Contacts of the strand formed by residues 285 - 294 (chain N) in PDB entry 2X1W
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 MET 285 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224N TYR* 3.9 30.7 - - + -
249N ARG* 3.9 41.1 - - + +
250N THR 3.2 7.4 - - - +
252N LEU* 3.8 10.3 - - - +
279N THR* 3.1 33.9 - - + +
280N GLN* 4.4 5.4 - - - +
283N SER* 3.2 11.0 + - - +
284N GLU* 1.3 86.1 - - + +
286N LYS* 1.3 67.5 + - - +
287N LYS* 5.2 6.7 - - + +
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Residues in contact with LYS 286 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A GLU* 3.3 29.6 + - - +
148B THR* 2.9 35.3 + - - +
151B PHE* 4.7 1.4 - - - -
248N ALA 3.8 0.8 - - - +
249N ARG* 3.4 5.4 - - - +
250N THR* 2.8 41.2 + - - +
251N GLU 3.7 11.9 - - - +
252N LEU* 3.9 12.6 - - + -
254N VAL* 3.0 33.6 + - - +
276N ASP* 4.8 2.2 - - - +
279N THR* 4.2 3.8 - - - -
285N MET* 1.3 81.2 - - - +
287N LYS* 1.3 60.7 + - - +
288N PHE* 3.5 16.1 - - + -
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Residues in contact with LYS 287 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247N THR* 3.8 16.8 - - + -
248N ALA 3.5 1.8 - - - -
249N ARG* 3.6 32.8 - - + +
276N ASP* 3.9 4.9 + - - +
277N LEU* 2.9 62.2 + - + +
278N LYS 4.6 6.7 - - - -
279N THR* 3.2 27.4 + - - +
285N MET* 5.2 5.7 - - + +
286N LYS* 1.3 74.0 - - - +
288N PHE* 1.3 65.2 + - - +
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Residues in contact with PHE 288 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B THR* 4.8 0.4 - - - -
149B ASN* 4.4 10.3 - - + -
246N CYS 3.6 0.5 - - - +
247N THR* 3.2 7.4 - - - +
248N ALA* 2.8 46.2 + - + +
250N THR* 3.6 21.8 - - + -
254N VAL* 3.4 24.2 - - + -
256N ILE* 3.4 42.4 - - + -
258N PHE* 3.7 22.1 - + + -
275N ARG 3.9 4.9 - - - -
276N ASP* 3.3 30.3 - - - -
277N LEU* 4.8 2.2 - - - -
286N LYS* 3.5 22.9 - - + -
287N LYS* 1.3 75.9 - - - +
289N LEU* 1.3 61.5 + - - +
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Residues in contact with LEU 289 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245N ASN* 3.9 20.2 - - + +
246N CYS 3.4 19.1 - - - +
247N THR* 3.4 16.8 - - - +
258N PHE* 4.0 3.9 - - - -
273N VAL 4.0 0.8 - - - +
274N ASN* 3.3 4.0 - - - +
275N ARG* 2.8 63.1 + - + +
277N LEU* 3.9 18.1 - - + +
287N LYS 4.3 0.4 + - - -
288N PHE* 1.3 75.2 - - - +
290N SER* 1.3 62.2 + - - +
291N THR* 3.7 16.6 - - - +
1601N NAG 3.5 35.0 - - - +
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Residues in contact with SER 290 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244N LEU 3.7 1.2 - - - +
245N ASN* 3.7 0.5 - - - -
246N CYS* 2.7 43.2 + - - +
258N PHE* 3.5 36.0 - - - +
260N TRP* 3.2 24.1 + - - -
272N LEU* 4.2 3.8 - - - +
273N VAL 3.7 3.4 - - - -
274N ASN* 2.8 18.6 + - - -
289N LEU* 1.3 74.3 - - - +
291N THR* 1.3 61.1 + - - +
292N LEU 4.1 0.2 - - - -
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Residues in contact with THR 291 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243N VAL* 3.9 21.3 - - + -
244N LEU 3.3 6.5 - - - +
245N ASN* 2.7 25.7 + - - +
271N LYS 3.4 6.2 - - - +
272N LEU* 3.5 3.4 - - - -
273N VAL* 3.0 41.2 + - + +
289N LEU* 3.7 15.4 - - - +
290N SER* 1.3 73.1 + - - +
292N LEU* 1.3 61.4 + - - +
293N THR* 3.9 11.4 + - - +
1601N NAG 4.6 0.6 - - - -
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Residues in contact with LEU 292 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242N LEU* 3.7 3.8 - - + +
243N VAL* 3.4 2.6 - - - -
244N LEU* 2.7 41.9 + - + +
260N TRP* 3.8 32.9 - - + -
262N TYR* 4.4 11.4 - - + -
270N LYS* 3.9 26.2 - - + -
271N LYS 3.5 8.1 - - - +
272N LEU* 3.8 18.8 - - + -
290N SER 4.1 1.2 + - - -
291N THR* 1.3 74.4 - - - +
293N THR* 1.3 71.8 + - - +
294N ILE* 4.9 4.5 - - + -
305N TYR* 3.5 38.4 - - + -
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Residues in contact with THR 293 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241N LYS* 3.5 31.2 - - - +
242N LEU 3.3 9.8 + - - +
243N VAL* 4.4 5.5 - - + +
270N LYS* 3.4 3.2 - - - -
271N LYS* 2.8 61.5 + - + +
273N VAL* 6.0 0.9 - - - +
291N THR* 3.9 15.2 + - - +
292N LEU* 1.3 78.3 + - - +
294N ILE* 1.3 70.9 + - - +
295N ASP* 4.2 4.1 + - + +
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Residues in contact with ILE 294 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240N GLU 4.1 0.3 - - - +
241N LYS* 3.5 2.3 - - - +
242N LEU* 2.9 48.0 + - + +
270N LYS* 3.6 43.3 - - + +
292N LEU* 4.9 4.5 - - + -
293N THR* 1.3 76.6 - - - +
295N ASP* 1.3 61.1 + - - +
296N GLY 3.1 10.7 + - - +
297N VAL* 3.6 26.0 - - + -
301N ASP* 3.9 16.8 - - + +
305N TYR* 3.4 29.6 - - + +
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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