Contacts of the helix formed by residues 319 - 339 (chain Y) 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 Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312Y ALA 3.1 27.7 + - - +
313Y TRP* 3.4 13.2 + - - -
316Y LYS* 2.8 41.8 + - - +
318Y ALA* 1.3 87.9 - - - +
320Y LYS* 1.3 63.8 + - - -
321Y GLU* 2.9 4.7 + - - +
322Y ALA* 3.2 12.3 + - + +
323Y THR* 3.0 22.4 + - - -
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Residues in contact with LYS 320 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61Y ILE* 3.9 30.3 - - + +
64Y SER* 3.2 26.5 + - - -
313Y TRP* 4.8 0.6 - - - -
316Y LYS 4.4 0.2 + - - -
317Y ALA* 3.7 14.6 + - - +
318Y ALA 3.3 4.0 - - - +
319Y ASN* 1.3 75.7 - - - +
321Y GLU* 1.3 65.7 + - - +
323Y THR* 3.6 2.2 - - - -
324Y GLN* 3.1 48.2 + - - +
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Residues in contact with GLU 321 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318Y ALA 4.5 5.3 + - - +
319Y ASN* 2.9 2.9 - - - -
320Y LYS* 1.3 80.6 - - - +
322Y ALA* 1.3 70.0 + - - +
324Y GLN* 3.2 13.6 + - - +
325Y GLU* 3.1 34.2 + - - +
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Residues in contact with ALA 322 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312Y ALA* 4.2 17.9 - - + +
319Y ASN* 3.2 19.1 + - + +
321Y GLU* 1.3 78.1 - - - +
323Y THR* 1.3 65.5 + - - +
325Y GLU* 2.8 29.9 + - - +
326Y ALA* 3.2 5.2 + - - +
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Residues in contact with THR 323 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58Y PHE* 3.9 14.6 - - + -
61Y ILE* 3.5 22.0 - - + -
62Y LEU* 4.6 4.7 - - + -
309Y ALA* 3.0 27.7 - - + +
312Y ALA* 4.3 6.0 - - - +
313Y TRP* 2.7 34.6 - - + +
319Y ASN 3.0 11.0 + - - -
320Y LYS* 3.6 4.7 - - - -
322Y ALA* 1.3 78.5 - - - +
324Y GLN* 1.3 66.6 + - - +
325Y GLU 2.9 1.6 + - - -
326Y ALA* 3.1 3.5 + - - +
327Y PHE* 3.1 18.0 + - - +
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Residues in contact with GLN 324 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61Y ILE* 3.4 26.9 - - + +
62Y LEU* 5.3 0.9 - - - -
64Y SER* 3.1 26.2 + - - -
65Y VAL* 3.1 33.3 - - + +
66Y ASP* 4.4 2.6 + - - +
320Y LYS* 3.1 44.8 + - - +
321Y GLU* 3.2 8.8 + - - +
323Y THR* 1.3 80.2 - - - +
325Y GLU* 1.3 61.2 + - - +
327Y PHE* 4.0 4.5 - - - -
328Y MET* 3.1 30.2 + - - +
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Residues in contact with GLU 325 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321Y GLU* 3.1 41.7 + - - +
322Y ALA* 2.8 25.0 + - - +
324Y GLN* 1.3 69.5 - - - +
326Y ALA* 1.3 52.5 + - - +
328Y MET* 3.1 8.6 + - - +
329Y LYS* 2.7 36.6 + - - +
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Residues in contact with ALA 326 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308Y SER* 3.5 25.4 - - - +
309Y ALA* 3.7 18.2 - - - +
312Y ALA* 5.0 5.8 - - + -
322Y ALA 3.2 4.6 + - - +
323Y THR 3.1 3.4 + - - +
