Contacts of the strand formed by residues 302 - 314 (chain N) in PDB entry 5DST
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 302 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319L HIS* 3.2 13.9 + - - -
320L LYS* 3.0 30.3 + - - +
227N GLU* 3.8 11.2 - - - +
269N VAL* 3.6 21.5 - - + +
300N ARG* 2.8 45.7 + - + +
301N ASN* 1.3 76.2 - - - +
303N TYR* 1.3 80.8 + - - +
348N VAL* 3.0 31.0 + - - +
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Residues in contact with TYR 303 (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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105L HIS* 2.5 46.2 + + + +
106L ASN* 3.1 13.0 + - - -
319L HIS* 3.7 12.1 - - - +
320L LYS* 4.1 36.0 + - + +
227N GLU* 3.0 30.1 + - + +
269N VAL* 4.0 0.3 - - - +
302N ASP* 1.3 88.9 + - - +
304N VAL* 1.3 65.7 + - - +
305N HIS* 3.8 22.4 - + + -
345N TYR* 3.7 27.1 - + + -
346N LEU 3.2 9.4 - - - +
347N THR* 3.8 22.7 - - + -
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Residues in contact with VAL 304 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225N ALA* 3.9 20.4 - - + -
226N ILE 3.2 9.9 - - - +
269N VAL* 3.9 26.2 - - + -
298N ILE* 5.2 0.2 - - + -
303N TYR* 1.3 75.9 - - - +
305N HIS* 1.3 63.5 + - - +
306N ALA 3.8 16.6 - - - +
307N LEU* 5.1 1.1 - - + -
342N LEU* 4.1 15.7 - - + +
345N TYR* 3.1 5.1 - - - -
346N LEU* 2.7 53.8 + - + +
348N VAL* 4.2 14.1 - - + -
354N ILE* 4.6 6.5 - - + -
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Residues in contact with HIS 305 (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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226N ILE 2.9 4.6 + - - -
227N GLU* 3.8 9.6 - - + +
228N ASP* 3.2 34.9 + - + +
229N ARG* 3.0 41.8 - - + +
232N LYS* 4.1 23.0 + - + +
303N TYR* 3.8 26.0 - + + -
304N VAL* 1.3 75.7 - - - +
306N ALA* 1.3 61.0 + - + +
341N TYR* 4.0 4.8 - - + -
342N LEU* 3.0 31.6 + - - +
345N TYR* 3.6 33.0 - + + +
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Residues in contact with ALA 306 (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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225N ALA* 3.4 6.6 - - - +
226N ILE* 2.9 38.6 + - + +
228N ASP* 5.2 0.4 - - + -
304N VAL* 3.6 4.6 - - - +
305N HIS* 1.3 82.5 - - + +
307N LEU* 1.3 66.1 + - - +
339N VAL* 3.7 25.6 - - + -
340N PHE 3.4 16.4 - - - +
341N TYR* 4.0 9.6 - - + -
342N LEU* 4.2 4.7 - - - -
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Residues in contact with LEU 307 (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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223N VAL* 4.6 15.5 - - + -
224N VAL 3.4 4.0 - - - +
225N ALA* 3.9 19.3 - - + -
294N PHE* 4.0 18.6 - - + -
296N LEU* 4.1 14.4 - - + -
304N VAL* 5.1 4.0 - - + -
306N ALA* 1.3 82.6 - - - +
308N VAL* 1.3 65.7 + - - +
339N VAL* 3.5 0.2 - - - -
340N PHE* 2.7 49.4 + - + +
342N LEU* 4.7 7.2 - - + +
354N ILE* 5.2 2.2 - - + -
358N ILE* 6.4 0.9 - - + -
374N VAL* 3.8 33.0 - - + -
376N LEU* 4.3 19.5 - - + -
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Residues in contact with VAL 308 (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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223N VAL* 3.3 3.5 - - - -
224N VAL* 2.8 40.5 + - + +
226N ILE* 3.5 44.2 - - + -
263N VAL* 4.1 7.9 - - + -
307N LEU* 1.3 81.2 - - - +
