Contacts of the helix formed by residues 319 - 340 (chain W) 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 W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311W ALA 5.4 0.2 + - - -
312W ALA* 3.0 25.5 + - - +
313W TRP* 3.9 5.6 + - - -
316W LYS* 2.7 61.4 + - + +
318W ALA* 1.3 81.7 - - - +
320W LYS* 1.3 66.0 + - - +
321W GLU 3.4 1.8 - - - -
322W ALA* 3.2 12.9 + - + +
323W THR* 2.9 20.4 + - - -
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Residues in contact with LYS 320 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60W GLU* 5.5 2.0 + - - +
61W ILE* 4.6 22.3 - - + +
64W SER* 3.5 21.8 + - - -
317W ALA 3.2 14.0 + - - +
318W ALA 3.0 7.1 + - - +
319W ASN* 1.3 77.8 - - - +
321W GLU* 1.3 69.7 + - + +
323W THR* 3.0 3.4 + - - -
324W GLN* 2.9 46.2 + - - +
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Residues in contact with GLU 321 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318W ALA 4.8 1.2 + - - -
319W ASN 3.4 0.2 - - - -
320W LYS* 1.3 81.5 - - + +
322W ALA* 1.3 56.0 + - - +
324W GLN* 2.7 12.0 + - - +
325W GLU* 2.6 59.0 + - + +
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Residues in contact with ALA 322 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312W ALA* 3.2 36.0 - - + +
319W ASN* 3.2 17.8 + - + +
321W GLU* 1.3 79.4 - - - +
323W THR* 1.3 63.1 + - - +
325W GLU* 3.3 15.5 + - - +
326W ALA* 3.3 9.7 + - - +
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Residues in contact with THR 323 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58W PHE* 3.4 26.5 - - + -
61W ILE* 3.5 21.8 - - + -
62W LEU* 4.7 4.3 - - + -
309W ALA* 3.1 47.1 + - + +
312W ALA* 4.0 0.4 - - - -
313W TRP* 2.7 36.9 - - + +
319W ASN 2.9 8.2 + - - -
320W LYS 3.4 8.1 - - - -
322W ALA* 1.3 75.3 - - - +
324W GLN* 1.3 58.1 + - - +
327W PHE* 3.2 9.5 + - - +
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Residues in contact with GLN 324 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61W ILE* 2.6 41.6 + - + +
62W LEU* 5.5 1.3 - - - -
64W SER* 3.0 20.2 + - - -
65W VAL* 3.5 28.8 - - + +
320W LYS* 2.9 39.0 + - - +
321W GLU* 2.7 17.5 + - - +
323W THR* 1.3 71.8 - - - +
325W GLU* 1.3 59.0 + - - +
327W PHE* 4.5 5.4 - - - -
328W MET* 2.8 34.2 + - - +
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Residues in contact with GLU 325 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321W GLU* 2.6 53.7 + - + +
322W ALA* 3.3 8.9 + - - +
324W GLN* 1.3 73.3 - - - +
326W ALA* 1.3 60.1 + - - +
328W MET* 3.7 4.9 - - - +
329W LYS* 2.9 28.5 + - - +
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Residues in contact with ALA 326 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308W SER* 3.5 17.3 - - - +
309W ALA* 3.2 33.7 - - - +
312W ALA* 4.6 2.2 - - + -
322W ALA 3.3 8.3 + - - +
325W GLU* 1.3 77.9 - - - +
327W PHE* 1.3 65.9 + - - +
329W LYS* 2.9 11.2 + - - +
330W ARG* 2.9 28.9 + - - +
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Residues in contact with PHE 327 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30W LEU* 3.5 43.3 - - + -
62W LEU* 3.5 48.2 - - + -
63W PHE* 6.0 0.7 - + - -
65W VAL* 4.3 9.0 - - + -
69W ILE* 3.1 34.3 - - + -
73W ILE* 4.7 3.4 - - + -
305W LEU* 3.7 24.2 - - + -
306W GLN* 5.3 0.4 - - - -
309W ALA* 3.4 12.5 - - + +
323W THR 3.2 16.2 + - - +
324W GLN* 4.3 3.6 - - - +
326W ALA* 1.3 77.9 - - - +
328W MET* 1.3 64.2 + - - +
329W LYS 3.2 0.9 + - - -
331W ALA* 3.3 28.3 + - + +
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Residues in contact with MET 328 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65W VAL* 3.4 25.4 - - + -
66W ASP* 4.9 9.9 - - + -
68W SER* 3.6 22.9 - - - +
69W ILE* 4.6 18.4 - - - -
324W GLN 2.8 23.4 + - - +
325W GLU* 3.8 7.9 - - - +
327W PHE* 1.3 79.1 - - - +
329W LYS* 1.3 56.7 + - - +
331W ALA* 4.7 1.5 - - - +
332W MET* 3.2 65.5 + - + +
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Residues in contact with LYS 329 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308W SER* 6.0 1.3 - - - +
325W GLU 2.9 19.0 + - - +
326W ALA* 2.9 12.2 + - - +
328W MET* 1.3 77.4 - - - +
330W ARG* 1.3 86.1 + - - +
332W MET* 3.1 8.6 + - - +
333W ALA* 3.0 20.7 + - + +
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Residues in contact with ARG 330 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276W GLU* 2.8 56.1 + - - +
277W GLU* 4.1 9.6 + - - +
280W THR* 2.4 30.0 + - - -
304W ALA 3.4 10.5 + - - +
305W LEU* 3.6 24.9 - - + +
308W SER* 3.8 9.4 - - - +
