Contacts of the helix formed by residues 319 - 338 (chain Z) in PDB entry 1XDM
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 ASN 319 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312Z ALA 3.8 11.8 + - - +
313Z TRP 3.4 9.9 + - - -
316Z LYS* 3.0 48.1 + - - +
317Z ALA 3.7 0.2 - - - -
318Z ALA* 1.3 85.3 + - - +
320Z LYS* 1.3 52.6 + - - +
321Z GLU* 2.7 19.7 + - - +
322Z ALA* 2.8 22.3 + - + +
323Z THR* 3.0 13.4 + - - -
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Residues in contact with LYS 320 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61Z ILE* 4.3 22.6 - - + +
317Z ALA* 3.1 28.2 - - - +
318Z ALA* 3.1 9.1 + - - +
319Z ASN* 1.3 75.2 - - - +
321Z GLU* 1.3 54.8 + - + +
323Z THR* 4.0 9.4 - - - -
324Z GLN* 2.6 57.9 + - - +
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Residues in contact with GLU 321 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318Z ALA 5.7 2.7 - - - +
319Z ASN* 2.7 3.3 + - - +
320Z LYS* 1.3 77.9 - - + +
322Z ALA* 1.3 52.0 + - - +
324Z GLN* 3.5 2.1 - - - -
325Z GLU* 2.6 44.0 + - - +
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Residues in contact with ALA 322 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312Z ALA* 3.1 30.5 - - + +
319Z ASN* 2.8 19.0 + - + +
321Z GLU* 1.3 74.2 - - - +
323Z THR* 1.3 56.8 + - - +
325Z GLU* 3.2 8.6 - - - +
326Z ALA* 2.9 25.6 + - - +
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Residues in contact with THR 323 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58Z PHE* 3.9 14.6 - - + -
61Z ILE* 3.4 28.9 - - + -
62Z LEU* 4.4 6.3 - - + -
309Z ALA* 3.1 27.6 - - + +
312Z ALA* 2.9 28.8 + - - +
313Z TRP* 3.6 13.2 - - - +
319Z ASN 3.0 9.1 + - - -
320Z LYS* 3.6 7.3 - - - -
322Z ALA* 1.3 72.2 - - - +
324Z GLN* 1.3 57.2 + - - +
325Z GLU 2.9 9.6 + - - -
326Z ALA 3.0 2.3 + - - -
327Z PHE* 3.0 20.6 + - - +
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Residues in contact with GLN 324 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61Z ILE* 2.8 42.3 - - + +
62Z LEU* 5.5 0.9 - - - -
64Z SER* 2.9 10.3 + - - -
65Z VAL* 3.1 38.9 - - + +
66Z ASP 4.4 1.2 - - - +
320Z LYS* 2.6 43.1 + - - +
321Z GLU* 3.5 2.7 - - - +
323Z THR* 1.3 70.1 - - - +
325Z GLU* 1.3 55.7 + - - +
327Z PHE* 4.4 6.5 - - - -
328Z MET* 2.9 31.2 + - - +
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Residues in contact with GLU 325 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321Z GLU 2.6 25.6 + - - +
322Z ALA* 3.2 9.9 - - - +
324Z GLN* 1.3 72.2 - - - +
326Z ALA* 1.3 61.2 + - - +
327Z PHE 3.2 1.6 - - - -
328Z MET* 3.5 3.2 + - - +
329Z LYS* 2.9 39.6 + - + +
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Residues in contact with ALA 326 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305Z LEU 4.3 0.9 - - - +
308Z SER* 2.8 36.4 + - - +
309Z ALA* 3.0 31.5 + - - +
312Z ALA* 4.4 1.3 - - + -
322Z ALA 2.9 14.6 + - - +
325Z GLU* 1.3 74.2 - - + +
327Z PHE* 1.3 58.5 - - - +
329Z LYS* 4.0 8.2 - - - +
330Z ARG* 3.2 18.0 - - - +
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Residues in contact with PHE 327 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Z LEU* 3.8 37.9 - - + -
62Z LEU* 3.6 43.5 - - + -
65Z VAL* 4.1 11.9 - - + -
69Z ILE* 3.2 37.0 - - + -
73Z ILE* 4.5 5.4 - - + -
305Z LEU* 3.4 20.2 - - + -
306Z GLN* 5.8 0.4 - - + -
309Z ALA* 3.3 19.0 - - + +
323Z THR 3.0 9.8 + - - +
324Z GLN* 4.4 2.9 - - - -
326Z ALA* 1.3 77.1 - - - +
328Z MET* 1.3 67.2 + - - +
329Z LYS 3.0 2.7 + - - -
330Z ARG* 3.0 12.1 + - - +
331Z ALA* 3.1 20.2 + - + +
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Residues in contact with MET 328 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65Z VAL* 3.9 15.3 - - + -
66Z ASP* 3.8 17.0 - - + +
68Z SER* 2.9 28.5 - - - +
69Z ILE* 3.3 45.1 - - + +
324Z GLN 2.9 21.6 + - - +
325Z GLU* 4.1 4.5 - - - +
327Z PHE* 1.3 81.8 - - - +
329Z LYS* 1.3 60.8 + - - +
330Z ARG 3.6 0.2 + - - -
331Z ALA* 4.1 5.2 - - - -
332Z MET* 2.9 53.7 + - + +
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Residues in contact with LYS 329 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325Z GLU* 2.9 28.3 + - + +
326Z ALA* 4.3 8.3 - - - +
327Z PHE 3.0 0.4 + - - -
328Z MET* 1.3 79.3 - - - +
330Z ARG* 1.3 76.3 + - - +
332Z MET* 4.2 7.5 - - - +
