Contacts of the helix formed by residues 349 - 367 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348D PRO* 1.3 78.5 - - - +
350D LYS* 1.3 67.3 + - - +
351D GLU* 3.5 11.4 + - - +
352D GLU* 3.1 33.6 + - - +
353D MET* 3.0 18.2 + - - +
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Residues in contact with LYS 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B GLU* 4.5 8.3 + - - +
310D GLU* 3.8 21.1 + - + +
311D ASP* 3.2 31.5 + - - +
348D PRO 3.9 0.4 + - - -
349D SER* 1.3 73.4 - - - +
351D GLU* 1.3 64.8 + - - +
353D MET* 3.2 17.9 + - + +
354D LYS* 3.0 47.2 + - + +
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Residues in contact with GLU 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349D SER* 3.2 9.6 + - - +
350D LYS* 1.3 80.6 - - - +
352D GLU* 1.3 59.8 + - + +
354D LYS* 3.2 7.1 + - - +
355D ALA* 3.0 27.8 + - - +
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Residues in contact with GLU 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348D PRO* 3.8 19.4 - - + +
349D SER* 3.1 37.7 + - - +
351D GLU* 1.3 78.8 - - + +
353D MET* 1.3 61.2 + - - +
355D ALA* 3.3 6.8 + - - +
356D ASP* 3.0 25.5 + - - +
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Residues in contact with MET 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304D TYR* 3.6 42.9 - - + -
308D VAL* 4.8 5.6 - - - -
310D GLU* 3.4 40.6 - - + +
313D PRO* 4.6 15.0 - - + -
347D LEU* 4.3 13.5 - - + -
348D PRO* 3.9 21.3 - - + +
349D SER 3.0 10.6 + - - +
350D LYS* 3.2 24.9 + - + +
352D GLU* 1.3 73.9 - - - +
354D LYS* 1.3 66.0 + - - +
356D ASP* 3.3 3.3 + - - +
357D SER* 2.9 26.5 + - - -
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Residues in contact with LYS 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B GLY 5.0 6.3 - - - +
35B GLU* 3.2 44.2 + - + +
301D LEU* 6.2 0.6 - - - +
302D ASN* 2.9 29.3 + - - +
310D GLU* 3.0 28.4 + - + +
311D ASP* 4.9 1.3 + - - -
350D LYS* 3.0 40.8 + - + +
351D GLU* 3.5 10.5 - - - +
353D MET* 1.3 78.1 - - - +
355D ALA* 1.3 56.4 + - - +
357D SER* 3.4 2.6 + - - -
358D MET* 2.9 31.8 + - - +
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Residues in contact with ALA 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351D GLU 3.0 16.1 + - - +
352D GLU* 3.7 7.9 - - - +
354D LYS* 1.3 75.2 - - - +
356D ASP* 1.3 63.3 + - - +
358D MET* 3.3 17.7 + - + +
359D ALA* 3.1 23.7 + - - +
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Residues in contact with ASP 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299D TRP* 5.5 0.3 - - - -
304D TYR* 3.9 26.0 + - + -
305D LYS* 4.4 20.8 + - - +
352D GLU 3.0 17.7 + - - +
353D MET 3.6 3.8 - - - +
355D ALA* 1.3 78.6 - - - +
357D SER* 1.3 63.1 + - - +
359D ALA* 3.4 5.8 + - - +
360D TRP* 3.0 47.6 + - - -
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Residues in contact with SER 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299D TRP* 3.3 27.0 + - - +
301D LEU* 4.4 11.2 - - - +
302D ASN 5.1 2.2 - - - -
303D LEU 3.6 14.4 + - - -
304D TYR* 4.0 4.2 - - - -
305D LYS 5.0 0.2 + - - -
310D GLU* 2.7 33.4 + - - -
353D MET 2.9 9.5 + - - -
354D LYS* 3.9 3.8 - - - -
356D ASP* 1.3 73.6 - - - +
358D MET* 1.3 60.9 + - - +
360D TRP 3.3 0.9 + - - -
361D ARG* 2.9 25.9 + - - +
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Residues in contact with MET 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LYS 3.6 16.6 - - - +
33B GLY* 4.0 23.3 + - - +
34B ALA* 4.7 7.6 - - - -
344B ARG* 6.3 0.2 - - - -
354D LYS 2.9 16.9 + - - +
355D ALA* 3.3 15.5 + - + +
357D SER* 1.3 76.8 - - - +
359D ALA* 1.3 53.4 + - - +
361D ARG* 2.9 7.5 + - - +
