Contacts of the helix formed by residues 319 - 339 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B ALA 3.0 27.6 + - - +
313B TRP* 3.4 13.4 + - - -
316B LYS* 2.8 41.5 + - - +
318B ALA* 1.3 87.1 - - - +
320B LYS* 1.3 63.9 + - - -
321B GLU* 2.9 6.0 + - - +
322B ALA* 3.2 10.3 + - + +
323B THR* 3.0 22.0 + - - -
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Residues in contact with LYS 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ILE* 4.0 30.6 - - + +
64B SER* 3.3 25.9 + - - -
313B TRP* 5.0 0.2 - - - -
316B LYS 4.4 0.2 + - - -
317B ALA* 3.7 13.9 + - - +
318B ALA 3.3 4.6 + - - +
319B ASN* 1.3 75.0 - - - +
321B GLU* 1.3 64.8 + - - +
323B THR* 3.6 1.4 - - - -
324B GLN* 3.1 48.8 + - - +
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Residues in contact with GLU 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ALA 4.5 6.0 + - - +
319B ASN* 2.9 2.0 - - - -
320B LYS* 1.3 80.9 - - - +
322B ALA* 1.3 69.3 + - - +
324B GLN* 3.2 13.3 + - - +
325B GLU* 3.1 34.2 + - - +
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Residues in contact with ALA 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ALA* 4.2 18.3 - - + +
319B ASN* 3.2 20.8 + - + +
321B GLU* 1.3 77.0 - - - +
323B THR* 1.3 57.7 + - - +
325B GLU* 2.7 39.4 + - - +
326B ALA* 3.2 5.4 + - - +
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Residues in contact with THR 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B PHE* 3.9 14.4 - - + -
61B ILE* 3.5 23.1 - - + -
62B LEU* 4.7 4.3 - - + -
309B ALA* 3.0 30.1 + - + +
312B ALA* 4.3 5.6 - - - +
313B TRP* 2.7 35.6 - - + +
319B ASN 3.0 10.4 + - - -
320B LYS* 3.6 5.4 - - - -
322B ALA* 1.3 78.1 - - - +
324B GLN* 1.3 66.1 + - - +
325B GLU 2.9 2.1 + - - -
326B ALA* 3.1 2.3 + - - +
327B PHE* 3.1 18.2 + - - +
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Residues in contact with GLN 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ILE* 3.5 24.7 - - + +
62B LEU* 5.3 0.7 - - - -
64B SER* 3.1 20.1 + - - -
65B VAL* 3.1 39.8 - - + +
66B ASP* 4.3 2.8 + - - +
320B LYS* 3.1 45.5 + - - +
321B GLU* 3.2 8.6 + - - +
323B THR* 1.3 80.0 - - - +
325B GLU* 1.3 61.2 + - - +
327B PHE* 4.0 5.6 - - - -
328B MET* 3.1 29.7 + - - +
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Residues in contact with GLU 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B GLU* 3.1 42.6 + - - +
322B ALA* 2.7 25.0 + - - +
324B GLN* 1.3 68.5 - - - +
326B ALA* 1.3 53.3 + - - +
328B MET* 3.1 9.4 + - - +
329B LYS* 2.7 36.8 + - - +
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Residues in contact with ALA 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B SER* 3.5 26.5 - - - +
309B ALA* 3.6 17.3 - - - +
312B ALA* 5.1 6.7 - - + -
322B ALA 3.2 4.5 + - - +
323B THR 3.1 3.6 + - - +
325B GLU* 1.3 79.1 - - - +
327B PHE* 1.3 63.2 + - - +
329B LYS* 3.2 13.5 - - + +
330B ARG* 2.9 26.9 + - - +
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Residues in contact with PHE 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LEU* 3.6 40.6 - - + -
62B LEU* 3.9 34.1 - - + -
63B PHE* 6.2 0.4 - + - -
65B VAL* 4.0 22.0 - - + -
69B ILE* 3.7 26.5 - - + -
73B ILE* 4.2 11.0 - - + -
305B LEU* 3.8 32.1 - - + -
306B GLN* 5.4 0.4 - - + -
309B ALA* 3.5 18.2 - - + +
323B THR 3.1 12.0 + - - +
324B GLN* 4.0 4.5 - - - +
326B ALA* 1.3 75.6 - - - +
328B MET* 1.3 55.5 + - - +
330B ARG* 2.8 4.3 + - - -
331B ALA* 2.6 36.4 + - + +
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Residues in contact with MET 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL* 3.3 31.4 - - + -
66B ASP* 4.7 9.0 - - + +
68B SER* 3.1 28.7 - - - +
69B ILE* 3.5 28.7 - - - -
324B GLN 3.1 11.8 + - - +
325B GLU* 3.3 7.6 - - - +
327B PHE* 1.3 78.1 - - - +
329B LYS* 1.3 56.1 + - - +
331B ALA* 3.4 4.9 - - - +
332B MET* 2.9 68.1 + - + +
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Residues in contact with LYS 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B SER* 5.7 0.4 - - - +
325B GLU 2.7 17.0 + - - +
326B ALA* 3.2 17.5 - - + +
327B PHE 2.8 0.8 + - - -
328B MET* 1.3 73.3 - - - +
330B ARG* 1.3 87.5 + - - +
332B MET* 4.0 7.7 - - - +
333B ALA* 3.0 31.3 + - + +
