Contacts of the helix formed by residues 349 - 365 (chain A) in PDB entry 2X14
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 ALA 349 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343A PHE* 3.6 29.8 - - - +
345A TRP 3.3 3.8 + - - +
346A GLU* 3.3 29.0 + - - +
348A PHE* 1.3 76.6 - - - +
350A ARG* 1.3 65.4 + - - +
351A GLY 3.4 2.7 - - - -
352A THR* 3.3 6.2 + - - -
353A LYS* 3.0 22.8 + - + +
383A TRP* 4.0 13.9 - - + -
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Residues in contact with ARG 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ASP* 3.3 6.3 + - - +
346A GLU 4.6 8.3 + - - -
347A ALA* 5.2 6.8 + - - +
349A ALA* 1.3 77.3 - - - +
351A GLY* 1.3 57.8 + - - +
353A LYS* 3.8 5.9 - - - +
354A ALA* 2.9 32.9 + - + +
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Residues in contact with GLY 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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315A ASP* 2.9 27.3 + - - -
316A CYS* 3.9 19.6 + - - -
321A SER* 3.9 11.2 + - - -
324A TYR* 5.4 0.9 - - - -
340A VAL* 3.6 8.0 - - - +
350A ARG* 1.3 73.1 - - - +
352A THR* 1.3 57.4 + - - +
354A ALA* 3.8 2.4 - - - +
355A LEU* 3.1 27.7 + - - +
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Residues in contact with THR 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ASP* 4.2 1.2 + - - -
336A TRP* 3.9 17.8 - - + -
339A PRO* 3.8 6.6 - - + +
340A VAL* 3.1 27.3 + - - +
341A GLY* 3.2 14.2 + - - -
343A PHE* 4.1 9.8 - - + +
349A ALA 3.3 7.8 + - - -
351A GLY* 1.3 73.2 - - - +
353A LYS* 1.3 62.2 + - - +
355A LEU* 3.4 2.3 + - - +
356A MET* 2.9 28.1 + - - +
379A CYS* 3.7 21.1 - - - -
383A TRP* 3.6 19.1 - - + -
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Residues in contact with LYS 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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349A ALA* 3.0 17.5 + - + +
350A ARG* 3.8 6.5 - - - +
352A THR* 1.3 77.8 - - - +
354A ALA* 1.3 58.2 + - - +
356A MET* 3.4 4.7 + - + +
357A ASP* 2.9 55.4 + - - +
383A TRP* 3.7 56.0 - - + +
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Residues in contact with ALA 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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321A SER* 4.1 20.6 - - - +
350A ARG* 2.9 22.8 + - + +
351A GLY 3.8 3.6 - - - +
353A LYS* 1.3 76.0 - - - +
355A LEU* 1.3 62.4 + - - +
357A ASP* 3.3 13.4 + - - +
358A GLU* 3.0 30.0 + - + +
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Residues in contact with LEU 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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211A ILE* 4.0 16.8 - - + -
235A ILE* 5.0 0.4 - - + -
324A TYR* 4.3 26.2 - - + +
328A VAL* 3.7 29.6 - - + -
336A TRP* 3.7 32.8 - - + -
340A VAL* 3.8 24.5 - - + -
351A GLY 3.1 17.2 + - - +
352A THR* 3.8 4.3 - - - +
353A LYS 3.3 0.2 - - - -
354A ALA* 1.3 72.4 - - - +
356A MET* 1.3 55.3 + - - +
358A GLU* 3.2 8.1 + - + -
359A VAL* 2.7 43.6 + - + +
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Residues in contact with MET 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A TRP* 3.8 24.8 - - + -
352A THR 2.9 16.8 + - - +
353A LYS* 3.5 9.9 - - + +
355A LEU* 1.3 76.8 - - - +
357A ASP* 1.3 65.3 + - - +
359A VAL* 3.0 4.3 + - - +
360A VAL* 2.9 26.3 + - - +
371A ILE* 4.2 13.5 - - + -
376A THR* 4.7 1.3 - - + +
379A CYS* 3.6 32.3 - - + -
380A CYS* 3.8 20.9 - - - +
383A TRP* 4.5 12.8 - - + -
385A THR* 3.2 35.9 - - + +
389A VAL* 4.8 1.6 - - - -
