4.6 13.2 - - + -
347A LEU* 4.3 15.7 - - + -
348A PRO* 3.9 22.0 - - + +
349A SER 3.0 14.2 + - - +
350A LYS* 3.6 26.7 - - + +
352A GLU* 1.4 73.7 - - - +
354A LYS* 1.3 63.6 + - - +
356A ASP* 3.3 4.0 + - - +
357A SER* 3.0 25.5 + - - -
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Residues in contact with LYS 354 (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 LEU* 6.1 2.6 - - - +
302A ASN* 2.9 28.1 + - - +
310A GLU* 3.1 32.9 + - + +
311A ASP* 5.1 2.9 + - - -
350A LYS* 3.0 43.4 + - + +
351A GLU* 3.6 10.5 - - - +
353A MET* 1.3 76.7 - - - +
355A ALA* 1.3 55.6 + - - +
357A SER* 3.2 4.4 + - - +
358A MET* 2.8 30.5 + - - +
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Residues in contact with ALA 355 (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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351A GLU 3.0 16.0 + - - +
352A GLU* 3.7 7.4 - - - +
353A MET 3.3 0.4 - - - -
354A LYS* 1.3 75.3 - - - +
356A ASP* 1.3 63.8 + - - +
358A MET* 3.2 16.8 + - + +
359A ALA* 3.1 23.2 + - - +
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Residues in contact with ASP 356 (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 TRP* 5.5 0.3 - - - -
304A TYR* 3.8 26.0 + - + -
305A LYS* 4.2 21.1 + - - +
352A GLU 3.0 17.1 + - - +
353A MET 3.5 4.9 - - - +
355A ALA* 1.3 77.0 - - - +
357A SER* 1.3 60.9 + - - +
359A ALA* 3.4 5.3 + - - +
360A TRP* 3.2 47.6 + - - -
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Residues in contact with SER 357 (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 TRP* 3.3 25.8 + - - +
301A LEU* 4.4 10.9 - - - +
302A ASN 5.2 2.9 - - - -
303A LEU 3.5 14.3 + - - -
304A TYR* 4.0 4.5 - - - -
305A LYS 4.9 0.3 + - - -
310A GLU* 2.7 31.8 + - - -
353A MET 3.0 8.9 + - - -
354A LYS* 3.2 4.7 + - - -
356A ASP* 1.3 74.0 - - - +
358A MET* 1.3 65.7 + - - +
360A TRP 3.3 0.7 + - - -
361A ARG* 2.9 21.7 + - - +
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Residues in contact with MET 358 (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 LEU* 5.3 3.1 - - - -
354A LYS 2.8 16.9 + - - +
355A ALA* 3.6 13.7 - - + +
357A SER* 1.3 77.1 - - - +
359A ALA* 1.3 52.8 + - - +
361A ARG* 2.8 10.8 + - + +
362A GLU* 2.7 58.4 + - + +
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Residues in contact with ALA 359 (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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355A ALA 3.1 11.6 + - - +
356A ASP* 3.7 9.9 - - - +
357A SER 3.3 0.2 - - - -
358A MET* 1.3 75.8 - - - +
360A TRP* 1.3 66.3 + - + +
362A GLU* 3.4 15.3 + - - +
363A LYS* 3.0 24.4 + - - +
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Residues in contact with TRP 360 (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 TRP* 3.3 45.9 - + + +
305A LYS* 5.2 6.2 - - + +
356A ASP* 3.2 45.7 + - - -
357A SER 3.7 1.6 - - - +
358A MET 3.2 0.2 - - - -
359A ALA* 1.3 80.8 - - + +
361A ARG* 1.3 56.9 + - - +
363A LYS* 3.4 4.2 + - + +
364A GLU* 3.0 17.0 + - - +
376A TYR* 2.9 60.4 + + - -
379A ASP* 4.2 11.2 - - + -
380A TYR* 3.6 43.1 - + + -
383A ASN* 4.5 21.1 - - + -
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Residues in contact with ARG 361 (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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294A THR* 5.3 0.8 + - - -
297A ARG* 3.1 33.8 - - - +
299A TRP* 2.8 29.5 + - + -
300A PRO* 4.0 0.2 - - - +
301A LEU* 3.6 49.7 - - + +
357A SER 2.9 13.2 + - - +
358A MET* 2.8 11.9 + - + +
360A TRP* 1.3 72.7 - - - +
362A GLU* 1.3 69.3 + - + +
364A GLU* 2.9 34.9 + - - +
365A LEU* 3.1 29.2 + - + +
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Residues in contact with GLU 362 (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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358A MET* 2.7 45.4 + - + +
359A ALA* 3.6 21.1 + - - +
361A ARG* 1.3 74.5 - - + +
363A LYS* 1.3 62.9 + - - +
365A LEU* 3.2 20.4 + - + +
366A THR* 3.4 12.2 + - - -
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Residues in contact with LYS 363 (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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359A ALA 3.0 16.3 + - - +
360A TRP* 3.8 6.5 - - + +
362A GLU* 1.3 77.3 - - - +
364A GLU* 1.3 59.1 + - - +
366A THR* 2.9 42.7 - - + +
367A LEU* 3.3 12.9 - - + +
376A TYR* 3.7 24.5 - - + -
379A ASP* 5.7 3.6 + - - -
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Residues in contact with GLU 364 (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 ARG* 3.0 26.4 + - - +
298A LEU* 3.5 19.6 + - + +
299A TRP* 3.0 31.6 + - + +
360A TRP 3.0 13.3 + - - +
361A ARG* 2.9 36.7 + - - +
363A LYS* 1.3 77.4 - - - +
365A LEU* 1.3 61.4 + - - +
367A LEU* 3.3 31.3 + - + +
376A TYR* 3.7 11.6 - - + +
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Residues in contact with LEU 365 (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 ARG* 4.1 22.0 - - - +
361A ARG* 3.1 28.3 + - + +
362A GLU* 3.2 12.9 + - + +
364A GLU* 1.3 77.7 - - - +
366A THR* 1.3 60.3 + - - +
367A LEU 3.2 4.5 + - - +
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Residues in contact with THR 366 (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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362A GLU 3.4 9.0 + - - -
363A LYS* 2.9 31.7 + - + +
365A LEU* 1.3 76.8 - - - +
367A LEU* 1.3 73.6 + - + +
368A VAL* 3.5 12.4 + - - +
372A GLU* 4.6 8.1 - - - +
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Residues in contact with LEU 367 (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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298A LEU* 3.7 22.2 - - + -
363A LYS* 3.3 22.2 - - + +
364A GLU* 3.3 25.6 + - + +
365A LEU 3.2 6.8 - - - +
366A THR* 1.3 89.7 - - + +
368A VAL* 1.3 61.3 + - - +
372A GLU* 4.0 28.0 - - + +
373A MET* 3.9 24.2 - - + +
376A TYR* 3.7 32.3 - - + -
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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
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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