Contacts of the helix formed by residues 319 - 340 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312X ALA 3.4 26.0 + - - +
313X TRP* 3.6 7.7 + - - -
316X LYS* 2.7 48.9 + - - +
318X ALA* 1.3 83.5 - - - +
320X LYS* 1.3 62.8 + - - +
321X GLU 3.3 2.5 - - - -
322X ALA* 4.1 15.6 - - + +
323X THR* 3.0 26.0 + - - +
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Residues in contact with LYS 320 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60X GLU* 5.0 10.1 + - - +
61X ILE* 3.8 28.3 - - + +
64X SER* 3.5 26.3 + - - -
313X TRP* 5.2 0.2 - - - -
317X ALA 4.4 12.4 + - - +
318X ALA 3.3 4.6 + - - -
319X ASN* 1.3 76.0 - - - +
321X GLU* 1.3 62.6 + - + +
323X THR* 4.7 0.2 - - - -
324X GLN* 2.9 48.4 + - - +
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Residues in contact with GLU 321 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318X ALA 5.3 0.2 + - - -
319X ASN 3.3 0.4 - - - -
320X LYS* 1.3 79.1 - - + +
322X ALA* 1.3 67.9 + - - +
323X THR 3.0 1.6 - - - -
324X GLN* 2.8 25.5 + - - +
325X GLU* 3.1 20.9 + - + +
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Residues in contact with ALA 322 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312X ALA* 3.7 17.2 - - + +
319X ASN* 3.6 23.4 + - + +
321X GLU* 1.3 78.4 - - - +
323X THR* 1.3 59.4 + - - +
325X GLU* 3.6 20.0 - - - +
326X ALA* 3.9 3.8 + - - +
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Residues in contact with THR 323 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58X PHE* 4.0 10.5 - - + -
61X ILE* 3.8 21.5 - - + -
62X LEU* 5.2 1.6 - - + -
309X ALA* 2.9 48.5 - - + +
312X ALA* 3.1 7.8 - - - -
313X TRP* 2.7 45.7 + - + +
319X ASN 3.0 15.3 + - - -
320X LYS 3.9 2.2 - - - -
321X GLU 2.8 1.6 + - - -
322X ALA* 1.3 74.7 - - - +
324X GLN* 1.3 63.8 + - - +
325X GLU 3.1 2.7 + - - -
326X ALA 3.5 3.5 + - - -
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Residues in contact with GLN 324 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61X ILE* 2.7 41.2 + - + +
62X LEU* 5.4 1.8 - - - -
64X SER* 3.4 7.3 + - - -
65X VAL* 3.2 38.8 - - + +
66X ASP* 6.2 0.2 - - - -
320X LYS* 2.9 40.7 + - - +
321X GLU* 2.8 15.6 + - - +
323X THR* 1.3 70.8 - - - +
325X GLU* 1.3 56.7 + - - +
327X PHE* 3.4 8.5 + - - +
328X MET* 2.8 38.4 + - - +
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Residues in contact with GLU 325 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321X GLU* 3.1 22.6 + - + +
322X ALA* 3.6 13.5 - - - +
323X THR 3.1 0.2 - - - -
324X GLN* 1.3 72.9 - - - +
326X ALA* 1.3 54.4 + - - +
327X PHE 2.7 15.4 + - - -
328X MET* 2.7 21.4 + - - +
329X LYS* 2.8 19.6 + - - +
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Residues in contact with ALA 326 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305X LEU 4.5 0.5 - - - +
308X SER* 3.0 32.2 + - - +
309X ALA* 3.2 23.8 - - - +
312X ALA* 4.7 2.9 - - + -
322X ALA 3.9 7.4 + - - +
323X THR 3.5 1.9 + - - +
325X GLU* 1.3 78.3 - - - +
327X PHE* 1.3 55.9 + - - +
329X LYS* 4.2 9.0 - - - -
