Contacts of the helix formed by residues 282 - 296 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A TYR* 1.3 76.0 - - - +
283A GLU* 1.3 66.8 + - - +
284A ALA* 3.8 13.7 - - - +
285A THR* 2.7 27.9 + - - -
286A VAL* 3.0 21.8 + - - +
324A THR* 3.5 26.5 - - + +
325A PHE* 3.5 9.9 - - - -
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Residues in contact with GLU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A ASP* 1.3 75.0 - - - +
284A ALA* 1.3 57.2 + - - +
286A VAL* 2.8 27.9 + - + +
287A ASN* 2.8 37.1 + - - +
324A THR 4.0 2.3 + - - +
325A PHE* 3.5 8.1 - - + -
326A PRO* 6.4 1.3 - - + -
327A ASP* 5.3 1.7 - - - +
331A MET* 3.4 40.7 - - + +
334A ARG* 2.6 39.7 + - - +
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Residues in contact with ALA 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ASP* 3.3 13.9 + - - +
283A GLU* 1.3 76.9 - - - +
285A THR* 1.3 57.9 + - - +
287A ASN* 3.6 7.8 + - - +
288A SER* 2.9 30.1 + - - -
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Residues in contact with THR 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A THR* 6.1 0.4 - - + -
280A ASN* 4.0 8.7 + - - +
281A TYR* 3.5 21.1 - - + -
282A ASP* 2.7 37.3 + - - -
284A ALA* 1.3 75.6 - - - +
286A VAL* 1.3 64.3 + - - +
288A SER* 3.2 8.5 + - - -
289A PHE* 3.1 50.6 + - + -
545A TYR* 4.2 4.6 + - - +
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Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A THR* 4.7 6.3 - - + -
281A TYR* 5.5 1.1 - - + -
282A ASP 3.0 17.9 + - - +
283A GLU* 2.8 13.5 + - + +
285A THR* 1.3 77.2 - - - +
287A ASN* 1.3 63.5 + - - +
289A PHE* 3.0 8.3 + - - +
290A ILE* 3.0 26.6 + - + +
303A PHE* 3.7 31.6 - - + -
305A PHE* 3.8 25.6 - - + -
325A PHE* 4.6 1.8 - - + -
331A MET* 4.8 0.9 - - - -
335A LEU* 3.9 32.3 - - + -
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Residues in contact with ASN 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A GLU* 2.8 51.6 + - - +
284A ALA* 4.1 5.8 - - - +
286A VAL* 1.3 74.5 - - - +
288A SER* 1.3 55.0 + - - +
290A ILE* 4.4 5.6 - - - +
291A ASP* 2.7 50.7 + - - +
334A ARG* 5.9 2.8 - - - +
335A LEU* 4.0 15.6 - - - +
338A LYS* 3.9 16.7 + - - +
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Residues in contact with SER 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ALA 2.9 19.9 + - - -
285A THR* 3.4 8.5 - - - -
287A ASN* 1.3 75.6 - - - +
289A PHE* 1.3 65.7 + - - +
291A ASP* 4.3 3.7 - - - +
292A GLY* 2.9 24.3 + - - -
295A GLU* 5.3 0.2 - - - +
549A TRP* 4.5 3.8 - - - -
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Residues in contact with PHE 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A LEU* 4.4 23.1 - - + -
274A THR 4.5 8.1 - - - -
275A THR* 4.7 5.4 - - + -
285A THR* 3.1 28.9 + - + -
286A VAL* 3.0 9.6 + - - +
288A SER* 1.3 84.0 - - - +
290A ILE* 1.3 59.9 + - + +
292A GLY* 3.2 1.4 + - - -
293A MET* 2.9 34.6 + - + +
303A PHE* 4.8 7.0 - + + -
545A TYR* 3.2 58.6 - + + -
547A VAL* 3.6 31.2 - - + -
549A TRP* 3.6 13.0 - + - -
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Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A LEU* 6.2 0.2 - - + -
286A VAL* 3.0 24.0 + - + +
287A ASN* 3.9 5.2 - - - +
289A PHE* 1.3 74.8 - - + +
291A ASP* 1.3 64.4 + - - +
293A MET* 3.2 8.9 + - + +
294A ALA* 3.1 23.0 + - + +
300A LEU* 5.2 8.5 - - + -
303A PHE* 4.5 16.8 - - + -
335A LEU* 3.1 34.3 - - + -
338A LYS* 4.0 28.3 - - + +
340A LEU* 3.3 26.2 - - + -
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Residues in contact with ASP 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ASN* 2.7 35.2 + - - +
288A SER* 4.3 3.8 - - - +
290A ILE* 1.3 73.9 - - - +
292A GLY* 1.3 54.1 + - - +
294A ALA* 3.3 6.3 + - - +
295A GLU* 2.8 55.7 + - + +
338A LYS* 3.4 21.2 + - - -
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Residues in contact with GLY 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A SER 2.9 20.2 + - - -
289A PHE 3.2 2.4 + - - -
290A ILE 3.1 0.2 - - - -
291A ASP* 1.3 78.7 - - - +
293A MET* 1.3 59.7 + - - +
295A GLU* 3.6 8.6 + - - +
296A ARG* 3.1 39.6 + - - +
549A TRP* 3.5 17.4 - - - -
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Residues in contact with MET 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A LEU* 3.8 17.7 - - + -
273A LEU* 5.4 9.0 - - + -
289A PHE* 2.9 21.0 + - + +
290A ILE* 3.6 7.6 - - - +
291A ASP 3.2 0.2 - - - -
292A GLY* 1.3 73.9 - - - +
294A ALA* 1.3 64.7 + - - +
296A ARG 3.1 3.1 + - - -
297A ASN 3.1 4.0 + - - -
298A LEU* 2.8 72.6 + - + +
299A PRO 3.8 13.0 - - - +
300A LEU* 3.9 27.1 - - + -
539A LEU* 5.1 3.6 - - + -
547A VAL* 5.2 4.0 - - + -
548A PRO* 4.3 10.1 - - - -
549A TRP* 4.1 12.1 - - + -
559A VAL* 5.0 2.7 - - + -
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Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ILE* 3.1 14.2 + - + +
291A ASP* 3.8 6.7 - - - +
293A MET* 1.3 77.9 - - - +
295A GLU* 1.3 65.9 + - + +
297A ASN* 2.9 20.6 + - - +
298A LEU 4.3 3.6 + - - +
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Residues in contact with GLU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ASP* 2.8 47.6 + - + +
292A GLY* 3.6 11.2 + - - +
294A ALA* 1.3 75.2 - - + +
296A ARG* 1.3 67.1 + - + +
297A ASN* 3.2 8.7 + - - +
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Residues in contact with ARG 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A GLY* 3.1 30.3 + - - +
293A MET 3.1 3.4 + - - -
295A GLU* 1.3 87.1 + - + +
297A ASN* 1.3 68.4 + - - +
298A LEU* 3.2 13.2 + - + +
549A TRP* 3.4 61.7 - - - +
556A CYS* 3.7 17.3 - - + -
560A ARG* 2.5 36.4 + - - +
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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