Contacts of the helix formed by residues 363 - 376 (chain C) in PDB entry 1XV9
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 ASP 363 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315C HIS* 3.9 4.5 - - - -
361C GLN* 3.3 4.3 + - - +
362C MET* 1.3 75.9 - - - +
364C LYS* 1.3 58.7 + - - +
365C THR* 2.9 41.0 + - - +
366C GLU* 2.9 15.3 + - - +
367C LEU* 3.0 28.4 + - - +
403C TYR* 2.7 15.3 + - - -
408C TYR* 2.3 38.8 + - - +
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Residues in contact with LYS 364 (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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236C LEU* 3.0 23.8 - - + +
239C GLU* 3.5 21.8 - - + +
240C LEU* 3.8 22.2 - - + -
243C GLU* 4.1 19.5 - - - +
315C HIS* 4.0 18.4 - - + +
363C ASP* 1.3 74.7 - - - +
365C THR* 1.3 59.8 + - - +
367C LEU* 4.0 13.9 - - + -
368C GLY 3.8 2.6 + - - -
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Residues in contact with THR 365 (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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232C VAL* 3.3 37.9 - - + +
235C ILE* 4.8 2.8 - - + +
236C LEU* 3.0 31.6 - - + +
363C ASP* 2.9 14.1 + - - -
364C LYS* 1.3 77.3 - - - +
366C GLU* 1.3 64.0 + - - +
367C LEU 3.1 1.5 + - - -
368C GLY* 3.5 3.3 + - - -
369C CYS* 3.3 23.0 + - - -
403C TYR* 3.4 31.2 + - + -
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Residues in contact with GLU 366 (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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362C MET* 3.4 13.0 - - + +
363C ASP* 2.9 33.5 + - - +
365C THR* 1.3 69.8 - - - +
367C LEU* 1.3 70.0 + - - +
369C CYS* 3.4 3.3 + - - +
370C LEU* 3.3 21.8 + - - +
400C LEU* 4.1 12.1 - - - +
403C TYR* 3.4 13.6 - - + -
404C CYS* 3.4 19.6 - - - -
408C TYR* 3.8 8.6 - - - -
414C ARG* 2.6 46.4 + - - -
418C LEU* 3.8 17.6 - - + +
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Residues in contact with LEU 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C GLU* 3.3 20.6 - - - +
311C ALA* 4.1 10.1 - - + +
312C SER* 5.4 4.7 - - - -
315C HIS* 3.7 26.5 - - + +
357C MET* 3.5 20.6 - - + -
362C MET* 3.1 34.4 - - + +
363C ASP 3.0 13.6 + - - +
364C LYS* 4.0 9.2 - - + -
366C GLU* 1.3 81.3 - - - +
368C GLY* 1.3 54.1 + - - +
369C CYS 2.8 0.9 + - - -
370C LEU* 2.8 24.7 + - + +
371C ARG* 3.0 25.0 + - + +
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Residues in contact with GLY 368 (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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235C ILE* 3.8 13.9 - - - +
239C GLU* 2.8 33.1 + - - -
282C TRP* 3.9 4.4 - - - -
364C LYS 3.8 1.8 + - - -
365C THR 3.5 5.6 + - - -
367C LEU* 1.3 78.3 - - - +
369C CYS* 1.3 59.9 + - - +
371C ARG* 3.4 9.9 + - - +
372C ALA* 3.0 21.1 + - - +
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Residues in contact with CYS 369 (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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232C VAL* 4.8 16.2 - - - -
235C ILE* 4.1 23.6 - - - -
365C THR* 3.3 14.8 + - - -
366C GLU 3.6 5.6 - - - +
367C LEU 2.8 5.3 + - - -
368C GLY* 1.3 70.1 - - - +
370C LEU* 1.3 60.9 + - - +
372C ALA* 2.8 20.6 + - - +
373C ILE* 2.9 12.4 + - - +
396C VAL* 3.3 13.7 - - + +
399C SER* 5.1 0.7 - - - -
400C LEU* 3.6 46.4 - - + -
403C TYR* 5.9 0.2 - - - -
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Residues in contact with LEU 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C MET* 5.4 9.0 - - - -
366C GLU 3.3 9.4 + - - +
367C LEU* 2.8 12.0 + - + +
369C CYS* 1.3 75.8 - - - +
371C ARG* 1.3 59.5 + - + +
373C ILE* 2.9 27.4 + - + +