362D GLU* 2.6 58.6 + - - +
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Residues in contact with ALA 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355D ALA 3.1 13.3 + - - +
356D ASP* 3.7 10.5 - - - +
358D MET* 1.3 76.8 - - - +
360D TRP* 1.3 64.0 + - + +
362D GLU* 3.3 15.1 + - - +
363D LYS* 3.0 24.1 + - - +
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Residues in contact with TRP 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299D TRP* 3.4 43.3 - + + -
305D LYS* 5.3 6.0 - - + +
356D ASP* 3.0 43.3 + - - -
357D SER 3.3 2.6 + - - +
358D MET 3.2 0.4 - - - -
359D ALA* 1.3 77.0 - - + +
361D ARG* 1.3 66.4 + - - +
363D LYS* 3.5 4.6 + - + +
364D GLU* 3.0 12.3 + - - +
376D TYR* 2.9 55.5 + + - -
379D ASP* 4.1 11.2 - - + -
380D TYR* 3.7 43.1 - + + -
383D ASN* 4.5 22.7 - - + -
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Residues in contact with ARG 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B GLN 3.7 8.3 + - - -
31B GLU* 2.7 49.5 + - - +
32B LYS* 3.7 16.2 - - - -
33B GLY* 3.8 1.6 - - - +
294D THR* 5.4 0.4 + - - -
297D ARG* 3.1 30.5 - - - +
299D TRP* 2.8 32.6 + - + -
301D LEU* 3.6 33.3 - - + +
357D SER 2.9 12.7 + - - +
358D MET* 2.9 10.6 + - - +
360D TRP* 1.3 73.6 - - - +
362D GLU* 1.3 68.9 + - - +
364D GLU* 2.8 34.7 + - - +
365D LEU* 3.0 18.1 + - + +
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Residues in contact with GLU 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LYS* 4.2 15.3 - - + +
358D MET* 2.6 45.9 + - - +
359D ALA* 3.6 18.7 + - - +
361D ARG* 1.3 74.6 - - - +
363D LYS* 1.3 63.2 + - - +
365D LEU* 3.2 19.0 + - + +
366D THR* 3.4 12.5 + - - -
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Residues in contact with LYS 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359D ALA 3.0 15.3 + - - +
360D TRP* 3.8 7.2 - - + +
362D GLU* 1.3 76.3 - - - +
364D GLU* 1.3 61.9 + - - +
366D THR* 3.1 37.2 - - + +
367D LEU* 3.4 13.5 - - + +
376D TYR* 3.7 23.6 - - + -
379D ASP* 6.0 2.0 - - - -
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Residues in contact with GLU 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297D ARG* 3.0 31.2 + - - +
298D LEU* 3.4 20.1 + - + -
299D TRP* 3.1 27.0 + - + +
360D TRP 3.0 14.3 + - - +
361D ARG* 2.8 39.0 + - - +
363D LYS* 1.3 78.4 - - - +
365D LEU* 1.3 61.0 + - - +
367D LEU* 3.3 29.9 + - + +
376D TYR* 3.7 11.2 - - + +
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Residues in contact with LEU 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B GLU* 3.7 42.8 - - + +
32B LYS* 3.9 26.0 - - + -
297D ARG* 4.0 12.8 - - - +
361D ARG* 3.0 21.2 + - + +
362D GLU* 3.2 11.2 + - + +
364D GLU* 1.3 77.0 - - - +
366D THR* 1.3 61.8 + - - +
367D LEU 3.5 3.5 + - - +
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Residues in contact with THR 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362D GLU 3.4 8.4 + - - -
363D LYS* 3.1 32.2 + - + +
365D LEU* 1.3 76.9 - - - +
367D LEU* 1.3 73.6 + - + +
368D VAL* 3.4 14.3 + - - +
372D GLU* 4.6 9.1 - - - +
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Residues in contact with LEU 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298D LEU* 3.8 21.1 - - + -
363D LYS* 3.4 22.7 - - + +
364D GLU* 3.3 24.0 + - + +
365D LEU 3.3 6.4 - - - +
366D THR* 1.3 89.9 - - + +
368D VAL* 1.3 60.6 + - - +
372D GLU* 4.0 27.1 - - + +
373D MET* 3.9 23.8 - - + +
376D TYR* 3.7 35.9 - - + -
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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
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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