Contacts of the strand formed by residues 302 - 315 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319J HIS* 3.1 11.6 - - - -
320J LYS* 2.9 31.6 + - - +
227L GLU* 3.7 12.5 - - - +
269L VAL* 3.6 18.8 - - + +
300L ARG* 2.9 44.5 + - + +
301L ASN* 1.3 75.3 - - - +
303L TYR* 1.3 84.3 + - - +
347L THR 3.9 0.5 - - - -
348L VAL* 2.9 32.9 + - - +
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Residues in contact with TYR 303 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105J HIS* 2.6 46.4 + + + +
106J ASN* 3.1 14.0 + - - -
319J HIS* 3.5 11.8 - - - +
320J LYS* 4.0 32.8 + - + +
227L GLU* 3.2 27.7 + - + +
269L VAL* 4.0 0.3 - - - +
302L ASP* 1.3 92.0 + - - +
304L VAL* 1.3 65.7 + - - +
305L HIS* 3.8 22.9 - + + -
345L TYR* 3.7 25.1 - + + -
346L LEU 3.3 5.6 - - - +
347L THR* 3.8 28.0 - - + -
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Residues in contact with VAL 304 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225L ALA* 3.9 18.2 - - + -
226L ILE 3.4 4.9 - - - +
269L VAL* 3.9 30.1 - - + -
303L TYR* 1.3 78.4 - - - +
305L HIS* 1.3 64.0 + - - +
306L ALA 3.8 21.8 - - - +
307L LEU* 5.2 1.6 - - + -
342L LEU* 4.2 15.3 - - + +
345L TYR* 3.2 4.2 - - - -
346L LEU* 2.8 54.8 + - + +
348L VAL* 4.1 13.0 - - + -
354L ILE* 4.6 5.8 - - + -
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Residues in contact with HIS 305 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226L ILE 2.9 5.5 + - - -
227L GLU* 3.8 10.0 - - + +
228L ASP* 3.2 33.3 + - + +
229L ARG* 3.1 41.9 - - + +
232L LYS* 4.2 23.5 + - + +
303L TYR* 3.8 25.1 - + + -
304L VAL* 1.3 74.6 - - - +
306L ALA* 1.3 61.3 + - + +
341L TYR* 4.0 4.4 - - + -
342L LEU* 3.0 31.6 + - - +
345L TYR* 3.6 34.2 - + + +
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Residues in contact with ALA 306 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225L ALA* 3.4 4.3 - - - -
226L ILE* 3.0 36.9 + - + +
228L ASP* 5.4 0.2 - - + -
304L VAL* 3.6 7.9 - - - +
305L HIS* 1.3 82.1 - - + +
307L LEU* 1.3 66.5 + - - +
339L VAL* 3.8 25.4 - - + -
340L PHE 3.2 18.2 - - - +
341L TYR* 4.0 9.9 - - + -
342L LEU* 4.1 4.7 - - - -
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Residues in contact with LEU 307 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223L VAL* 4.6 15.5 - - + -
224L VAL 3.4 7.2 - - - +
225L ALA* 3.9 18.2 - - + -
294L PHE* 4.0 19.1 - - + -
296L LEU* 4.2 11.7 - - + -
304L VAL* 5.2 4.0 - - + -
306L ALA* 1.3 82.8 - - - +
308L VAL* 1.3 65.1 + - - +
339L VAL* 3.5 0.3 - - - -
340L PHE* 2.7 45.8 + - + +
342L LEU* 4.7 7.9 - - + -
354L ILE* 5.2 2.7 - - + -
358L ILE* 6.3 1.1 - - + -
374L VAL* 3.7 32.5 - - + -
376L LEU* 4.3 20.9 - - + -
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Residues in contact with VAL 308 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223L VAL* 3.3 4.2 - - - -
224L VAL* 2.8 42.9 + - + +
226L ILE* 3.6 40.2 - - + -
263L VAL* 4.2 7.4 - - + -
307L LEU* 1.3 79.6 - - - +
309L THR* 1.3 70.0 + - - +
310L TYR* 5.0 2.2 - - + -
328L PRO* 4.8 8.7 - - + -
337L GLN* 3.6 31.9 - - + -
338L THR 3.2 10.1 - - - +
339L VAL* 4.1 12.6 - - + -
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Residues in contact with THR 309 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190L CYS* 3.3 18.2 - - - +