326W ALA 2.9 21.9 + - - +
327W PHE 4.3 0.4 - - - +
329W LYS* 1.3 86.2 - - - +
331W ALA* 1.3 56.0 + - - +
332W MET 2.8 4.3 - - - -
333W ALA* 2.7 41.8 + - - +
334W ASN* 2.9 23.1 + - - +
342W TYR* 4.7 5.7 + - - -
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Residues in contact with ALA 331 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69W ILE* 4.9 4.7 - - + -
72W SER* 2.7 28.6 - - - +
73W ILE* 3.3 36.6 - - + -
299W PHE* 4.5 0.6 - - - -
305W LEU* 3.1 16.2 - - + +
327W PHE* 3.3 20.4 + - + +
328W MET* 5.2 1.1 - - - +
330W ARG* 1.3 76.8 - - - +
332W MET* 1.3 58.8 + - - +
334W ASN* 4.2 4.7 - - - +
335W CYS 3.4 9.4 + - - -
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Residues in contact with MET 332 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68W SER* 5.0 5.2 - - - +
69W ILE* 6.2 0.7 - - - -
72W SER* 3.3 17.2 - - - +
328W MET* 3.2 66.7 + - + +
329W LYS* 3.1 7.5 + - - +
330W ARG 2.8 0.8 - - - -
331W ALA* 1.3 78.3 - - - +
333W ALA* 1.3 66.4 + - - +
334W ASN 3.4 0.2 - - - -
335W CYS* 3.5 4.7 + - - +
336W GLN* 3.2 21.5 + - - +
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Residues in contact with ALA 333 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280W THR* 4.5 2.0 - - - +
329W LYS* 3.0 12.1 + - + +
330W ARG* 2.7 33.0 + - - +
332W MET* 1.3 70.2 - - - +
334W ASN* 1.3 53.0 + - - +
336W GLN* 2.8 12.0 - - - +
337W ALA* 2.6 33.9 + - - +
342W TYR* 3.8 28.1 - - + -
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Residues in contact with ASN 334 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279W ALA 4.4 0.2 - - - +
280W THR* 3.6 17.9 + - - -
283W LEU* 4.4 2.1 - - - +
299W PHE* 3.4 28.5 - - + -
301W TYR* 2.9 35.1 - - - -
304W ALA 4.4 1.8 + - - -
305W LEU* 3.5 18.2 - - - +
330W ARG* 2.9 39.8 + - - +
331W ALA* 4.6 1.1 - - - +
333W ALA* 1.3 70.7 - - - +
335W CYS* 1.3 58.0 + - - +
336W GLN 3.0 1.6 - - - -
337W ALA* 3.7 6.8 - - + +
338W ALA* 2.5 35.5 + - - +
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Residues in contact with CYS 335 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25W ASN 3.8 14.8 - - - -
26W GLY 3.0 24.6 - - - +
71W GLN* 3.9 15.0 - - - -
72W SER* 3.4 28.5 - - - +
299W PHE* 3.8 3.3 - - - -
331W ALA 3.4 10.5 + - - +
332W MET 3.6 4.3 - - - +
333W ALA 3.2 0.6 - - - -
334W ASN* 1.3 77.3 - - - +
336W GLN* 1.3 62.9 + - - +
339W LYS* 3.1 30.6 + - - +
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Residues in contact with GLN 336 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332W MET 3.2 12.4 + - - +
333W ALA* 2.8 16.4 - - - +
335W CYS* 1.3 84.3 - - - +
337W ALA* 1.3 50.8 + - - +
339W LYS* 2.9 8.9 + - - +
340W GLY 2.8 30.7 + - - -
341W GLN* 2.9 45.5 + - - +
342W TYR* 3.8 22.9 - - + +
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Residues in contact with ALA 337 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280W THR* 3.4 45.5 - - + +
283W LEU* 3.6 10.6 - - + +
284W ASN* 3.2 30.3 + - + +
287W ASN* 3.1 9.5 - - - +
333W ALA 2.6 12.3 + - - +
334W ASN* 3.2 9.2 + - - +
336W GLN* 1.3 72.9 - - - +
338W ALA* 1.3 61.8 + - - +
340W GLY 3.3 4.5 + - - -
342W TYR* 4.0 1.7 - - - +
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Residues in contact with ALA 338 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26W GLY* 3.0 34.6 - - - +
283W LEU* 3.9 6.7 - - - +
287W ASN* 2.3 31.7 + - - +
297W LEU 4.1 4.4 + - - +
298W SER* 4.5 11.4 - - - -
299W PHE* 4.3 11.2 - - + -
334W ASN 2.5 22.4 + - - +
335W CYS 3.4 0.4 - - - +
337W ALA* 1.3 68.7 - - - +
339W LYS* 1.3 58.7 + - - +
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Residues in contact with LYS 339 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25W ASN* 3.3 48.1 - - - +
26W GLY* 3.8 4.2 - - - +
287W ASN* 3.7 10.2 - - - +
296W LYS* 5.1 5.4 - - - +
335W CYS* 3.1 23.2 + - - +
336W GLN* 2.9 12.8 + - - +
338W ALA* 1.3 79.3 - - - +
340W GLY* 1.3 56.0 + - - +
341W GLN* 2.8 37.5 + - + +
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Residues in contact with GLY 340 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284W ASN* 2.8 24.1 + - - +
287W ASN* 3.9 12.8 - - - -
288W LEU* 3.9 23.8 - - - +
336W GLN 2.8 3.4 + - - -
337W ALA 3.3 7.5 + - - -
339W LYS* 1.3 78.2 - - - +
341W GLN* 1.3 65.7 + - - +
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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
------------------------------------------------------------
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