Contacts of the strand formed by residues 337 - 348 (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 GLN 337 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260D VAL* 3.3 7.8 - - - +
261D ASP 3.0 30.7 + - - +
262D ILE* 3.4 9.6 - - - +
263D VAL* 2.9 35.5 + - + +
308D VAL* 3.6 18.6 - - + -
309D THR 3.9 7.0 - - - +
310D TYR* 4.6 1.6 - - + -
326D THR 2.6 27.6 + - - +
327D ALA 3.1 15.0 + - - -
328D PRO* 3.7 29.0 - - + +
335D TRP 4.1 1.1 - - - -
336D LYS* 1.3 85.9 + - - +
338D THR* 1.3 65.0 + - - +
339D VAL* 4.9 0.4 - - - -
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Residues in contact with THR 338 (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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189D TYR* 4.7 2.8 - - - +
190D CYS* 3.3 37.3 + - + -
258D PRO* 4.0 15.9 - - + -
259D LEU 3.4 4.3 - - - +
260D VAL* 4.6 8.9 - - + +
308D VAL* 3.3 5.2 - - - -
309D THR* 3.0 43.8 + - - -
335D TRP 4.9 1.7 + - - -
337D GLN* 1.3 80.3 + - - +
339D VAL* 1.3 63.5 - - - +
340D PHE* 3.8 19.8 - - + -
393D MET* 4.3 9.4 - - - -
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Residues in contact with VAL 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D ILE* 4.7 5.6 - - + -
228D ASP* 4.7 2.2 - - - +
258D PRO* 3.1 6.9 - - - +
259D LEU* 2.7 48.3 + - + +
261D ASP* 4.7 9.2 - - + +
263D VAL* 3.9 27.8 - - + -
306D ALA* 3.8 23.6 - - + -
307D LEU 3.6 4.0 - - - +
308D VAL* 4.1 6.5 - - + -
338D THR* 1.3 77.6 - - - +
340D PHE* 1.3 63.1 + - - +
341D TYR* 3.9 27.2 + - + +
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Residues in contact with PHE 340 (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* 4.2 2.7 - - - -
258D PRO* 3.6 18.8 - - + -
306D ALA* 3.2 3.1 - - - +
307D LEU* 2.7 50.1 + - + +
309D THR* 3.7 33.2 - - + -
338D THR* 3.8 22.9 - - + -
339D VAL* 1.3 76.1 - - - +
341D TYR* 1.3 65.0 + - - +
342D LEU* 4.6 2.5 - - + +
358D ILE* 5.3 3.4 - - + -
372D PHE* 3.8 45.3 - + + -
374D VAL* 4.8 9.4 - - + -
391D TYR* 3.8 36.2 + + + +
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Residues in contact with TYR 341 (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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228D ASP* 2.7 31.4 + - + -
231D TYR* 3.6 19.2 - - - -
232D LYS* 3.6 36.9 - - + -
235D LYS* 4.8 1.6 - - + -
236D ILE* 3.9 21.1 - - + -
255D MET* 3.7 31.7 + - - +
257D GLU 5.6 1.8 - - - -
258D PRO* 5.7 0.8 - - + +
259D LEU* 3.9 34.1 - - + +
305D HIS* 3.8 14.1 - - + -
306D ALA* 3.9 11.2 - - + -
339D VAL* 3.9 12.5 + - + +
340D PHE* 1.3 71.5 - - - +
342D LEU* 1.3 56.9 + - - +
389D ASN* 4.5 0.2 + - - -
391D TYR* 2.3 38.9 + - - -
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Residues in contact with LEU 342 (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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232D LYS* 2.9 25.3 + - - -
255D MET* 3.5 8.1 - - - +
304D VAL* 4.2 20.4 - - + +
305D HIS 3.1 15.7 + - - +
306D ALA* 4.2 5.8 - - - +
307D LEU* 4.7 9.4 - - + -
340D PHE* 4.6 3.8 - - + +
341D TYR* 1.3 79.2 - - - +
343D GLU* 1.3 61.9 + - - +
344D ASP 3.6 18.8 - - - +
346D LEU* 4.2 28.0 - - + -
374D VAL* 5.8 2.7 - - + -
376D LEU* 4.3 24.5 - - + -
389D ASN* 4.1 17.5 - - - +
391D TYR* 4.2 4.3 - - - +
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Residues in contact with GLU 343 (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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232D LYS* 3.2 14.9 + - - -
237D HIS* 5.2 4.3 - - - -
255D MET* 3.8 20.1 - - + +
256D LYS* 5.6 13.4 - - - -
342D LEU* 1.3 73.5 - - - +
344D ASP* 1.3 72.1 + - - +
387D VAL* 4.3 9.6 - - + +
389D ASN* 3.5 26.2 - - - +
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Residues in contact with ASP 344 (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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232D LYS* 4.7 1.8 - - - +
342D LEU* 3.6 19.4 - - - +
343D GLU* 1.3 88.1 - - - +
345D TYR* 1.3 70.1 + - + +
346D LEU* 3.8 9.5 + - + +
385D THR* 5.8 6.3 - - + +
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Residues in contact with TYR 345 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104B TYR 2.6 28.6 + - - -
105B HIS* 3.5 15.8 - + - -
107B LYS* 3.7 24.2 + - + +
232D LYS* 4.8 3.8 - - - +
303D TYR* 3.7 32.3 - + - -
304D VAL 3.3 15.7 - - - +
305D HIS* 3.6 37.9 - + + +
344D ASP* 1.3 80.4 - - - +
346D LEU* 1.3 63.1 + - - +
347D THR* 4.0 11.6 + - - -
383D CYS* 4.9 2.9 - - - -
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Residues in contact with LEU 346 (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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303D TYR* 3.3 7.4 - - - +
304D VAL* 2.8 38.8 + - + -
342D LEU* 4.2 18.4 - - + -
344D ASP* 4.0 11.0 - - + +
345D TYR* 1.3 78.6 - - - +
347D THR* 1.3 61.6 + - - +
348D VAL* 3.7 14.2 + - + -
354D ILE* 4.1 27.4 - - + -
376D LEU* 4.1 24.7 - - + -
378D PHE* 4.4 17.3 - - + -
383D CYS* 4.0 9.2 - - - -
385D THR* 4.2 20.2 - - + +
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Residues in contact with THR 347 (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 5.2 0.2 + - - -
108B HIS* 3.9 25.8 + - + +
319B HIS* 3.7 30.3 - - + +
302D ASP 4.1 2.0 - - - -
303D TYR* 3.9 22.0 - - + -
345D TYR* 4.0 10.8 + - - -
346D LEU* 1.3 71.9 - - - +
348D VAL* 1.3 60.6 + - - +
352D GLU* 4.2 1.7 - - - +
378D PHE* 3.9 6.6 - - - -
382D LEU* 3.9 24.3 + - + +
383D CYS* 3.4 25.3 + - - +
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Residues in contact with VAL 348 (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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319B HIS* 3.1 9.1 - - - -
269D VAL* 4.1 11.0 - - + -
298D ILE* 3.7 35.9 - - + -
301D ASN* 3.5 0.2 - - - -
302D ASP 3.1 48.6 + - - +
304D VAL* 4.1 11.0 - - + -
346D LEU* 3.7 26.5 - - + +
347D THR* 1.3 79.6 - - - +
349D ARG* 1.3 61.6 + - - +
352D GLU* 3.9 2.9 - - - -
354D ILE* 5.2 0.2 - - + -
378D PHE* 3.8 18.6 - - + -
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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