330X ARG* 3.0 29.2 - - - +
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Residues in contact with PHE 327 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30X LEU* 3.9 38.6 - - + -
62X LEU* 3.7 41.7 - - + -
65X VAL* 4.5 7.2 - - + -
69X ILE* 3.2 36.6 - - + -
73X ILE* 4.4 7.2 - - + -
305X LEU* 3.5 32.3 - - + -
306X GLN* 5.4 1.1 - - + -
309X ALA* 3.6 19.1 - - + +
323X THR 4.1 1.6 - - - +
324X GLN* 3.4 9.4 + - - +
325X GLU 2.7 4.8 + - - -
326X ALA* 1.3 76.1 - - - +
328X MET* 1.3 61.7 + - - +
329X LYS 3.1 1.8 - - - -
331X ALA* 3.0 29.0 + - + +
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Residues in contact with MET 328 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65X VAL* 3.6 22.7 - - + -
66X ASP* 4.8 10.3 - - + +
68X SER* 2.8 31.0 - - - +
69X ILE* 4.1 24.7 - - - -
324X GLN 2.8 20.1 + - - +
325X GLU* 2.7 18.9 + - - +
327X PHE* 1.3 74.6 - - + +
329X LYS* 1.3 56.4 + - - +
331X ALA* 3.9 3.8 - - - +
332X MET* 3.2 65.7 + - + +
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Residues in contact with LYS 329 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325X GLU 2.8 15.2 + - - +
326X ALA* 4.5 6.5 - - - +
328X MET* 1.3 75.3 - - - +
330X ARG* 1.3 74.4 + - - +
331X ALA 3.0 1.1 - - - -
332X MET* 3.1 8.8 + - - +
333X ALA* 2.6 39.3 + - + +
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Residues in contact with ARG 330 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276X GLU* 2.9 52.2 + - - +
277X GLU* 3.8 15.0 + - - +
280X THR* 2.5 35.2 + - - +
304X ALA 4.1 5.6 - - - +
305X LEU* 3.4 24.4 - - + +
308X SER* 4.4 1.8 - - - -
326X ALA* 3.0 22.2 - - - +
327X PHE 3.6 2.1 + - - +
329X LYS* 1.3 98.2 - - - +
331X ALA* 1.3 62.9 + - - +
333X ALA* 3.7 17.1 - - - +
334X ASN* 2.9 32.0 + - - +
342X TYR* 4.6 3.6 + - - -
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Residues in contact with ALA 331 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69X ILE* 3.3 29.6 - - + -
72X SER* 2.8 22.5 + - - -
73X ILE* 4.3 11.4 - - + -
299X PHE* 4.5 4.5 - - - -
305X LEU* 3.6 10.3 - - + +
327X PHE* 3.0 21.4 + - + +
328X MET 3.9 4.3 - - - +
330X ARG* 1.3 80.6 - - - +
332X MET* 1.3 61.5 + - + +
334X ASN* 4.1 1.3 - - - -
335X CYS* 3.4 11.8 + - - +
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Residues in contact with MET 332 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68X SER* 5.3 7.6 - - - +
69X ILE* 6.3 0.4 - - - -
71X GLN* 6.5 0.2 - - + -
72X SER* 3.0 16.6 - - - +
328X MET* 3.2 54.7 + - + +
329X LYS* 3.1 7.6 + - - +
331X ALA* 1.3 74.8 - - + +
333X ALA* 1.3 67.0 + - - +
335X CYS* 3.0 11.1 + - - +
336X GLN* 3.1 22.3 + - + +
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Residues in contact with ALA 333 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280X THR* 3.6 7.8 - - + +
329X LYS* 2.6 24.0 + - + +
330X ARG* 3.4 34.5 - - - +
332X MET* 1.3 71.3 - - - +
334X ASN* 1.3 58.2 + - - +
335X CYS 2.9 5.9 + - - -
336X GLN* 3.0 12.6 + - - +
337X ALA 3.0 17.8 + - - -
342X TYR* 3.9 19.6 - - + -