325Y GLU* 1.3 78.0 - - - +
327Y PHE* 1.3 66.5 + - - +
329Y LYS* 3.2 14.3 - - + +
330Y ARG* 2.9 24.4 + - - +
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Residues in contact with PHE 327 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Y LEU* 3.5 41.3 - - + -
62Y LEU* 3.9 33.2 - - + -
63Y PHE* 5.8 0.9 - + - -
65Y VAL* 4.0 22.4 - - + -
69Y ILE* 3.7 25.6 - - + -
73Y ILE* 4.2 11.2 - - + -
305Y LEU* 3.8 32.5 - - + -
306Y GLN* 5.4 0.2 - - - -
309Y ALA* 3.5 17.6 - - + +
323Y THR 3.1 11.5 + - - +
324Y GLN* 3.9 4.7 - - - +
326Y ALA* 1.3 75.2 - - - +
328Y MET* 1.3 55.5 + - - +
330Y ARG* 2.8 4.9 + - - -
331Y ALA* 2.6 37.0 + - + +
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Residues in contact with MET 328 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65Y VAL* 3.2 30.1 - - + -
66Y ASP* 4.7 9.6 - - + +
68Y SER* 3.1 29.8 - - - +
69Y ILE* 3.6 28.5 - - - -
324Y GLN 3.1 11.4 + - - +
325Y GLU* 3.3 8.5 - - - +
327Y PHE* 1.3 77.7 - - - +
329Y LYS* 1.3 57.1 + - - +
331Y ALA* 3.5 5.6 - - - +
332Y MET* 2.9 67.7 + - + +
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Residues in contact with LYS 329 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308Y SER* 5.7 0.9 - - - +
325Y GLU 2.7 17.4 + - - +
326Y ALA* 3.2 16.2 - - + +
327Y PHE 2.8 0.8 + - - -
328Y MET* 1.3 75.1 - - - +
330Y ARG* 1.3 86.3 + - - +
332Y MET* 4.0 8.0 - - - +
333Y ALA* 2.9 30.9 + - + +
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Residues in contact with ARG 330 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276Y GLU* 3.4 54.7 + - - +
277Y GLU* 3.7 19.1 + - - -
280Y THR* 2.8 32.9 + - - +
304Y ALA 4.0 6.4 + - - +
305Y LEU* 3.7 21.8 - - + +
308Y SER* 3.7 5.4 - - - +
326Y ALA 2.9 14.5 + - - +
327Y PHE 2.8 7.9 + - - +
329Y LYS* 1.3 105.7 - - - +
331Y ALA* 1.3 62.5 + - - +
333Y ALA* 3.5 22.5 - - - +
334Y ASN* 3.1 32.5 + - - +
342Y TYR* 4.9 3.2 + - - -
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Residues in contact with ALA 331 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69Y ILE* 3.3 33.0 - - + -
72Y SER* 2.8 20.2 - - - -
73Y ILE* 4.1 14.6 - - + -
299Y PHE* 4.4 5.0 - - - -
305Y LEU* 3.6 13.6 - - + +
327Y PHE* 2.6 23.0 + - + +
328Y MET 3.5 3.1 - - - +
330Y ARG* 1.3 74.6 - - - +
332Y MET* 1.3 62.3 + - + +
334Y ASN 4.0 0.2 + - - -
335Y CYS 3.6 8.3 + - - -
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Residues in contact with MET 332 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68Y SER 5.8 2.7 - - - +
69Y ILE* 6.2 0.4 - - + -
72Y SER* 3.1 18.6 - - - +
328Y MET* 2.9 62.8 + - + +
329Y LYS* 4.0 6.5 - - - +
331Y ALA* 1.3 73.6 - - + +
333Y ALA* 1.3 66.2 + - - +
335Y CYS* 2.8 16.5 + - - +
336Y GLN* 3.0 17.8 + - + +
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Residues in contact with ALA 333 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280Y THR* 3.8 3.7 - - - +
329Y LYS* 2.9 20.3 + - + +