333Z ALA* 3.3 24.9 + - + +
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Residues in contact with ARG 330 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276Z GLU* 2.3 67.8 + - - +
277Z GLU* 3.6 17.5 + - - -
280Z THR* 2.5 19.0 + - - +
304Z ALA 3.6 13.3 + - - +
305Z LEU* 3.9 11.4 - - + -
308Z SER* 3.8 2.2 - - - +
326Z ALA 3.2 19.7 - - - +
327Z PHE 3.0 5.3 + - - +
329Z LYS* 1.3 100.2 + - - +
331Z ALA* 1.3 60.0 + - - +
332Z MET 3.2 1.6 - - - -
333Z ALA* 3.7 19.2 - - - +
334Z ASN* 2.8 39.5 + - - +
342Z TYR* 4.1 5.1 + - - -
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Residues in contact with ALA 331 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69Z ILE* 4.5 10.3 - - + -
72Z SER* 2.9 21.1 - - - +
73Z ILE* 4.1 24.0 - - + -
299Z PHE* 4.2 2.0 - - - -
305Z LEU* 3.9 11.3 - - - +
327Z PHE* 3.1 21.2 + - + +
328Z MET* 4.2 7.2 - - - +
329Z LYS 3.6 0.2 - - - -
330Z ARG* 1.3 75.9 - - - +
332Z MET* 1.3 57.8 + - - +
334Z ASN 3.9 0.5 - - - -
335Z CYS* 2.9 28.6 + - - +
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Residues in contact with MET 332 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68Z SER* 5.7 2.7 - - - +
72Z SER* 3.1 16.6 - - - +
328Z MET* 2.9 52.1 + - + +
329Z LYS* 4.2 7.4 - - - +
330Z ARG 3.2 0.2 - - - -
331Z ALA* 1.3 75.4 - - - +
333Z ALA* 1.3 66.8 + - - +
335Z CYS* 2.9 13.8 + - - +
336Z GLN* 3.0 27.8 + - + +
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Residues in contact with ALA 333 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280Z THR* 4.0 1.1 - - - +
329Z LYS* 3.3 19.6 + - + +
330Z ARG* 3.3 25.7 + - - +
332Z MET* 1.3 78.2 - - - +
334Z ASN* 1.3 57.0 + - - +
336Z GLN* 2.8 33.7 + - - +
337Z ALA 3.1 7.8 + - - -
342Z TYR* 3.5 29.6 - - + -
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Residues in contact with ASN 334 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276Z GLU 4.6 1.4 + - - -
279Z ALA 3.6 5.4 - - - +
280Z THR* 2.8 39.2 + - - +
283Z LEU* 4.9 0.2 - - + -
299Z PHE* 2.9 41.3 - - + -
301Z TYR* 3.6 20.5 - - + -
304Z ALA* 3.8 20.4 + - - +
305Z LEU* 4.1 4.4 - - + +
330Z ARG* 2.8 32.7 + - - +
333Z ALA* 1.3 69.6 - - - +
335Z CYS* 1.3 60.7 + - - +
336Z GLN 3.1 1.3 - - - -
337Z ALA* 3.6 9.1 - - + +
338Z ALA* 3.5 10.9 + - - +
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Residues in contact with CYS 335 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25Z ASN 5.0 5.2 - - - -
26Z GLY* 3.9 13.3 - - - +
71Z GLN 3.6 15.7 - - - -
72Z SER* 3.2 23.8 - - - +
299Z PHE* 3.8 7.4 - - - -
331Z ALA 2.9 20.5 + - - +
332Z MET* 2.9 9.8 + - - +
334Z ASN* 1.3 78.9 - - - +
336Z GLN* 1.3 62.8 + - - +
337Z ALA 3.3 0.2 - - - -
338Z ALA* 3.6 10.0 - - - +
339Z LYS* 3.5 23.4 - - - +
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Residues in contact with GLN 336 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284Z ASN* 3.3 2.4 - - - +
332Z MET* 3.0 31.3 + - + +
333Z ALA* 2.8 14.9 + - - +
335Z CYS* 1.3 81.9 - - - +
337Z ALA* 1.3 54.2 + - - +
338Z ALA 3.1 1.3 - - - -
339Z LYS* 3.2 12.5 + - + -
340Z GLY 2.7 26.5 + - - -
341Z GLN* 3.1 26.7 + - + +
342Z TYR* 3.3 18.5 + - + +
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Residues in contact with ALA 337 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280Z THR* 3.8 21.1 - - + +
283Z LEU* 2.7 54.7 - - + +
284Z ASN* 3.6 11.5 - - - +
287Z ASN* 3.3 5.0 - - - +
333Z ALA 3.1 4.4 + - - -
334Z ASN* 3.7 15.3 - - - +
335Z CYS 3.3 0.2 - - - -
336Z GLN* 1.3 72.5 - - - +
338Z ALA* 1.3 58.0 + - - +
339Z LYS 2.9 8.8 + - - -
340Z GLY 3.2 7.6 + - - -
342Z TYR* 4.3 1.1 - - - -
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Residues in contact with ALA 338 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26Z GLY* 3.3 36.2 - - - +
283Z LEU* 4.1 0.9 - - + +
287Z ASN* 2.7 22.1 + - - +
296Z LYS* 6.0 1.7 - - - +
297Z LEU 3.8 16.7 + - - +
298Z SER* 4.1 11.7 - - - -
299Z PHE* 4.6 1.6 - - + -
334Z ASN 3.5 8.4 + - - +
335Z CYS 3.6 6.3 - - - +
336Z GLN 3.1 0.2 - - - -
337Z ALA* 1.3 77.4 - - - +
339Z LYS* 1.3 59.3 + - - +
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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
------------------------------------------------------------
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