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Residues in contact with ASN 334 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276X GLU 3.9 1.2 + - - +
280X THR* 2.4 42.6 + - - -
283X LEU* 3.6 1.9 - - - +
299X PHE* 3.1 33.2 - - + -
301X TYR* 3.5 27.7 - - + -
304X ALA 3.8 20.8 + - - -
305X LEU* 3.9 3.6 - - - +
330X ARG* 2.9 30.1 + - - +
331X ALA 4.1 0.2 - - - -
333X ALA* 1.3 75.6 - - - +
335X CYS* 1.3 59.7 + - - +
337X ALA* 3.6 9.4 - - + +
338X ALA 3.5 9.7 + - - -
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Residues in contact with CYS 335 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25X ASN 4.0 5.2 - - - -
26X GLY 2.9 29.2 - - - +
71X GLN 3.9 17.0 - - - -
72X SER* 3.6 12.8 - - - +
299X PHE* 4.3 2.5 - - - -
331X ALA 3.4 14.5 + - - +
332X MET* 3.0 11.8 + - - +
333X ALA 2.9 1.2 + - - -
334X ASN* 1.3 76.6 - - - +
336X GLN* 1.3 65.1 + - + +
338X ALA* 2.9 21.0 + - - +
339X LYS* 3.0 26.6 + - - +
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Residues in contact with GLN 336 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332X MET* 3.3 17.1 + - + +
333X ALA* 3.0 7.6 + - - +
335X CYS* 1.3 75.7 - - + +
337X ALA* 1.3 55.2 + - - +
339X LYS* 2.6 28.7 + - + +
340X GLY 2.7 16.1 + - - -
341X GLN* 3.0 33.1 + - + +
342X TYR* 3.7 29.6 - - - +
343X VAL 5.6 0.2 - - - +
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Residues in contact with ALA 337 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280X THR* 3.2 45.3 - - + +
283X LEU* 3.4 17.3 - - + +
284X ASN* 2.9 33.3 + - - -
287X ASN* 3.7 1.7 - - - +
333X ALA 3.0 4.6 + - - -
334X ASN* 3.6 11.7 - - - -
336X GLN* 1.3 78.1 - - - +
338X ALA* 1.3 59.1 + - - +
339X LYS 3.3 0.7 + - - -
340X GLY 3.3 4.5 + - - -
342X TYR* 3.7 2.9 - - - +
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Residues in contact with ALA 338 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26X GLY* 3.8 23.1 - - - +
283X LEU* 3.6 20.8 - - + +
287X ASN* 2.6 27.1 + - - +
297X LEU 3.8 9.2 - - - +
298X SER* 4.3 10.3 - - - +
299X PHE* 4.7 0.2 - - + -
334X ASN 3.5 5.5 + - - +
335X CYS 2.9 12.3 + - - +
337X ALA* 1.3 78.6 - - - +
339X LYS* 1.3 57.1 + - - +
340X GLY 3.4 0.4 - - - -
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Residues in contact with LYS 339 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25X ASN* 3.7 33.8 + - - +
26X GLY* 4.6 4.9 - - - +
287X ASN* 4.7 2.5 - - - -
335X CYS* 3.0 25.4 + - - +
336X GLN* 2.6 19.3 + - + +
338X ALA* 1.3 80.8 - - - +
340X GLY* 1.3 59.1 + - - -
341X GLN* 3.3 38.8 + - + +
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Residues in contact with GLY 340 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284X ASN* 3.1 19.2 - - - +
287X ASN* 4.2 10.0 - - - +
288X LEU* 3.7 35.9 - - - +
336X GLN 2.7 3.2 + - - -
337X ALA 3.3 7.0 + - - -
338X ALA 3.4 0.8 - - - -
339X LYS* 1.3 80.0 - - - +
341X GLN* 1.3 58.8 + - - +
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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