Contacts of the helix formed by residues 319 - 342 (chain C) in PDB entry 1SZU
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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315C PHE 3.2 12.5 + - - -
316C GLU 3.6 5.6 + - - +
317C GLN 3.3 5.4 - - - +
318C GLU* 1.3 81.4 - - - +
320C LEU* 1.3 64.1 + - - +
321C LEU* 3.2 4.2 - - - +
322C GLN* 3.2 42.1 + - - +
323C LYS* 3.2 15.7 + - - +
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Residues in contact with LEU 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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54C ASN 4.6 2.9 - - - +
55C THR* 3.7 31.2 - - + -
314C VAL* 3.8 24.0 - - + +
315C PHE* 3.2 35.8 + - + -
318C GLU* 3.8 20.2 - - + +
319C ASN* 1.3 72.8 - - - +
321C LEU* 1.3 61.7 + - - +
322C GLN 3.3 0.2 - - - -
323C LYS* 3.8 21.4 - - + +
324C ALA* 2.9 28.4 + - - +
403C LEU* 4.0 14.3 - - + +
404C THR* 4.1 23.3 - - + -
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Residues in contact with LEU 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C GLY* 3.7 19.7 - - - +
249C GLY 3.3 23.1 - - - +
250C THR* 3.5 20.9 - - + -
251C LEU* 3.6 18.4 - - + +
315C PHE* 4.0 19.6 + - + +
319C ASN* 3.2 3.0 - - - +
320C LEU* 1.3 75.8 - - - +
322C GLN* 1.3 63.7 + - - +
324C ALA* 3.1 17.3 + - - +
325C ASN* 3.1 17.5 + - - -
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Residues in contact with GLN 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C ASN* 3.2 35.8 + - - +
321C LEU* 1.3 80.8 - - - +
323C LYS* 1.3 62.7 + - + +
325C ASN* 3.1 27.1 + - - +
326C ASP* 3.1 38.1 + - - +
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Residues in contact with LYS 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C GLU* 3.2 38.4 + - - +
319C ASN* 3.2 13.3 + - - +
320C LEU* 3.8 21.4 - - + +
322C GLN* 1.3 77.7 - - - +
324C ALA* 1.3 53.1 + - - +
326C ASP* 3.7 10.3 - - - +
327C LEU* 2.7 37.6 + - - +
403C LEU 4.2 17.5 - - - +
404C THR* 5.6 2.7 - - - +
405C ILE 6.2 0.4 - - - +
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Residues in contact with ALA 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C GLY 3.9 19.3 - - - +
249C GLY* 4.2 8.1 - - - +
320C LEU 2.9 14.9 + - - +
321C LEU 3.1 11.9 - - - +
322C GLN 3.1 0.2 - - - -
323C LYS* 1.3 77.9 - - - +
325C ASN* 1.3 58.4 + - - +
327C LEU* 3.6 1.8 - - - +
328C GLY 2.9 24.9 + - - -
352C GLY 4.2 0.2 - - - -
353C ALA* 3.6 15.5 + - + +
403C LEU* 3.8 28.2 - - + +
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Residues in contact with ASN 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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248C THR 4.0 1.9 - - - +
249C GLY* 3.4 27.6 + - - -
321C LEU 3.1 22.4 + - - -
322C GLN* 3.1 21.0 + - - +
324C ALA* 1.3 77.0 - - - +
326C ASP* 1.3 60.2 + - - +
328C GLY* 3.4 1.9 + - - -
329C GLN* 3.1 26.6 + - - +
352C GLY* 3.9 14.6 + - - +
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Residues in contact with ASP 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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322C GLN* 3.1 40.3 + - - +
323C LYS* 3.8 9.4 - - - +
325C ASN* 1.3 75.2 - - - +
327C LEU* 1.3 67.0 + - - +
329C GLN* 3.2 6.6 + - - +
330C LYS* 2.9 39.2 + - + +
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Residues in contact with LEU 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C ARG* 4.5 0.2 - - - +
