Contacts of the helix formed by residues 319 - 338 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A ALA 3.8 12.1 + - - +
313A TRP* 3.4 9.5 + - - -
316A LYS* 3.0 47.8 + - - +
317A ALA 3.7 0.2 - - - -
318A ALA* 1.3 85.1 + - - +
320A LYS* 1.3 51.6 + - - +
321A GLU* 2.7 19.8 + - - +
322A ALA* 2.8 23.0 + - + +
323A THR* 3.1 13.1 + - - -
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Residues in contact with LYS 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ILE* 4.2 22.8 - - + +
313A TRP* 6.1 0.2 - - - -
317A ALA* 3.1 28.7 - - - +
318A ALA* 3.1 8.9 + - - +
319A ASN* 1.3 75.6 - - - +
321A GLU* 1.3 53.6 + - + +
323A THR* 4.1 9.6 - - - -
324A GLN* 2.6 58.7 + - - +
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Residues in contact with GLU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A ALA 5.7 2.0 - - - +
319A ASN* 2.7 4.9 + - - +
320A LYS* 1.3 79.0 - - + +
322A ALA* 1.3 51.4 + - - +
324A GLN* 3.5 2.5 - - - -
325A GLU* 2.6 44.4 + - - +
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Residues in contact with ALA 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A ALA* 3.1 31.7 - - + +
319A ASN* 2.8 18.2 + - + +
321A GLU* 1.3 76.3 - - - +
323A THR* 1.3 57.1 + - - +
325A GLU* 3.2 7.8 - - - +
326A ALA* 2.9 25.8 + - - +
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Residues in contact with THR 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PHE* 3.8 15.7 - - + -
61A ILE* 3.4 27.6 - - + -
62A LEU* 4.4 6.5 - - + -
309A ALA* 3.1 27.6 - - + +
312A ALA* 2.9 31.1 + - - +
313A TRP* 3.6 13.5 - - - +
319A ASN 3.1 9.1 + - - -
320A LYS* 3.6 6.9 - - - -
322A ALA* 1.3 72.1 - - - +
324A GLN* 1.3 58.7 + - - +
325A GLU 2.9 9.4 + - - -
326A ALA 3.0 2.3 + - - -
327A PHE* 3.0 21.0 + - - +
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Residues in contact with GLN 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ILE* 2.7 43.9 - - + +
62A LEU* 5.4 0.7 - - - -
64A SER* 2.9 10.5 + - - -
65A VAL* 3.1 39.7 - - + +
66A ASP 4.4 1.0 - - - +
320A LYS* 2.6 41.5 + - - +
321A GLU* 3.5 2.5 - - - +
323A THR* 1.3 70.5 - - - +
325A GLU* 1.3 56.2 + - - +
327A PHE* 4.4 7.0 - - - -
328A MET* 2.9 31.2 + - - +
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Residues in contact with GLU 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A GLU 2.6 24.5 + - - +
322A ALA* 3.2 10.8 - - - +
324A GLN* 1.3 74.7 - - - +
326A ALA* 1.3 61.0 + - - +
328A MET* 3.5 2.4 + - - +
329A LYS* 2.9 41.8 + - + +
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Residues in contact with ALA 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A LEU 4.4 0.5 - - - +
308A SER* 2.8 33.9 + - - +
309A ALA* 3.0 34.0 + - - +
312A ALA* 4.4 1.6 - - + -
322A ALA 2.9 14.4 + - - +
325A GLU* 1.3 75.3 - - - +
327A PHE* 1.3 57.4 - - - +
329A LYS* 4.1 7.9 - - - -
330A ARG* 3.2 18.4 - - - +
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Residues in contact with PHE 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 3.8 39.7 - - + -
62A LEU* 3.5 45.1 - - + -
65A VAL* 4.2 10.3 - - + -
69A ILE* 3.2 35.7 - - + -
73A ILE* 4.6 5.2 - - + -
305A LEU* 3.4 20.4 - - + -
306A GLN* 5.8 0.2 - - + -
309A ALA* 3.4 18.8 - - + -
323A THR 3.0 9.3 + - - +
324A GLN* 4.4 2.7 - - - -
326A ALA* 1.3 77.4 - - - +
328A MET* 1.3 68.1 + - - +
329A LYS 3.0 2.1 + - - -
330A ARG* 3.0 12.3 + - - +
331A ALA* 3.1 21.4 + - + +
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Residues in contact with MET 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A VAL* 3.8 15.5 - - + -
66A ASP* 3.7 16.8 - - + +
68A SER* 3.0 28.9 - - - +
69A ILE* 3.2 46.0 - - + +
72A SER* 6.2 0.2 - - - -
324A GLN 2.9 21.2 + - - +
325A GLU* 4.1 3.6 - - - +
327A PHE* 1.3 81.0 - - - +
329A LYS* 1.3 60.2 + - - +
330A ARG 3.4 0.2 - - - -
331A ALA* 4.1 4.7 - - - -
332A MET* 2.8 53.7 + - + +
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Residues in contact with LYS 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A GLU* 2.9 27.4 + - + +
326A ALA* 4.3 8.5 - - - +
327A PHE 3.0 0.2 - - - -
328A MET* 1.3 79.8 - - - +
330A ARG* 1.3 75.7 + - - +
332A MET* 4.2 6.8 - - - +
333A ALA* 3.3 25.4 + - + +
