Contacts of the helix formed by residues 319 - 340 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312D ALA 2.9 26.6 + - - +
313D TRP* 3.9 5.0 + - - -
316D LYS* 2.7 62.7 + - + +
318D ALA* 1.3 81.8 - - - +
320D LYS* 1.3 66.7 + - - +
321D GLU 3.4 1.6 - - - -
322D ALA* 3.2 11.7 + - + +
323D THR* 2.9 21.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 320 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D GLU* 6.3 0.8 - - - +
61D ILE* 4.0 21.8 - - + +
64D SER* 3.6 22.3 + - - -
317D ALA 3.2 14.9 + - - +
318D ALA 3.0 5.8 + - - +
319D ASN* 1.3 78.4 - - - +
321D GLU* 1.3 69.2 + - + +
323D THR* 3.0 3.3 + - - -
324D GLN* 2.9 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 321 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318D ALA 4.8 1.2 + - - -
319D ASN 3.4 0.2 - - - -
320D LYS* 1.3 82.2 - - + +
322D ALA* 1.3 56.1 + - - +
324D GLN* 2.7 11.9 + - - +
325D GLU* 2.6 59.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 322 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312D ALA* 3.2 36.2 - - + +
319D ASN* 3.2 17.1 + - + +
321D GLU* 1.3 80.5 - - - +
323D THR* 1.3 62.9 + - - +
325D GLU* 3.2 15.1 + - - +
326D ALA* 3.3 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 323 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D PHE* 3.5 26.5 - - + -
61D ILE* 3.5 23.1 - - + -
62D LEU* 4.8 4.0 - - + -
309D ALA* 3.1 45.7 + - + +
312D ALA* 3.8 0.4 - - - +
313D TRP* 2.7 35.6 - - + +
319D ASN 2.9 8.5 + - - -
320D LYS 3.4 7.9 - - - -
322D ALA* 1.3 76.3 - - - +
324D GLN* 1.3 56.6 - - - +
327D PHE* 3.2 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 324 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D ILE* 2.7 41.3 + - + +
62D LEU* 5.5 1.1 - - + -
64D SER* 3.1 20.2 + - - -
65D VAL* 3.5 28.6 - - + +
320D LYS* 2.9 38.3 + - - +
321D GLU* 2.7 17.2 + - - +
323D THR* 1.3 72.4 - - - +
325D GLU* 1.3 58.2 + - + +
326D ALA 3.3 0.2 - - - -
327D PHE* 4.5 5.2 - - - -
328D MET* 2.8 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 325 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321D GLU* 2.6 52.3 + - + +
322D ALA* 3.2 8.3 + - - +
324D GLN* 1.3 71.8 - - - +
326D ALA* 1.3 60.2 + - - +
328D MET* 3.7 5.7 - - - +
329D LYS* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 326 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D SER* 3.6 16.2 - - - +
309D ALA* 3.2 34.3 - - - +
312D ALA* 4.7 2.5 - - + -
322D ALA 3.3 8.6 + - - +
324D GLN 3.3 0.2 - - - -
325D GLU* 1.3 79.0 - - - +
327D PHE* 1.3 60.3 + - - +
329D LYS* 2.9 23.8 + - + +
330D ARG* 2.9 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 327 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D LEU* 3.6 42.6 - - + -
62D LEU* 3.5 48.9 - - + -
63D PHE* 6.1 0.2 - + - -
65D VAL* 4.0 9.4 - - + -
69D ILE* 3.1 35.4 - - + +
73D ILE* 4.7 3.6 - - + -
305D LEU* 3.8 24.2 - - + -
309D ALA* 3.5 12.7 - - + +
323D THR 3.2 15.7 + - - +
324D GLN* 4.3 3.6 - - - +
326D ALA* 1.3 78.8 - - - +
328D MET* 1.3 62.6 - - - +
329D LYS 3.2 0.5 + - - -
331D ALA* 3.3 30.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 328 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D VAL* 3.5 24.9 - - + -
66D ASP* 4.9 9.0 - - + -
68D SER* 3.6 22.9 - - - +
69D ILE* 4.7 18.6 - - + -
324D GLN 2.8 23.4 + - - +
325D GLU* 3.8 7.6 - - - +
327D PHE* 1.3 77.9 - - - +
329D LYS* 1.3 57.4 + - - +
331D ALA* 5.2 1.3 - - - +
332D MET* 3.2 65.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 329 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D SER* 6.0 1.3 - - - +
325D GLU 2.9 18.4 + - - +
326D ALA* 2.9 13.4 + - + +
328D MET* 1.3 76.2 - - - +
330D ARG* 1.3 86.0 + - - +
332D MET* 3.1 8.6 + - - +
333D ALA* 3.0 21.0 + - + +
342D TYR* 5.9 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 330 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276D GLU* 2.8 48.2 + - - +
277D GLU* 4.1 3.8 + - - +
279D ALA* 5.4 0.2 - - - +
280D THR* 2.4 31.1 + - - -
304D ALA 3.4 16.8 + - - +