323C LYS 2.7 21.7 + - - +
324C ALA 3.6 2.9 - - - +
326C ASP* 1.3 72.0 - - - +
328C GLY* 1.3 59.2 + - - +
330C LYS* 3.2 6.0 + - - +
331C LEU* 2.9 53.2 + - + +
353C ALA* 3.9 19.7 - - + -
401C VAL* 4.1 21.5 - - + +
402C PRO 4.1 9.0 - - - +
403C LEU* 4.0 18.2 - - + +
405C ILE* 3.7 14.8 - - + -
410C ILE* 3.4 33.7 - - + -
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Residues in contact with GLY 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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324C ALA 2.9 11.2 + - - -
325C ASN 3.7 1.1 - - - -
326C ASP 3.2 0.2 - - - -
327C LEU* 1.3 78.5 - - - +
329C GLN* 1.3 55.6 + - - +
331C LEU* 3.5 2.8 + - - +
332C LYS* 2.9 36.4 + - - +
352C GLY 3.0 27.4 - - - -
353C ALA* 4.2 1.8 - - - +
355C ILE* 3.9 13.4 - - - +
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Residues in contact with GLN 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C ASN 3.1 13.7 + - - +
326C ASP* 3.6 10.1 - - - +
327C LEU 3.2 0.2 - - - -
328C GLY* 1.3 75.2 - - - +
330C LYS* 1.3 59.9 + - + +
332C LYS* 3.2 17.1 + - - +
333C ASP* 2.8 72.4 + - - +
336C LEU* 6.2 0.2 - - - +
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Residues in contact with LYS 330 (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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326C ASP* 2.9 29.9 + - + +
327C LEU* 3.7 3.6 - - - +
329C GLN* 1.3 75.8 - - + +
331C LEU* 1.3 63.6 + - - +
333C ASP* 3.6 7.0 + - - +
334C GLY 3.1 17.5 + - - -
407C ASP* 2.5 35.8 + - - +
410C ILE* 3.9 31.5 - - + +
414C LEU* 3.8 10.6 - - + +
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Residues in contact with LEU 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C PHE* 4.5 13.5 - - + -
327C LEU* 2.9 44.1 + - + +
328C GLY* 3.6 4.7 - - - +
330C LYS* 1.3 74.5 - - - +
332C LYS* 1.3 66.8 + - - +
334C GLY* 3.2 2.4 + - - -
335C LEU* 2.9 31.1 + - + +
353C ALA 5.1 3.1 - - - +
355C ILE* 4.2 24.9 - - + -
399C ILE* 3.8 38.1 - - + -
401C VAL* 4.6 1.1 - - + -
410C ILE* 4.1 19.7 - - + -
414C LEU* 4.0 15.2 - - + +
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Residues in contact with LYS 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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328C GLY 2.9 20.9 + - - +
329C GLN* 3.7 21.4 + - - +
331C LEU* 1.3 75.3 - - - +
333C ASP* 1.3 58.8 + - - +
335C LEU* 3.1 3.9 + - - +
336C LEU* 2.8 41.6 + - + +
348C VAL* 4.0 24.7 - - + +
349C ARG* 3.9 6.7 - - - +
350C GLY 2.9 43.1 + - - +
355C ILE* 4.0 15.9 - - + +
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Residues in contact with ASP 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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329C GLN* 2.8 53.3 + - - +
330C LYS* 3.9 7.0 - - - +
332C LYS* 1.3 74.4 - - - +
334C GLY* 1.3 63.7 + - - +
336C LEU* 3.2 12.6 + - - +
337C ALA* 3.0 22.7 + - - +
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Residues in contact with GLY 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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330C LYS 3.1 9.3 + - - -
331C LEU 3.7 2.9 - - - -
333C ASP* 1.3 79.8 - - - +
335C LEU* 1.3 57.6 + - - +
337C ALA* 3.4 7.8 - - - +
338C ILE* 3.2 32.6 + - - +
414C LEU* 3.9 25.4 - - - -
