Contacts of the helix formed by residues 282 - 296 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B TYR* 1.3 75.7 - - - +
283B GLU* 1.3 68.1 + - - +
284B ALA* 2.6 38.7 + - - +
285B THR* 2.9 22.1 + - - -
286B VAL* 3.0 13.4 + - - +
324B THR* 3.5 29.5 - - + +
325B PHE* 3.5 8.3 - - - -
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Residues in contact with GLU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ASP* 1.3 76.3 + - - +
284B ALA* 1.3 60.8 + - - +
286B VAL* 3.8 9.4 - - + -
287B ASN* 3.1 43.0 + - - +
324B THR 4.4 2.5 + - - +
325B PHE* 3.5 9.1 - - + -
326B PRO* 5.9 4.4 - - + +
327B ASP* 4.9 3.3 - - - +
331B MET* 3.8 38.5 - - + +
334B ARG* 3.3 33.8 + - - +
335B LEU* 5.7 0.2 - - + -
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Residues in contact with ALA 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ASP* 2.6 27.0 + - - +
283B GLU* 1.3 70.9 - - - +
285B THR* 1.3 65.3 + - - +
287B ASN* 4.1 2.2 - - - +
288B SER* 2.9 25.7 + - - -
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Residues in contact with THR 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ASN 3.7 18.2 + - - +
281B TYR* 3.1 12.2 - - + -
282B ASP* 2.9 31.9 + - - -
284B ALA* 1.3 77.1 - - - +
286B VAL* 1.3 65.7 - - - +
288B SER* 3.0 21.2 - - - -
289B PHE* 3.0 35.7 + - + -
545B TYR* 4.4 5.4 - - + +
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Residues in contact with VAL 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B THR* 4.8 5.6 - - + -
281B TYR* 5.2 0.7 - - + -
282B ASP 3.0 20.8 + - - +
283B GLU* 3.6 10.5 - - - +
285B THR* 1.3 76.4 - - - +
287B ASN* 1.3 65.9 + - - +
289B PHE* 2.9 17.1 + - - +
290B ILE* 3.1 20.0 + - + +
303B PHE* 4.0 32.4 - - + -
305B PHE* 3.7 25.4 - - + -
325B PHE* 4.8 0.7 - - + -
335B LEU* 3.6 33.9 - - + -
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Residues in contact with ASN 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B GLU* 3.1 48.0 + - - +
284B ALA* 4.3 2.2 - - - +
286B VAL* 1.3 78.9 - - - +
288B SER* 1.3 62.8 + - - +
290B ILE* 4.3 4.0 - - - -
291B ASP* 2.5 40.8 + - - +
334B ARG* 5.2 7.2 - - - +
335B LEU* 3.5 19.6 - - - +
338B LYS* 2.6 29.0 + - - +
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Residues in contact with SER 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B ALA 2.9 17.4 + - - -
285B THR* 3.0 19.3 - - - -
286B VAL 3.0 0.2 + - - -
287B ASN* 1.3 77.6 - - - +
289B PHE* 1.3 62.5 + - - +
291B ASP* 3.3 4.8 + - - +
292B GLY* 2.9 25.1 + - - -
295B GLU* 5.3 0.3 - - - +
549B TRP* 5.1 0.6 - - - -
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Residues in contact with PHE 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B LEU* 4.4 23.1 - - + -
274B THR 4.8 7.0 - - - -
275B THR* 5.0 4.5 - - + -
281B TYR* 6.1 0.4 - - + -
285B THR* 3.0 28.4 + - + -
286B VAL 2.9 6.3 + - - +
288B SER* 1.3 81.8 - - - +
290B ILE* 1.3 66.3 + - + +
292B GLY* 2.8 12.5 + - - +
293B MET* 2.9 19.6 + - + +
300B LEU* 5.7 0.7 - - + -
303B PHE* 4.6 11.9 - + + -
545B TYR* 3.4 50.9 - + + -
547B VAL* 3.5 35.2 - - + -
549B TRP* 3.7 14.9 - + - -
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Residues in contact with ILE 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B VAL* 3.1 20.3 + - + +
287B ASN* 3.8 8.5 - - - +
289B PHE* 1.3 76.0 - - - +
291B ASP* 1.3 58.0 + - - +
293B MET* 3.5 4.3 + - - +
294B ALA* 3.2 25.1 + - + +
300B LEU* 4.5 17.8 - - + +
303B PHE* 4.7 11.2 - - + -
335B LEU* 3.3 34.8 - - + -
338B LYS* 3.8 27.1 - - + +
340B LEU* 3.4 33.2 - - + -
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Residues in contact with ASP 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ASN* 2.5 30.9 + - - +
288B SER* 3.7 5.0 - - - +
290B ILE* 1.3 73.7 - - - +
292B GLY* 1.3 60.6 + - - +
293B MET 3.2 0.7 - - - -
294B ALA* 3.8 7.4 - - - +
295B GLU* 2.9 47.5 + - + +
338B LYS* 3.5 23.4 + - - +
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Residues in contact with GLY 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B SER 2.9 11.0 + - - -
289B PHE 2.8 8.0 + - - -
291B ASP* 1.3 76.5 - - - +
293B MET* 1.3 61.9 + - - +
295B GLU* 4.0 8.2 + - - +
296B ARG* 3.2 42.8 + - - +
549B TRP* 3.6 17.3 - - - -
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Residues in contact with MET 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B LEU* 3.7 20.0 - - + -
273B LEU* 5.4 7.9 - - + -
289B PHE* 2.9 18.0 + - + +
290B ILE 3.6 7.9 - - - +
291B ASP 3.2 0.2 - - - -
292B GLY* 1.3 78.0 - - - +
294B ALA* 1.3 59.0 + - - +
296B ARG 3.2 1.6 + - - -
297B ASN 3.0 4.3 + - - -
298B LEU* 2.7 64.7 + - + +
299B PRO 3.5 24.2 - - - +
300B LEU* 3.9 30.3 - - + -
539B LEU* 5.2 4.3 - - + -
547B VAL* 5.5 1.6 - - + -
548B PRO* 4.3 9.2 - - - -
549B TRP* 3.8 20.6 - - + -
559B VAL* 5.0 3.4 - - + -
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Residues in contact with ALA 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B ILE* 3.2 14.7 + - + +
291B ASP* 3.8 9.2 - - - +
293B MET* 1.3 77.6 - - - +
295B GLU* 1.3 65.8 + - + +
297B ASN* 3.1 17.7 + - - +
298B LEU 4.8 2.9 - - - +
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Residues in contact with GLU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ASP* 2.9 38.8 + - + +
292B GLY* 4.0 9.9 + - - +
294B ALA* 1.3 77.3 - - + +
296B ARG* 1.3 67.5 + - + +
297B ASN* 3.5 9.0 + - - -
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Residues in contact with ARG 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B GLY* 3.2 27.2 + - - +
293B MET 3.2 1.4 + - - -
294B ALA 3.2 0.6 - - - -
295B GLU* 1.3 83.7 + - + +
297B ASN* 1.3 69.0 + - - +
298B LEU* 3.3 13.2 + - + -
549B TRP* 3.5 52.6 - - - +
553B ASP* 5.8 3.2 + - - -
556B CYS* 3.3 25.0 - - - -
560B ARG* 2.7 34.4 + - - +
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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