305D LEU* 3.5 26.2 - - + +
308D SER* 3.8 9.4 - - - +
326D ALA 2.9 20.2 + - - +
327D PHE 4.3 0.7 - - - +
329D LYS* 1.3 88.1 - - - +
331D ALA* 1.3 54.8 + - - +
332D MET 2.7 5.5 + - - -
333D ALA* 2.7 42.2 + - - +
334D ASN* 3.0 22.5 + - - +
342D TYR* 4.2 13.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 331 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D ILE* 4.9 4.3 - - + -
72D SER* 2.7 32.9 + - - +
73D ILE* 3.3 36.6 - - + -
299D PHE* 4.5 1.0 - - - -
305D LEU* 3.2 15.3 - - + +
327D PHE* 3.3 21.3 + - + +
328D MET* 5.2 1.3 - - - +
330D ARG* 1.3 76.5 - - - +
332D MET* 1.3 55.1 + - - +
334D ASN* 4.2 4.3 - - - +
335D CYS 3.5 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 332 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D SER* 5.0 4.5 - - - +
69D ILE* 6.3 0.7 - - - -
72D SER* 3.3 16.8 - - - +
328D MET* 3.2 66.5 + - + +
329D LYS* 3.1 8.2 + - - +
330D ARG 2.8 0.6 - - - -
331D ALA* 1.3 78.6 - - - +
333D ALA* 1.3 64.4 + - - +
335D CYS* 3.5 4.3 + - - +
336D GLN* 3.2 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 333 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D THR* 4.5 2.5 - - - +
329D LYS* 3.0 12.9 + - + +
330D ARG* 2.7 33.1 + - - +
332D MET* 1.3 69.8 - - - +
334D ASN* 1.3 52.3 + - - +
336D GLN* 2.8 12.6 - - - +
337D ALA* 2.6 33.4 + - - +
342D TYR* 3.7 28.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 334 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D THR* 3.6 17.1 + - - -
283D LEU* 4.4 3.1 - - - +
299D PHE* 3.4 29.0 - - + -
301D TYR* 3.0 35.4 - - - -
304D ALA 4.4 1.4 + - - -
305D LEU* 3.5 18.6 - - - +
330D ARG* 3.0 39.2 + - - +
331D ALA* 4.6 0.9 - - - +
333D ALA* 1.3 71.2 - - - +
335D CYS* 1.3 56.9 + - - +
336D GLN 3.0 1.6 - - - -
337D ALA* 3.4 7.0 - - + +
338D ALA* 2.5 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 335 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ASN 3.9 14.8 - - - -
26D GLY 3.0 23.7 - - - +
71D GLN* 3.9 14.6 - - - -
72D SER* 3.4 28.5 - - - +
299D PHE* 3.8 2.8 - - - -
331D ALA 3.5 10.0 + - - +
332D MET 3.6 4.3 - - - +
333D ALA 3.2 0.4 - - - -
334D ASN* 1.3 78.6 - - - +
336D GLN* 1.3 61.8 + - - +
339D LYS* 3.1 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 336 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332D MET 3.2 12.2 + - - +
333D ALA* 2.8 17.5 + - - +
335D CYS* 1.3 84.2 - - - +
337D ALA* 1.3 56.3 + - - -
339D LYS* 2.9 9.0 + - - +
340D GLY 2.8 25.1 + - - -
341D GLN* 2.9 61.6 + - - +
342D TYR* 4.5 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 337 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D THR* 3.5 45.5 - - + +
283D LEU* 3.7 10.4 - - + +
284D ASN* 3.3 31.6 + - - +
287D ASN* 3.1 10.2 - - - +
333D ALA 2.6 12.4 + - - +
334D ASN* 3.7 8.5 - - - +
336D GLN* 1.3 72.2 - - - +
338D ALA* 1.3 61.8 + - - +
340D GLY 3.3 4.9 + - - -
342D TYR* 4.6 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 338 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D GLY* 3.0 33.7 - - - +
283D LEU* 3.9 6.7 - - - +
287D ASN* 2.4 29.3 + - - +
297D LEU 4.1 5.0 + - - +
298D SER* 4.5 12.3 - - - -
299D PHE* 4.3 10.5 - - + -
334D ASN 2.5 22.6 + - - +
335D CYS 3.4 0.4 - - - +
337D ALA* 1.3 68.5 - - - +
339D LYS* 1.3 60.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 339 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ASN* 3.3 50.4 - - - +
26D GLY* 3.7 4.6 - - - +
287D ASN* 3.8 9.4 + - - +
296D LYS* 4.8 6.9 - - - +
335D CYS* 3.1 20.5 + - - +
336D GLN* 2.9 12.0 + - - +
338D ALA* 1.3 80.4 - - - +
340D GLY* 1.3 54.9 + - - +
341D GLN* 2.9 29.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 340 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D ASN* 2.9 16.6 - - - -
287D ASN* 3.8 13.9 - - - -
288D LEU* 3.7 25.7 - - - +
336D GLN 2.8 6.3 + - - -
337D ALA 3.3 6.6 + - - -
339D LYS* 1.3 79.5 - - - +
341D GLN* 1.3 65.9 + - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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