Contacts of the strand formed by residues 302 - 315 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319B HIS* 3.1 15.5 + - - -
320B LYS* 2.9 34.5 + - - +
227D GLU* 3.9 13.1 - - - +
269D VAL* 3.5 22.6 - - + +
300D ARG* 2.9 43.6 + - + +
301D ASN* 1.3 76.8 - - - +
303D TYR* 1.3 71.4 + - - +
347D THR 4.0 0.2 - - - -
348D VAL* 3.1 32.2 + - - +
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Residues in contact with TYR 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B HIS* 2.5 47.2 + + + +
106B ASN* 2.9 16.3 + - - -
319B HIS* 3.6 11.7 - - - +
320B LYS* 4.2 29.9 + - + +
227D GLU* 3.1 28.3 + - + +
269D VAL* 4.1 0.2 - - - +
302D ASP* 1.3 89.8 + - - +
304D VAL* 1.3 64.5 + - - +
305D HIS* 3.9 21.8 - + + -
345D TYR* 3.7 27.8 - + + -
346D LEU 3.3 6.7 - - - +
347D THR* 3.9 25.1 - - + -
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Residues in contact with VAL 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D ALA* 3.9 21.3 - - + -
226D ILE 3.3 10.5 - - - +
269D VAL* 4.0 26.2 - - + -
298D ILE* 5.2 0.7 - - + -
303D TYR* 1.3 76.5 - - - +
305D HIS* 1.3 63.8 + - - +
306D ALA 3.8 15.7 - - - +
307D LEU* 5.0 1.6 - - + -
342D LEU* 4.2 15.6 - - + +
345D TYR* 3.3 5.3 - - - -
346D LEU* 2.8 50.6 + - + -
348D VAL* 4.1 13.9 - - + -
354D ILE* 4.7 5.8 - - + -
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Residues in contact with HIS 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D ILE 2.9 5.3 + - - -
227D GLU* 3.8 9.1 - - + +
228D ASP* 3.2 33.5 + - + +
229D ARG* 3.1 41.6 - - + +
232D LYS* 4.2 23.8 - - + +
303D TYR* 3.9 26.2 + + + -
304D VAL* 1.3 74.4 - - - +
306D ALA* 1.3 62.5 + - + +
341D TYR* 3.8 5.7 - - + -
342D LEU* 3.1 30.1 + - - +
345D TYR* 3.6 34.8 - + + +
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Residues in contact with ALA 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D ALA* 3.4 4.3 - - - -
226D ILE* 2.9 37.6 + - + +
228D ASP* 5.3 0.2 - - + -
304D VAL* 3.6 6.8 - - - +
305D HIS* 1.3 84.4 - - + +
307D LEU* 1.3 64.9 + - - +
339D VAL* 3.8 25.4 - - + -
340D PHE 3.2 17.0 - - - +
341D TYR* 3.9 9.4 - - + -
342D LEU* 4.2 4.7 - - - -
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Residues in contact with LEU 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D VAL* 4.7 14.8 - - + -
224D VAL 3.3 7.9 - - - +
225D ALA* 3.9 19.3 - - + -
294D PHE* 4.1 18.4 - - + -
296D LEU* 4.1 10.5 - - + -
304D VAL* 5.0 3.8 - - + -
306D ALA* 1.3 81.7 - - - +
308D VAL* 1.3 63.1 + - - +
339D VAL 3.6 0.2 - - - -
340D PHE* 2.7 48.1 + - + +
342D LEU* 4.7 9.6 - - + -
354D ILE* 5.1 2.5 - - + -
358D ILE* 6.4 1.1 - - + -
374D VAL* 3.8 31.4 - - + -
376D LEU* 4.3 20.9 - - + -
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Residues in contact with VAL 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D VAL* 3.2 4.6 - - - -
224D VAL* 2.8 39.9 + - + +
226D ILE* 3.6 43.7 - - + -
263D VAL* 4.2 7.4 - - + -
307D LEU* 1.3 80.3 - - - +
309D THR* 1.3 68.5 + - - +
310D TYR* 4.3 2.6 + - + -
328D PRO* 4.8 9.0 - - + -
337D GLN* 3.6 35.4 - - + -
338D THR 3.3 6.1 - - - +
339D VAL* 4.1 13.7 - - + -
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Residues in contact with THR 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D CYS* 3.3 19.5 - - - +