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Residues in contact with LEU 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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331C LEU 2.9 27.4 + - - +
332C LYS* 3.6 4.3 - - - +
334C GLY* 1.3 72.6 - - - +
336C LEU* 1.3 62.2 + - - +
337C ALA 3.2 0.2 - - - -
338C ILE* 3.4 8.9 + - + +
339C ALA* 2.9 28.9 + - - +
345C ILE* 4.5 4.7 - - + +
348C VAL* 4.1 12.7 - - + +
355C ILE* 3.7 26.9 - - + -
356C ALA* 5.2 0.4 - - - -
357C ILE* 3.7 35.4 - - + -
399C ILE* 4.1 14.1 - - + -
414C LEU* 4.3 15.5 - - + -
417C ILE* 4.6 25.6 - - + -
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Residues in contact with LEU 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 LYS* 2.8 30.8 + - + +
333C ASP* 3.6 13.2 - - - +
335C LEU* 1.3 72.1 - - - +
337C ALA* 1.3 62.1 + - - +
339C ALA* 3.2 15.6 + - + +
340C GLU* 3.2 19.7 + - - +
348C VAL* 3.5 32.1 - - + +
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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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333C ASP 3.0 12.4 + - - +
334C GLY* 3.4 13.2 - - - +
336C LEU* 1.3 76.2 - - - +
338C ILE* 1.3 64.5 + - + +
340C GLU* 3.0 30.8 + - - +
341C LYS* 3.9 3.3 + - - +
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Residues in contact with ILE 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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334C GLY 3.2 20.0 + - - +
335C LEU* 3.8 11.4 - - + +
337C ALA* 1.3 76.5 - - + +
339C ALA* 1.3 63.2 + - - +
341C LYS* 3.2 13.1 + - - +
342C HIS* 3.2 29.3 + - + +
345C ILE* 4.1 13.9 - - + -
414C LEU* 3.7 12.6 - - + +
417C ILE* 4.3 11.0 - - + -
418C SER* 3.4 52.5 - - - +
421C PHE* 4.4 9.4 - - + -
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Residues in contact with ALA 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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335C LEU 2.9 15.2 + - - +
336C LEU* 3.2 19.7 - - + +
337C ALA 3.1 0.2 - - - -
338C ILE* 1.3 78.1 - - - +
340C GLU* 1.3 59.9 + - + +
342C HIS 3.0 26.1 + - - +
343C PRO* 3.9 3.8 - - - +
345C ILE* 3.8 31.2 - - + +
348C VAL* 4.6 4.0 - - + -
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Residues in contact with GLU 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C LEU 3.2 14.1 + - - +
337C ALA* 3.0 17.7 + - - +
339C ALA* 1.3 78.5 - - + +
341C LYS* 1.3 58.5 + - - +
343C PRO* 5.1 5.5 - - - +
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Residues in contact with LYS 341 (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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337C ALA 3.9 2.6 + - - +
338C ILE* 3.2 5.6 + - - +
340C GLU* 1.3 78.4 - - - +
342C HIS* 1.3 73.8 + - + +
343C PRO* 3.8 3.8 - - - +
422C ASP* 3.0 38.5 + - - +
425C LYS* 3.3 21.4 + - - +
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Residues in contact with HIS 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C ILE* 3.2 24.8 + - + +
339C ALA 3.0 14.4 + - - +
341C LYS* 1.3 94.9 - - + +
343C PRO* 1.3 60.5 - - - +
344C GLU* 3.1 19.5 + - - +
345C ILE* 3.2 16.9 + - + +
418C SER* 4.6 0.8 + - - -
421C PHE* 3.2 56.3 + - + +
422C ASP* 2.6 34.2 + - - -
425C LYS* 3.6 25.2 - - + +
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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