330Y ARG* 3.5 34.5 - - - +
332Y MET* 1.3 75.7 - - - +
334Y ASN* 1.3 61.6 + - - +
336Y GLN* 3.2 23.7 + - - +
337Y ALA 3.2 8.8 + - - -
342Y TYR* 3.7 18.6 - - + -
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Residues in contact with ASN 334 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276Y GLU 5.0 1.0 + - - -
279Y ALA 4.2 0.2 - - - +
280Y THR* 2.7 32.5 + - - -
283Y LEU* 4.2 1.5 - - + +
299Y PHE* 3.9 26.6 - - + -
301Y TYR* 3.3 37.7 - - - -
304Y ALA 4.6 6.3 + - - -
305Y LEU* 4.0 12.1 - - - +
330Y ARG* 3.1 23.7 + - - +
331Y ALA 4.5 0.2 - - - +
333Y ALA* 1.3 75.2 - - - +
335Y CYS* 1.3 67.6 + - - +
336Y GLN 3.0 1.8 - - - -
337Y ALA* 2.9 8.7 + - - +
338Y ALA* 2.9 21.3 + - - +
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Residues in contact with CYS 335 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25Y ASN 3.6 10.3 - - - -
26Y GLY* 3.0 32.9 - - - +
71Y GLN 3.8 13.2 - - - -
72Y SER* 3.7 22.0 - - - +
299Y PHE* 4.1 3.0 - - - -
331Y ALA 3.6 3.8 + - - -
332Y MET* 2.8 12.3 + - - +
334Y ASN* 1.3 76.3 - - - +
336Y GLN* 1.3 65.0 + - + +
338Y ALA* 3.0 14.4 + - - +
339Y LYS* 3.1 23.2 + - - +
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Residues in contact with GLN 336 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332Y MET* 3.0 13.1 + - + +
333Y ALA* 3.3 16.1 + - - +
334Y ASN 3.0 0.6 - - - -
335Y CYS* 1.3 79.3 - - + +
337Y ALA* 1.3 50.6 + - - +
339Y LYS* 2.6 31.0 + - + -
340Y GLY 2.7 13.5 + - - -
341Y GLN* 2.9 36.8 + - + +
342Y TYR* 3.6 21.1 - - + +
343Y VAL* 5.8 3.2 - - - +
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Residues in contact with ALA 337 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280Y THR* 3.3 41.1 - - + +
283Y LEU* 3.0 28.4 - - + +
284Y ASN* 3.2 22.9 - - + +
287Y ASN* 3.1 4.0 - - - +
333Y ALA 3.2 2.6 + - - -
334Y ASN* 2.9 11.1 + - - +
336Y GLN* 1.3 77.9 - - - +
338Y ALA* 1.3 56.8 + - - +
340Y GLY 3.0 12.3 + - - -
342Y TYR* 3.7 1.5 - - - +
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Residues in contact with ALA 338 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26Y GLY* 3.3 29.8 - - - +
283Y LEU* 4.1 3.5 - - + +
287Y ASN* 2.7 30.5 + - - +
297Y LEU 4.0 12.5 + - - +
298Y SER* 4.6 11.7 - - - +
299Y PHE* 4.8 0.7 - - + -
334Y ASN 2.9 9.5 + - - +
335Y CYS 3.1 12.1 - - - +
336Y GLN 3.0 0.2 - - - -
337Y ALA* 1.3 73.2 - - - +
339Y LYS* 1.3 57.6 + - - +
340Y GLY 3.3 0.4 - - - -
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Residues in contact with LYS 339 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Y ASN* 4.1 26.5 - - - +
26Y GLY* 4.3 6.5 - - - +
287Y ASN* 4.9 2.2 - - - -
288Y LEU* 5.3 1.0 - - - +
335Y CYS* 3.1 25.4 + - - +
336Y GLN* 2.6 18.1 + - + +
338Y ALA* 1.3 75.0 - - - +
340Y GLY* 1.3 50.7 + - - -
341Y GLN* 2.6 62.4 + - + +
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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