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Residues in contact with ARG 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A GLU* 2.4 64.8 + - - +
277A GLU* 3.6 17.5 + - - -
280A THR* 2.6 19.2 + - - +
304A ALA 3.6 13.1 + - - +
305A LEU* 4.0 10.5 - - + -
308A SER* 3.8 2.7 - - - +
326A ALA 3.2 19.1 - - - +
327A PHE 3.0 5.3 + - - +
329A LYS* 1.3 100.6 + - - +
331A ALA* 1.3 58.8 + - - +
332A MET 3.2 2.0 - - - -
333A ALA* 3.7 19.5 - - - +
334A ASN* 2.8 40.7 + - - +
342A TYR* 4.0 5.1 + - - -
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Residues in contact with ALA 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ILE* 4.4 10.5 - - + -
72A SER* 2.9 21.0 - - - +
73A ILE* 4.0 23.3 - - + -
299A PHE* 4.3 1.7 - - - -
305A LEU* 3.9 11.5 - - - +
327A PHE* 3.1 21.6 + - + +
328A MET* 4.3 6.3 - - - +
329A LYS 3.6 0.2 - - - -
330A ARG* 1.3 77.8 - - - +
332A MET* 1.3 58.4 + - - +
334A ASN 3.9 1.0 - - - -
335A CYS* 2.9 28.1 + - - +
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Residues in contact with MET 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A SER* 5.6 2.9 - - - +
69A ILE* 6.5 0.2 - - - -
72A SER* 3.1 17.7 - - - +
328A MET* 2.8 51.7 + - + +
329A LYS* 4.2 7.2 - - - +
330A ARG 3.2 0.4 - - - -
331A ALA* 1.3 74.7 - - - +
333A ALA* 1.3 66.1 + - - +
335A CYS* 2.9 13.3 + - - +
336A GLN* 3.0 28.7 + - - +
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Residues in contact with ALA 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A THR* 4.3 0.2 - - - -
329A LYS* 3.3 17.7 + - + +
330A ARG* 3.3 25.7 + - - +
332A MET* 1.3 78.3 - - - +
334A ASN* 1.3 57.8 + - - +
336A GLN* 2.8 31.8 + - - +
337A ALA 3.1 8.5 + - - -
342A TYR* 3.3 30.9 - - + -
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Residues in contact with ASN 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A GLU 4.5 1.2 + - - -
279A ALA 3.7 4.3 - - - +
280A THR* 2.8 40.8 + - - +
299A PHE* 2.9 39.6 - - + -
301A TYR* 3.7 20.9 - - + -
304A ALA* 3.8 20.4 + - - +
305A LEU* 4.1 3.2 - - + +
330A ARG* 2.8 32.8 + - - +
333A ALA* 1.3 69.0 - - - +
335A CYS* 1.3 61.9 + - - +
336A GLN 3.1 1.3 - - - -
337A ALA* 3.6 10.1 - - + +
338A ALA 3.5 11.1 + - - -
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Residues in contact with CYS 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ASN 5.0 4.7 - - - -
26A GLY* 3.9 12.6 - - - +
71A GLN 3.6 16.4 - - - -
72A SER* 3.1 24.5 - - - +
299A PHE* 3.9 7.4 - - - -
331A ALA 2.9 21.4 + - - +
332A MET 2.9 9.6 + - - +
334A ASN* 1.3 79.0 - - - +
336A GLN* 1.3 63.3 + - - +
337A ALA 3.3 0.2 - - - -
338A ALA* 3.6 14.7 + - - +
339A LYS* 3.6 17.5 - - - +
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Residues in contact with GLN 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A ASN* 3.4 2.9 - - - +
332A MET* 3.0 30.4 + - - +
333A ALA* 2.8 15.9 + - - +
335A CYS* 1.3 83.1 - - - +
337A ALA* 1.3 58.7 + - - +
338A ALA 3.1 0.9 - - - -
339A LYS* 3.2 9.5 + - + -
340A GLY 2.8 22.0 + - - -
341A GLN* 3.3 27.4 + - + +
342A TYR* 3.4 21.1 + - + +
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Residues in contact with ALA 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A THR* 3.8 22.7 - - + +
283A LEU* 2.8 50.3 - - + +
284A ASN* 3.6 11.4 - - - -
287A ASN* 3.4 5.7 - - - +
333A ALA 3.1 4.0 + - - -
334A ASN* 3.7 17.5 - - - +
336A GLN* 1.3 73.5 - - - +
338A ALA* 1.3 57.6 + - - +
339A LYS 2.9 9.5 + - - -
340A GLY 3.4 6.9 + - - -
342A TYR* 4.3 1.8 - - - -
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Residues in contact with ALA 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLY* 3.3 35.2 - - - +
283A LEU* 4.1 1.3 - - + +
287A ASN* 2.8 22.8 - - - +
296A LYS* 6.0 1.7 - - - +
297A LEU 3.8 15.6 + - - +
298A SER* 4.2 11.2 - - - -
299A PHE* 4.6 2.0 - - + -
334A ASN 3.5 8.1 + - - +
335A CYS 3.6 6.3 - - - +
336A GLN 3.1 0.2 - - - -
337A ALA* 1.3 76.7 - - - +
339A LYS* 1.3 60.8 + - - +
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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
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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