Contacts of the helix formed by residues 319 - 340 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312C ALA 3.4 25.9 + - - +
313C TRP* 3.6 8.6 + - - -
316C LYS* 2.7 48.6 + - - +
318C ALA* 1.3 84.6 - - - +
320C LYS* 1.3 64.5 + - - +
321C GLU 3.3 2.9 - - - +
322C ALA* 4.0 15.3 - - + +
323C THR* 3.0 24.7 + - - +
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Residues in contact with LYS 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C GLU* 5.0 10.7 + - - +
61C ILE* 3.8 27.0 - - + +
64C SER* 3.4 27.1 + - - -
313C TRP* 5.2 0.7 - - - +
317C ALA 4.4 11.7 + - - +
318C ALA* 3.3 4.9 + - - +
319C ASN* 1.3 76.9 - - - +
321C GLU* 1.3 63.2 + - + +
323C THR* 4.8 0.4 - - - -
324C GLN* 3.0 48.5 + - - +
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Residues in contact with GLU 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C ASN 3.3 0.4 - - - -
320C LYS* 1.3 78.2 - - + +
322C ALA* 1.3 68.5 + - - +
323C THR 3.0 1.6 - - - -
324C GLN* 2.8 25.2 + - - +
325C GLU* 3.1 21.0 + - + +
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Residues in contact with ALA 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C ALA* 3.7 17.5 - - + +
319C ASN* 4.0 23.6 - - + +
321C GLU* 1.3 78.9 - - - +
323C THR* 1.3 59.5 + - - +
325C GLU* 3.6 20.4 - - - +
326C ALA* 3.8 4.2 + - - +
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Residues in contact with THR 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C PHE* 4.0 9.9 - - + -
61C ILE* 3.7 22.7 - - + -
62C LEU* 5.2 1.6 - - + -
309C ALA* 3.0 48.5 - - + +
312C ALA* 3.1 7.8 - - - -
313C TRP* 2.7 45.0 + - + -
319C ASN 3.0 16.5 + - - -
320C LYS 3.9 2.2 - - - -
321C GLU 2.8 1.6 + - - -
322C ALA* 1.3 72.6 - - - +
324C GLN* 1.3 64.6 + - - +
325C GLU 3.1 2.4 + - - -
326C ALA 3.5 2.9 + - - -
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Residues in contact with GLN 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ILE* 2.7 40.7 + - + +
62C LEU* 5.4 1.6 - - - -
64C SER* 3.4 7.9 + - - -
65C VAL* 3.2 39.9 - - + +
66C ASP* 5.7 0.9 - - - +
320C LYS* 3.0 41.0 + - - +
321C GLU* 2.8 15.5 + - - +
323C THR* 1.3 71.3 - - - +
325C GLU* 1.3 56.4 + - - +
327C PHE* 3.7 7.4 - - - +
328C MET* 2.7 38.5 + - + +
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Residues in contact with GLU 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321C GLU* 3.1 22.6 + - + +
322C ALA* 3.6 12.6 - - - +
323C THR 3.1 0.4 - - - -
324C GLN* 1.3 73.2 - - - +
326C ALA* 1.3 54.1 + - - +
327C PHE 2.6 15.4 + - - -
328C MET* 2.7 21.4 + - - +
329C LYS* 2.8 18.0 + - - +
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Residues in contact with ALA 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305C LEU 4.4 0.5 - - - +
308C SER* 3.1 32.7 + - - +
309C ALA* 3.3 24.3 - - + +
312C ALA* 4.7 2.9 - - + -
322C ALA 3.8 5.8 + - - +
323C THR 3.5 2.8 + - - +
325C GLU* 1.3 77.9 - - - +
327C PHE* 1.3 56.1 + - - +
329C LYS* 4.2 9.4 - - - -
330C ARG* 3.0 29.3 + - - +