374C VAL* 3.0 17.2 + - - +
400C LEU* 3.1 28.9 - - + -
418C LEU* 3.0 37.5 - - + +
419C LEU* 3.4 23.6 - - + +
421C ARG* 5.0 5.8 - - + -
422C LEU* 4.6 17.5 - - + +
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Residues in contact with ARG 371 (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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239C GLU* 4.1 9.2 + - - -
242C VAL* 6.0 2.2 - - - +
279C LEU* 3.3 31.9 - - - +
282C TRP* 2.9 65.0 - - + +
308C LEU* 3.0 45.9 + - - +
309C LEU* 4.0 0.4 - - - +
311C ALA* 3.7 24.9 - - + -
312C SER* 3.0 28.5 + - - +
367C LEU* 3.0 29.1 + - + +
368C GLY* 3.4 10.1 - - - +
370C LEU* 1.3 76.1 - - + +
372C ALA* 1.3 57.4 + - - +
374C VAL* 4.2 2.7 - - - -
375C LEU* 3.6 5.9 + - - +
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Residues in contact with ALA 372 (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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235C ILE* 4.9 4.7 - - + -
282C TRP* 4.3 3.6 - - - -
286C ILE* 4.8 15.7 - - + -
368C GLY 3.0 11.0 + - - +
369C CYS* 2.8 13.3 + - - +
371C ARG* 1.3 77.6 - - - +
373C ILE* 1.3 57.6 + - - +
374C VAL 3.1 1.6 - - - -
375C LEU* 3.2 5.9 + - - +
376C PHE* 2.9 42.5 + - + +
396C VAL* 3.9 23.1 - - + -
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Residues in contact with ILE 373 (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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369C CYS 2.9 15.2 + - - +
370C LEU* 3.3 32.3 - - + +
372C ALA* 1.3 76.5 - - - +
374C VAL* 1.3 61.9 + - - +
376C PHE* 3.1 19.5 - - - +
377C ASN* 4.7 1.4 - - - +
393C ARG* 4.0 22.1 + - + +
396C VAL* 3.4 20.2 - - + +
397C TYR* 4.0 32.3 - - + +
400C LEU* 4.0 10.3 - - + -
419C LEU* 3.8 13.7 - - + -
422C LEU* 4.1 20.6 - - + -
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Residues in contact with VAL 374 (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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300C LEU 5.5 0.4 - - - +
304C GLY* 4.5 15.0 - - - +
307C GLU* 5.1 9.6 - - + +
308C LEU* 3.4 32.1 - - + -
370C LEU 3.0 13.5 + - - +
371C ARG* 4.1 1.1 - - - +
373C ILE* 1.3 77.2 - - - +
375C LEU* 1.3 72.2 + - - +
376C PHE 2.9 1.9 + - - -
377C ASN* 3.2 19.1 + - - +
422C LEU* 4.0 27.1 - - + -
425C LEU* 4.5 15.5 - - + -
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Residues in contact with LEU 375 (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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282C TRP* 4.2 15.5 - - + -
283C ALA* 4.1 15.9 - - + -
286C ILE* 4.6 9.0 - - + -
289C PHE* 3.5 44.0 - - + -
300C LEU* 3.2 37.9 - - + +
301C LEU* 3.8 18.4 - - + -
308C LEU* 5.1 9.9 - - + -
371C ARG 3.6 12.3 + - - +
372C ALA* 3.2 10.0 + - - +
374C VAL* 1.3 83.5 - - - +
376C PHE* 1.3 67.4 + - + +
377C ASN* 3.1 6.9 + - - +
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Residues in contact with PHE 376 (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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230C MET* 3.8 23.3 - - + -
286C ILE* 3.8 26.9 - - + -
287C PRO 4.6 2.5 - - - -
288C HIS 4.3 7.6 - - - -
289C PHE* 4.0 21.5 - + - -
292C LEU* 4.1 5.2 - - + -
300C LEU* 4.2 10.8 - - + -
372C ALA* 2.9 23.9 + - + +
373C ILE 3.1 3.6 - - - +
374C VAL 2.9 4.3 + - - -
375C LEU* 1.3 75.5 - - + +
377C ASN* 1.3 52.3 + - - +
389C VAL* 3.8 13.5 - - + +
392C LEU* 3.7 39.3 - - + -
393C ARG* 2.8 60.4 - - + +
396C VAL* 4.2 9.4 - - + -
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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
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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