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Residues in contact with ARG 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B GLU* 3.3 54.7 + - - +
277B GLU* 3.7 20.1 + - - -
280B THR* 2.8 32.5 + - - +
304B ALA 4.0 5.6 + - - +
305B LEU* 3.7 22.2 - - + +
308B SER* 3.7 5.8 - - - +
326B ALA 2.9 15.0 + - - +
327B PHE 2.8 7.9 + - - +
329B LYS* 1.3 105.8 - - - +
331B ALA* 1.3 62.8 + - - +
333B ALA* 3.5 23.2 - - - +
334B ASN* 3.1 31.5 + - - +
342B TYR* 4.7 3.6 + - - -
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Residues in contact with ALA 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ILE* 3.3 32.5 - - + -
72B SER* 2.9 19.8 - - - -
73B ILE* 4.0 14.1 - - + -
299B PHE* 4.5 5.7 - - - -
305B LEU* 3.6 13.4 - - + +
327B PHE* 2.6 24.1 + - + +
328B MET 3.4 3.1 - - - +
330B ARG* 1.3 74.3 - - - +
332B MET* 1.3 62.5 + - + +
335B CYS 3.6 8.5 + - - -
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Residues in contact with MET 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B SER 5.8 2.0 - - - +
69B ILE* 6.6 0.2 - - - -
72B SER* 3.1 17.7 - - - +
328B MET* 2.9 62.0 + - + +
329B LYS* 4.0 6.1 - - - +
331B ALA* 1.3 73.6 - - + +
333B ALA* 1.3 67.9 + - - +
335B CYS* 2.8 16.0 + - - +
336B GLN* 3.0 18.1 + - + +
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Residues in contact with ALA 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B THR* 3.8 3.4 - - - +
329B LYS* 3.0 21.4 + - + +
330B ARG* 3.5 33.2 - - - +
332B MET* 1.3 74.8 - - - +
334B ASN* 1.3 62.0 + - - +
336B GLN* 3.2 23.7 + - - +
337B ALA 3.2 8.1 + - - -
342B TYR* 3.6 19.7 - - + -
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Residues in contact with ASN 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B GLU 5.0 1.0 + - - -
279B ALA 4.2 0.2 - - - +
280B THR* 2.7 32.0 + - - -
283B LEU* 4.2 1.3 - - + +
299B PHE* 3.9 27.5 - - + -
301B TYR* 3.3 37.2 - - - -
304B ALA 4.5 6.5 + - - -
305B LEU* 4.0 12.9 - - - +
330B ARG* 3.1 24.2 + - - +
333B ALA* 1.3 74.6 - - - +
335B CYS* 1.3 68.1 + - - +
336B GLN 3.1 2.2 - - - -
337B ALA* 3.0 9.4 + - - +
338B ALA* 2.9 21.1 + - - +
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Residues in contact with CYS 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ASN 3.5 11.2 - - - -
26B GLY 3.0 32.8 - - - +
71B GLN 3.9 13.5 - - - -
72B SER* 3.8 23.1 - - - +
299B PHE* 4.1 3.0 - - - -
331B ALA 3.6 4.0 + - - +
332B MET* 2.8 10.2 + - - +
334B ASN* 1.3 76.7 - - - +
336B GLN* 1.3 65.3 + - + +
338B ALA* 3.0 17.7 + - - +
339B LYS* 3.2 22.1 + - - +
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Residues in contact with GLN 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B MET* 3.0 14.0 + - + +
333B ALA* 3.3 14.9 - - - +
334B ASN 3.1 0.2 - - - -
335B CYS* 1.3 78.9 - - + +
337B ALA* 1.3 49.8 + - - +
339B LYS* 2.6 31.5 + - + +
340B GLY 2.8 13.0 + - - -
341B GLN* 2.9 40.9 + - + +
342B TYR* 3.7 19.4 - - + +
343B VAL* 5.4 3.2 + - - +
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Residues in contact with ALA 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B THR* 3.3 42.2 - - + +
283B LEU* 3.0 29.2 - - + +
284B ASN* 3.2 23.1 - - + +
287B ASN* 3.2 2.4 - - - +
333B ALA 3.2 2.6 + - - -
334B ASN* 3.0 11.7 + - - +
336B GLN* 1.3 77.5 - - - +
338B ALA* 1.3 57.3 + - - +
340B GLY 2.9 13.3 + - - -
342B TYR* 3.7 1.4 - - - +
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Residues in contact with ALA 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLY* 3.3 30.2 - - - +
283B LEU* 4.2 7.4 - - + +
287B ASN* 2.7 31.1 + - - +
297B LEU 4.0 11.2 + - - +
298B SER* 4.7 7.0 - - - -
299B PHE* 4.8 1.3 - - + -
334B ASN 2.9 10.0 + - - +
335B CYS 3.1 12.3 - - - +
336B GLN 3.0 0.2 - - - -
337B ALA* 1.3 72.6 - - - +
339B LYS* 1.3 58.4 + - - +
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Residues in contact with LYS 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ASN* 3.7 35.2 + - - +
26B GLY* 4.3 5.6 - - - +
287B ASN* 4.8 3.4 - - - -
288B LEU* 5.1 1.9 - - - +
335B CYS* 3.2 26.0 + - - +
336B GLN* 2.6 17.6 + - + +
338B ALA* 1.3 74.2 - - - +
340B GLY* 1.3 54.6 + - - +
341B GLN* 2.7 55.9 + - + +
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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