221L LEU* 4.1 10.8 - - + -
222L TYR 3.1 17.0 - - - +
223L VAL* 3.6 20.9 - - + -
275L ILE* 4.6 8.7 - - + -
308L VAL* 1.3 76.2 - - - +
310L TYR* 1.3 61.3 + - - +
337L GLN* 3.9 4.0 - - - -
338L THR* 2.9 48.5 + - - -
340L PHE* 3.8 18.4 - - + -
358L ILE* 4.9 5.4 - - + -
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Residues in contact with TYR 310 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190L CYS* 6.4 0.2 - - - +
221L LEU* 3.5 6.6 - - - +
222L TYR* 2.8 62.7 + + + -
224L VAL* 4.2 26.7 - - + -
272L ALA* 3.2 22.3 - - - +
308L VAL* 5.0 1.8 - - + -
309L THR* 1.3 77.4 - - - +
311L PHE* 1.3 66.3 + - - +
312L ASN* 3.9 17.7 - - - -
326L THR* 3.5 15.5 - - - +
327L ALA* 3.5 38.1 - - + -
328L PRO* 3.8 18.4 - - + -
329L ASP* 5.8 0.9 - - - -
336L LYS 5.3 0.7 - - - -
337L GLN* 4.5 2.9 - - + -
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Residues in contact with PHE 311 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187L MET* 4.2 9.6 - - + -
188L GLY 3.8 5.8 - - - -
190L CYS* 4.4 6.5 - - - -
191L LEU* 3.5 46.9 - - + -
220L ALA 3.1 17.0 - - - +
221L LEU* 4.1 7.9 - - + -
310L TYR* 1.3 78.1 - - - +
312L ASN* 1.3 67.5 + - - +
313L ILE* 3.7 30.3 - - + -
324L PHE* 4.5 2.9 - + - -
326L THR* 2.9 52.9 + - + +
335L TRP* 3.6 43.3 - + + -
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Residues in contact with ASN 312 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218L ARG* 5.8 3.8 + - - +
219L ALA* 3.4 4.3 - - - -
220L ALA* 2.9 33.8 + - + +
222L TYR* 3.3 27.1 + - + -
310L TYR* 3.9 10.9 - - - -
311L PHE* 1.3 79.3 + - - +
313L ILE* 1.3 68.8 + - - +
324L PHE 3.4 7.0 - - - +
325L SER* 2.7 36.8 + - - -
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Residues in contact with ILE 313 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186L TRP* 5.0 0.7 - - + -
187L MET* 3.8 29.6 - - + -
191L LEU* 4.4 0.4 - - + -
216L PRO* 3.4 32.5 - - + -
218L ARG* 3.6 3.4 - - - +
219L ALA* 3.7 21.1 - - + -
311L PHE* 3.7 23.1 - - + -
312L ASN* 1.3 83.5 - - - +
314L GLU* 1.3 65.3 + - - +
315L PHE* 4.2 5.6 - - + -
321L LYS* 4.7 2.6 + - - -
323L GLY* 3.0 20.8 - - - -
324L PHE* 2.9 45.6 + - + +
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Residues in contact with GLU 314 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216L PRO* 3.3 2.9 - - - +
217L ASP* 3.2 8.1 + - - +
218L ARG* 2.9 68.4 + - + +
313L ILE* 1.3 76.8 - - - +
315L PHE* 1.3 72.8 + - - +
316L THR* 3.7 16.2 - - + +
321L LYS* 3.8 30.4 + - - +
322L MET 3.3 14.1 - - - +
323L GLY* 4.1 0.4 - - - -
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Residues in contact with PHE 315 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98L THR* 3.5 28.5 - - + -
99L TYR* 4.0 36.8 - + - -
102L SER* 3.8 15.7 - - - -
214L MET 5.5 0.7 - - - -
215L PHE* 3.6 27.1 - + + -
216L PRO* 3.4 40.6 - - + -
217L ASP* 4.0 3.1 - - - -
313L ILE* 4.2 10.5 - - + -
314L GLU* 1.3 73.0 - - - +
316L THR* 1.3 62.2 - - - +
317L LYS 3.3 2.8 + - - -
318L CYS* 3.5 31.5 + - - +
320L LYS 4.8 0.5 - - - +
321L LYS* 5.6 0.2 - - - -
322L MET* 2.9 30.5 + - + +
323L GLY* 4.3 1.8 - - - -
324L PHE* 4.6 2.7 - + - -
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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