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Residues in contact with PHE 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LEU* 3.9 37.2 - - + -
62C LEU* 3.7 44.9 - - + -
65C VAL* 4.4 7.9 - - + -
69C ILE* 3.2 36.1 - - + -
73C ILE* 4.4 7.0 - - + -
305C LEU* 3.5 32.5 - - + -
306C GLN* 5.4 0.9 - - + -
309C ALA* 3.6 19.3 - - + +
323C THR 4.1 1.3 - - - +
324C GLN* 3.4 8.9 + - - +
325C GLU 2.6 5.5 + - - -
326C ALA* 1.3 74.4 - - - +
328C MET* 1.3 60.7 + - - +
329C LYS 3.1 1.8 - - - -
330C ARG* 3.6 0.6 + - - +
331C ALA* 3.0 29.1 + - + +
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Residues in contact with MET 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C VAL* 3.6 24.0 - - + -
66C ASP* 4.9 11.0 - - + +
68C SER* 2.8 31.2 - - - +
69C ILE* 4.1 22.9 - - - -
324C GLN 2.7 19.9 + - - +
325C GLU* 2.7 18.3 + - - +
327C PHE* 1.3 75.0 - - - +
329C LYS* 1.3 56.5 + - - +
331C ALA* 3.8 3.8 - - - +
332C MET* 3.2 65.7 + - + +
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Residues in contact with LYS 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325C GLU 2.8 15.3 + - - +
326C ALA* 4.5 7.6 - - - +
328C MET* 1.3 76.2 - - - +
330C ARG* 1.3 75.2 + - - +
331C ALA 3.0 1.3 - - - -
332C MET* 3.1 8.2 + - - +
333C ALA* 2.6 38.9 + - + +
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Residues in contact with ARG 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C GLU* 2.9 52.9 + - - +
277C GLU* 3.8 14.6 + - - +
280C THR* 2.5 35.4 + - - +
304C ALA 4.1 5.8 - - - +
305C LEU* 3.4 24.1 - - + +
308C SER* 3.9 1.8 - - - +
326C ALA* 3.0 22.2 + - - +
327C PHE 3.6 1.7 + - - +
329C LYS* 1.3 97.7 - - - +
331C ALA* 1.3 62.6 + - - +
333C ALA* 3.6 17.3 - - - +
334C ASN* 2.9 32.1 + - - +
342C TYR* 4.6 2.4 + - - -
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Residues in contact with ALA 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C ILE* 3.3 30.1 - - + -
72C SER* 2.8 24.2 + - - -
73C ILE* 4.3 9.6 - - + -
299C PHE* 4.5 4.5 - - - -
305C LEU* 3.6 10.0 - - + +
327C PHE* 3.0 21.6 + - + +
328C MET 3.8 4.5 - - - +
329C LYS 3.0 0.2 - - - -
330C ARG* 1.3 81.3 - - - +
332C MET* 1.3 60.2 + - + +
334C ASN* 4.2 1.1 - - - -
335C CYS* 3.5 11.6 + - - +
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Residues in contact with MET 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C SER* 5.3 7.9 - - - +
69C ILE* 6.4 0.4 - - - -
71C GLN* 6.5 0.4 - - + -
72C SER* 3.0 16.8 - - - +
328C MET* 3.2 55.1 + - + +
329C LYS* 3.1 6.6 + - - +
331C ALA* 1.3 74.7 - - + +
333C ALA* 1.3 69.5 + - - +
335C CYS* 3.0 10.6 + - - +
336C GLN* 3.1 22.5 + - + +
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Residues in contact with ALA 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C THR* 3.7 7.6 - - + +
329C LYS* 2.6 25.2 + - + +
330C ARG* 3.4 34.3 - - - +
332C MET* 1.3 71.7 - - - +
334C ASN* 1.3 59.4 + - - +
335C CYS 2.9 6.1 + - - -
336C GLN* 3.0 11.9 + - - +
337C ALA 3.0 17.5 + - - -
342C TYR* 3.7 19.0 - - + -