309N THR* 1.3 68.7 + - - +
310N TYR* 4.3 2.4 + - + -
328N PRO* 4.8 9.0 - - + -
337N GLN* 3.7 29.6 - - + -
338N THR 3.2 11.0 - - - +
339N VAL* 4.1 11.7 - - + -
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Residues in contact with THR 309 (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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190N CYS* 3.3 16.0 - - - -
221N LEU* 4.2 11.0 - - + -
222N TYR 3.1 15.3 - - - +
223N VAL* 3.7 16.6 - - + -
275N ILE* 4.7 9.0 - - + -
308N VAL* 1.3 78.5 - - - +
310N TYR* 1.3 61.8 + - - +
337N GLN* 3.8 5.0 - - - +
338N THR* 2.9 50.2 + - - -
340N PHE* 3.7 20.6 - - + -
358N ILE* 4.9 4.9 - - + -
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Residues in contact with TYR 310 (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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190N CYS* 6.4 0.4 - - - +
221N LEU* 3.5 6.3 - - - +
222N TYR* 2.8 62.2 + + + -
224N VAL* 4.2 22.9 - - + -
272N ALA* 3.3 22.0 - - - +
308N VAL* 5.0 3.8 - - + -
309N THR* 1.3 77.0 - - - +
311N PHE* 1.3 64.8 + - - +
312N ASN* 3.9 18.6 - - - -
325N SER* 4.4 0.2 - - - -
326N THR* 3.5 24.2 - - - +
327N ALA* 3.5 29.2 - - + -
328N PRO* 3.8 16.8 - - + -
329N ASP* 5.6 1.9 + - - -
336N LYS 5.5 0.7 - - - -
337N GLN* 4.4 4.7 - - + -
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Residues in contact with PHE 311 (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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187N MET* 4.2 9.0 - - + -
188N GLY 3.8 6.1 - - - -
190N CYS* 4.4 5.8 - - - -
191N LEU* 3.5 47.8 - - + -
220N ALA 3.0 19.7 - - - +
221N LEU* 4.0 8.1 - - + -
310N TYR* 1.3 78.9 - - - +
312N ASN* 1.3 63.0 + - - +
313N ILE* 3.7 28.7 - - + -
324N PHE* 4.6 2.5 - + - -
326N THR* 2.9 51.5 + - + +
335N TRP* 3.6 43.7 - + + -
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Residues in contact with ASN 312 (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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218N ARG* 5.7 3.1 + - - +
219N ALA* 3.4 3.8 - - - +
220N ALA* 2.9 34.4 + - + +
222N TYR* 3.3 27.6 + - + -
310N TYR* 3.9 11.9 - - - -
311N PHE* 1.3 79.5 + - - +
313N ILE* 1.3 65.8 + - - +
324N PHE 3.4 9.6 - - - +
325N SER* 2.7 36.3 + - - -
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Residues in contact with ILE 313 (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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186N TRP* 4.8 1.8 - - + -
187N MET* 3.8 30.5 - - + -
216N PRO* 3.4 31.0 - - + -
218N ARG* 3.6 3.1 - - - +
219N ALA* 3.7 24.9 - - + -
311N PHE* 3.7 23.8 - - + -
312N ASN* 1.3 78.4 - - - +
314N GLU* 1.3 63.8 + - - +
315N PHE* 4.1 11.9 - - + -
321N LYS* 4.8 2.6 + - - -
323N GLY* 3.1 20.6 - - - -
324N PHE* 3.0 35.7 + - + +
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Residues in contact with GLU 314 (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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216N PRO* 3.3 3.3 - - - +
217N ASP* 3.2 22.2 + - - +
218N ARG* 2.8 53.1 + - + +
313N ILE* 1.3 76.4 - - - +
315N PHE* 1.3 72.8 + - - +
316N THR* 3.7 17.6 - - + +
321N LYS* 3.8 30.5 + - + +
322N MET 3.5 12.7 + - - +
323N GLY* 4.2 0.4 - - - -
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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