Contacts of the helix formed by residues 282 - 296 (chain C) in PDB entry 1XSK
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 282 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281C TYR* 1.3 74.6 - - - +
283C GLU* 1.3 69.1 + - - +
284C ALA* 3.3 15.9 + - - +
285C THR* 2.6 43.6 + - - -
286C VAL* 3.1 13.9 + - - +
324C THR* 3.4 27.8 - - + +
325C PHE* 3.7 8.5 - - - -
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Residues in contact with GLU 283 (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 ASP* 1.3 75.3 - - - +
284C ALA* 1.3 64.7 + - - +
286C VAL* 3.1 5.2 + - - +
287C ASN* 3.1 42.6 + - - +
324C THR 3.7 10.2 + - - +
325C PHE* 3.7 3.3 - - + -
326C PRO* 5.3 9.6 - - + +
327C ASP* 4.9 6.1 + - - +
331C MET* 3.4 41.2 - - + +
334C ARG* 2.6 37.9 + - - +
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Residues in contact with ALA 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C ASP* 3.2 16.5 + - - +
283C GLU* 1.3 78.3 - - - +
285C THR* 1.3 58.3 + - - +
287C ASN* 3.7 6.3 + - - +
288C SER* 2.9 28.5 + - - -
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Residues in contact with THR 285 (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 ASN 4.2 4.9 - - - +
281C TYR* 3.6 9.1 - - + -
282C ASP* 2.6 37.8 + - - -
284C ALA* 1.3 72.8 - - - +
286C VAL* 1.3 69.5 + - - +
288C SER* 3.3 8.3 + - - -
289C PHE* 3.1 41.2 + - + -
545C TYR* 4.1 20.2 - - + +
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Residues in contact with VAL 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C THR* 4.3 8.5 - - + -
281C TYR* 5.3 2.0 - - + -
282C ASP 3.1 16.7 + - - +
283C GLU* 3.1 10.4 + - - +
285C THR* 1.3 75.1 - - - +
287C ASN* 1.3 66.5 + - - +
289C PHE* 2.9 18.2 + - - +
290C ILE* 3.0 30.4 + - + +
303C PHE* 3.5 35.6 - - + -
305C PHE* 3.7 24.2 - - + -
325C PHE* 4.6 2.5 - - + -
331C MET* 5.0 2.9 - - + -
335C LEU* 3.9 16.6 - - + -
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Residues in contact with ASN 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C GLU* 3.1 43.6 + - - +
284C ALA* 4.0 5.6 - - - +
286C VAL* 1.3 80.3 - - - +
288C SER* 1.3 57.2 + - - +
290C ILE* 4.2 5.8 - - - -
291C ASP* 2.8 47.5 + - - +
331C MET* 5.5 0.8 - - - +
334C ARG* 5.4 6.5 - - - +
335C LEU* 3.6 19.6 - - - +
338C LYS* 3.0 21.6 + - - +
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Residues in contact with SER 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C ALA 2.9 20.2 + - - -
285C THR* 3.4 12.3 - - - +
287C ASN* 1.3 76.1 - - - +
289C PHE* 1.3 61.5 + - - +
291C ASP* 4.3 3.6 - - - +
292C GLY* 3.0 26.7 + - - -
295C GLU* 5.0 0.5 - - - +
549C TRP* 4.8 3.0 - - - -
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Residues in contact with PHE 289 (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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273C LEU* 4.6 22.0 - - + -
274C THR 4.8 7.0 - - - -
275C THR* 4.9 6.1 - - + -
281C TYR* 5.9 1.8 - - + -
285C THR* 3.1 33.9 + - + -
286C VAL* 2.9 10.1 + - - +
288C SER* 1.3 82.6 - - - +
290C ILE* 1.3 65.1 + - + +
292C GLY* 3.2 2.3 + - - -
293C MET* 3.0 29.2 + - + +
303C PHE* 5.0 5.8 - + + -
545C TYR* 3.2 57.0 - + + -
547C VAL* 3.4 34.5 - - + -
549C TRP* 3.6 12.3 - + - -
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Residues in contact with ILE 290 (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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273C LEU* 6.2 0.4 - - + -
286C VAL* 3.0 22.8 + - + +
287C ASN* 3.7 7.0 - - - +
289C PHE* 1.3 72.8 - - + +
291C ASP* 1.3 68.0 + - - +
293C MET* 3.2 9.1 + - - +
294C ALA* 3.1 21.4 + - + +
300C LEU* 5.9 7.2 - - + -
303C PHE* 4.4 15.9 - - + -
335C LEU* 3.2 34.1 - - + -
338C LYS* 3.8 27.8 - - + -
340C LEU* 3.2 30.3 - - + -
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Residues in contact with ASP 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C ASN* 2.8 30.7 + - - +
288C SER* 4.3 3.1 - - - +
290C ILE* 1.3 72.9 - - - +
292C GLY* 1.3 58.3 + - - +
294C ALA* 3.2 7.6 + - - +
295C GLU* 2.8 46.5 + - + +
338C LYS* 2.8 34.0 + - - +
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Residues in contact with GLY 292 (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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288C SER 3.0 17.1 + - - -
289C PHE 3.5 4.5 - - - -
290C ILE 3.1 0.2 - - - -
291C ASP* 1.3 79.2 - - - +
293C MET* 1.3 59.4 + - - +
295C GLU* 3.5 11.9 + - - +
296C ARG* 2.7 44.0 + - - +
549C TRP* 3.4 10.7 - - - -
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Residues in contact with MET 293 (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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271C LEU* 3.9 11.7 - - + -
273C LEU* 5.5 8.1 - - + -
289C PHE 3.0 19.5 + - - +
290C ILE* 3.6 8.3 - - - +
291C ASP 3.2 0.2 - - - -
292C GLY* 1.3 74.2 - - - +
294C ALA* 1.3 67.5 + - - +
296C ARG* 3.1 4.0 + - - -
297C ASN 3.0 4.7 + - - -
298C LEU* 2.9 70.9 + - + +
299C PRO 3.8 5.6 - - - +
300C LEU* 3.6 37.9 - - + -
539C LEU* 5.1 5.6 - - + -
547C VAL* 5.3 3.8 - - + -
548C PRO* 4.0 18.6 - - - -
549C TRP* 4.1 7.0 - - + -
559C VAL* 5.0 3.1 - - + -
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Residues in contact with ALA 294 (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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290C ILE* 3.1 11.3 + - + +
291C ASP* 3.6 10.8 - - - +
293C MET* 1.3 80.3 - - - +
295C GLU* 1.3 54.3 + - - +
297C ASN* 2.8 29.4 + - - +
298C LEU 4.7 3.8 - - - +
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Residues in contact with GLU 295 (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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288C SER 5.0 0.5 - - - +
291C ASP* 2.8 45.4 + - + +
292C GLY* 3.5 14.4 + - - +
294C ALA* 1.3 72.4 - - + +
296C ARG* 1.3 67.4 + - + +
297C ASN* 3.4 12.3 + - - +
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Residues in contact with ARG 296 (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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292C GLY* 2.7 37.7 + - - +
293C MET 3.1 8.3 + - - +
295C GLU* 1.3 86.4 + - + +
297C ASN* 1.3 66.1 + - - +
298C LEU* 3.3 11.6 + - + -
549C TRP* 3.4 58.0 - - - +
556C CYS* 3.8 19.5 - - + -
560C ARG* 2.4 37.7 + - - +
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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