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Residues in contact with ASN 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276C GLU 4.3 1.0 + - - -
279C ALA 3.8 0.2 - - - -
280C THR* 2.4 41.8 + - - -
283C LEU* 3.7 2.5 - - + +
299C PHE* 3.1 33.4 - - + -
301C TYR* 3.5 29.4 - - + -
304C ALA 3.7 20.6 + - - -
305C LEU* 3.9 3.8 - - - +
330C ARG* 2.9 30.7 + - - +
333C ALA* 1.3 76.0 - - - +
335C CYS* 1.3 60.5 + - - +
337C ALA* 3.6 8.5 - - + +
338C ALA* 3.5 9.9 + - - +
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Residues in contact with CYS 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ASN 4.0 0.7 - - - -
26C GLY 3.0 26.6 - - - +
71C GLN 4.0 17.5 - - - -
72C SER* 3.6 11.9 - - - +
299C PHE* 4.3 2.9 - - - -
331C ALA 3.5 15.5 + - - +
332C MET* 3.0 11.2 + - - +
333C ALA 2.9 0.8 + - - -
334C ASN* 1.3 76.2 - - - +
336C GLN* 1.3 64.5 + - - +
338C ALA* 2.9 20.3 + - - +
339C LYS* 2.9 35.2 + - - +
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Residues in contact with GLN 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332C MET* 3.3 17.7 + - + +
333C ALA* 3.0 7.6 + - - +
335C CYS* 1.3 75.9 - - + +
337C ALA* 1.3 55.6 + - - +
339C LYS* 2.7 15.3 + - + +
340C GLY* 2.6 33.8 + - - -
341C GLN* 3.1 41.1 + - + +
342C TYR* 3.7 21.1 - - + +
343C VAL 5.6 0.4 - - - +
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Residues in contact with ALA 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C THR* 3.2 43.7 - - + +
283C LEU* 3.4 19.1 - - + +
284C ASN* 3.0 32.3 + - - -
287C ASN* 3.7 2.1 - - - +
333C ALA 3.0 4.8 + - - -
334C ASN* 3.6 12.8 - - - -
336C GLN* 1.3 78.0 - - - +
338C ALA* 1.3 59.6 + - - +
339C LYS 3.3 0.3 + - - -
340C GLY 3.5 3.8 + - - -
342C TYR* 3.7 3.5 - - - +
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Residues in contact with ALA 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C GLY* 3.8 24.2 - - - +
283C LEU* 3.6 17.4 - - + +
287C ASN* 2.6 23.5 + - - +
297C LEU 3.8 12.6 - - - +
298C SER* 4.3 9.4 - - - +
299C PHE* 4.6 0.4 - - + -
334C ASN 3.5 9.7 + - - +
335C CYS 2.9 12.6 + - - +
337C ALA* 1.3 78.7 - - - +
339C LYS* 1.3 57.6 + - - +
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Residues in contact with LYS 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ASN* 3.6 36.4 + - - +
26C GLY* 4.4 5.4 - - - -
287C ASN* 4.6 3.6 - - - +
335C CYS* 2.9 33.4 + - - +
336C GLN* 2.7 21.6 + - + +
338C ALA* 1.3 80.8 - - - +
340C GLY* 1.3 54.6 + - - -
341C GLN* 3.0 44.9 + - + +
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Residues in contact with GLY 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284C ASN* 2.8 25.4 + - - +
287C ASN* 4.3 8.3 - - - -
288C LEU* 3.5 34.3 - - - +
336C GLN 2.6 8.1 + - - -
337C ALA 3.5 6.3 + - - -
338C ALA 3.5 0.2 - - - -
339C LYS* 1.3 74.7 - - - +
341C GLN* 1.3 54.8 + - - +
342C TYR 3.0 3.5 + - - +
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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