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Residues in contact with ASP 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A LYS* 2.9 55.7 + - - +
354A ALA* 3.3 14.9 + - - +
356A MET* 1.3 72.6 - - - +
358A GLU* 1.3 59.0 + - + +
360A VAL* 3.4 7.1 + - - +
361A LYS* 3.0 48.0 + - - +
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Residues in contact with GLU 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A SER 5.4 0.9 - - - +
325A ALA* 3.5 35.8 - - + +
328A VAL* 3.7 19.9 - - + +
329A THR* 4.9 4.3 + - - -
354A ALA* 3.0 22.8 + - + +
355A LEU* 3.4 12.6 - - + +
357A ASP* 1.3 76.3 - - - +
359A VAL* 1.3 59.5 + - - +
361A LYS* 3.3 26.5 + - - +
362A ALA* 2.9 28.2 + - - +
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Residues in contact with VAL 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ILE* 4.5 6.1 - - + -
328A VAL* 4.4 14.4 - - + -
334A ILE* 4.6 9.6 - - + -
336A TRP* 3.9 21.8 - - + -
355A LEU* 2.7 38.0 + - + +
356A MET* 3.6 7.0 - - - +
358A GLU* 1.3 73.1 - - - +
360A VAL* 1.3 53.6 - - - +
362A ALA* 3.5 2.8 + - - +
363A THR* 2.8 33.3 + - - -
369A THR* 3.8 26.2 - - + +
371A ILE* 4.6 9.4 - - + -
389A VAL* 4.1 13.2 - - + -
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Residues in contact with VAL 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A MET* 2.9 18.1 + - + +
357A ASP* 3.6 10.3 - - - +
359A VAL* 1.3 75.0 - - - +
361A LYS* 1.3 69.1 + - + +
363A THR* 3.3 5.5 + - - -
364A SER* 3.1 26.5 + - - +
385A THR* 3.8 36.1 - - + -
388A LYS* 3.9 37.6 - - + +
389A VAL* 4.5 5.6 - - + -
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Residues in contact with LYS 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A ASP* 3.0 32.6 + - - +
358A GLU* 3.5 32.9 + - - +
360A VAL* 1.3 79.6 - - + +
362A ALA* 1.3 61.1 + - - +
364A SER* 3.2 18.4 + - - -
365A ARG* 3.3 15.5 + - - +
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Residues in contact with ALA 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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328A VAL* 3.8 19.3 - - + -
334A ILE* 4.7 0.2 - - + -
358A GLU 2.9 17.1 + - - +
359A VAL* 3.7 6.1 - - - +
360A VAL 3.3 0.2 - - - -
361A LYS* 1.3 74.5 - - - +
363A THR* 1.3 63.8 + - - +
365A ARG* 3.1 30.6 + - - +
367A CYS* 2.9 40.0 + - + +
369A THR* 4.6 1.8 - - + -
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Residues in contact with THR 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 VAL 2.8 16.9 + - - -
360A VAL 3.4 7.6 - - - -
362A ALA* 1.3 77.5 - - - +
364A SER* 1.3 63.8 + - - +
366A GLY* 3.0 15.4 + - - -
367A CYS* 3.5 16.1 + - - +
369A THR* 2.7 27.3 + - - +
388A LYS 3.4 23.6 + - - +
389A VAL* 3.7 12.2 - - - -
390A SER* 4.2 5.4 - - - +
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Residues in contact with SER 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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360A VAL* 3.1 19.4 + - - +
361A LYS* 3.2 13.4 + - - -
363A THR* 1.3 76.6 - - - +
365A ARG* 1.3 59.4 + - - +
366A GLY 3.7 0.3 + - - -
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Residues in contact with ARG 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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328A VAL 3.0 22.0 + - - -
329A THR* 3.1 19.6 + - - +
331A ALA 2.7 29.7 + - - -
332A LYS* 3.8 20.1 - - - +
361A LYS 3.6 9.9 - - - +
362A ALA* 3.1 21.5 + - - +
364A SER* 1.3 78.4 - - - +
366A GLY* 1.3 54.8 + - - -
367A CYS* 3.4 20.7 - - - +
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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