221D LEU* 4.1 11.2 - - + -
222D TYR 3.1 16.4 - - - +
223D VAL* 3.7 16.6 - - + -
275D ILE* 4.6 9.9 - - + -
308D VAL* 1.3 79.0 - - - +
310D TYR* 1.3 61.5 + - - +
337D GLN* 3.9 5.0 - - - -
338D THR* 3.0 44.6 + - - -
340D PHE* 3.7 19.1 - - + -
358D ILE* 4.9 4.7 - - + -
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Residues in contact with TYR 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D CYS* 6.4 0.2 - - - +
221D LEU* 3.4 6.8 - - - +
222D TYR* 2.8 63.3 + + + +
224D VAL* 4.3 22.2 - - + -
272D ALA* 3.2 22.2 - - - +
308D VAL* 5.0 4.9 - - + -
309D THR* 1.3 77.1 - - - +
311D PHE* 1.3 66.5 + - - +
312D ASN* 3.9 19.1 - - - -
326D THR* 3.6 15.9 - - - +
327D ALA* 3.6 35.0 - - + -
328D PRO* 3.9 19.3 - - + -
329D ASP* 5.8 1.6 - - - -
336D LYS 5.5 0.4 - - - -
337D GLN* 4.6 2.5 - - + -
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Residues in contact with PHE 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D MET* 4.2 7.6 - - + -
188D GLY 3.8 7.2 - - - -
190D CYS* 4.4 6.3 - - - -
191D LEU* 3.5 46.2 - - + -
220D ALA 3.2 15.0 - - - +
221D LEU* 4.1 9.2 - - + -
222D TYR* 4.8 0.2 - - - -
310D TYR* 1.3 78.8 - - - +
312D ASN* 1.3 64.1 + - - +
313D ILE* 3.8 32.1 - - + -
324D PHE* 4.4 3.1 - + - +
325D SER* 3.8 0.2 - - - -
326D THR* 3.0 52.9 + - + +
335D TRP* 3.6 44.0 - + + -
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Residues in contact with ASN 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D ARG* 5.8 4.4 + - - +
219D ALA* 3.4 5.0 - - - +
220D ALA* 3.0 34.2 + - + +
222D TYR* 3.6 25.6 + - + -
310D TYR* 3.9 11.3 - - - -
311D PHE* 1.3 76.1 + - - +
313D ILE* 1.3 68.6 + - - +
324D PHE 3.4 7.2 - - - +
325D SER* 2.7 37.8 + - - +
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Residues in contact with ILE 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186D TRP* 4.9 0.7 - - + -
187D MET* 3.8 37.0 - - + -
191D LEU* 4.3 0.2 - - + -
216D PRO* 3.4 32.1 - - + -
218D ARG* 3.7 3.1 - - - +
219D ALA* 3.7 20.0 - - + -
311D PHE* 3.8 22.9 - - + -
312D ASN* 1.3 84.9 - - - +
314D GLU* 1.3 66.6 + - - +
315D PHE* 4.2 11.0 - - + -
321D LYS* 4.8 2.4 + - - -
323D GLY* 3.1 21.1 - - - -
324D PHE* 3.0 30.7 + - + +
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Residues in contact with GLU 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D PRO* 3.1 16.0 - - - +
217D ASP* 3.2 10.1 + - - +
218D ARG* 2.8 53.4 + - + +
313D ILE* 1.3 76.2 - - - +
315D PHE* 1.3 74.2 + - - +
316D THR* 3.7 18.8 - - + +
321D LYS* 4.0 28.2 + - + +
322D MET 3.5 13.0 - - - +
323D GLY* 4.2 0.4 - - - -
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Residues in contact with PHE 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D THR* 3.4 29.2 - - + -
99D TYR* 4.1 36.8 - + - -
102D SER* 3.7 16.4 - - - -
214D MET 5.4 0.4 - - - -
215D PHE* 3.6 26.5 - + + -
216D PRO* 3.5 40.4 - - + -
217D ASP* 3.8 4.0 - - - -
313D ILE* 4.2 10.3 - - + -
314D GLU* 1.3 74.4 - - - +
316D THR* 1.3 63.0 + - - +
317D LYS 3.3 2.2 + - - -
318D CYS* 3.6 30.9 + - - +
320D LYS 4.8 0.5 - - - +
321D LYS* 5.6 0.2 - - - -
322D MET* 3.1 27.8 + - + +
323D GLY* 4.3 1.8 - - - -
324D PHE* 4.7 2.2 - + - -
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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