Contacts of the strand formed by residues 302 - 314 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319D HIS* 3.0 24.0 - - - -
320D LYS* 2.6 37.7 + - - +
227F GLU* 3.8 8.3 - - - +
269F VAL* 3.9 24.5 - - + -
300F ARG* 2.7 44.7 + - - +
301F ASN* 1.3 75.0 - - - +
303F TYR* 1.3 75.6 + - - +
348F VAL* 3.0 21.2 + - - +
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Residues in contact with TYR 303 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D HIS* 2.8 44.1 + + + +
106D ASN* 3.1 13.5 + - - -
319D HIS* 3.5 12.2 - - - +
320D LYS* 3.7 39.9 + - + +
227F GLU* 3.1 29.3 - - + +
269F VAL* 4.1 0.3 - - - +
302F ASP* 1.3 84.5 + - - +
304F VAL* 1.3 63.9 + - - +
305F HIS* 3.8 22.0 - + + -
345F TYR* 3.7 27.4 - + + -
346F LEU 3.3 4.3 - - - +
347F THR* 3.8 27.4 - - + -
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Residues in contact with VAL 304 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225F ALA* 3.8 21.3 - - + -
226F ILE 3.3 9.4 - - - +
269F VAL* 3.9 28.0 - - + -
298F ILE* 5.3 0.2 - - + -
303F TYR* 1.3 76.4 - - - +
305F HIS* 1.3 62.3 + - - +
306F ALA 3.8 16.6 - - - +
307F LEU* 5.1 1.1 - - + -
342F LEU* 4.1 14.7 - - + +
345F TYR* 3.2 4.8 - - - -
346F LEU* 2.8 55.4 + - + -
348F VAL* 4.2 13.0 - - + -
354F ILE* 4.6 6.1 - - + -
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Residues in contact with HIS 305 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226F ILE 2.8 5.3 + - - -
227F GLU* 3.8 9.4 - - + +
228F ASP* 3.2 34.6 + - + +
229F ARG* 3.1 40.9 - - + +
232F LYS* 4.2 22.9 + - + +
303F TYR* 3.8 26.5 - + + -
304F VAL* 1.3 73.6 - - - +
306F ALA* 1.3 61.9 + - + +
341F TYR* 3.8 4.5 - - + -
342F LEU* 2.9 33.6 + - - +
345F TYR* 3.6 33.3 - + + +
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Residues in contact with ALA 306 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225F ALA* 3.4 4.2 - - - +
226F ILE* 3.0 37.6 + - + +
228F ASP* 5.3 0.2 - - + -
304F VAL* 3.7 5.9 - - - +
305F HIS* 1.3 81.4 - - + +
307F LEU* 1.3 65.4 + - - +
339F VAL* 3.8 20.9 - - + -
340F PHE 3.2 22.7 - - - +
341F TYR* 3.9 11.0 - - + -
342F LEU* 4.1 4.3 - - - -
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Residues in contact with LEU 307 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223F VAL* 4.6 15.9 - - + -
224F VAL 3.3 7.9 - - - +
225F ALA* 3.9 20.0 - - + -
294F PHE* 4.1 17.5 - - + -
296F LEU* 4.1 11.0 - - + -
304F VAL* 5.1 3.4 - - + -
306F ALA* 1.3 82.1 - - - +
308F VAL* 1.3 61.0 + - - +
339F VAL* 3.4 2.3 - - - -
340F PHE* 2.6 51.2 + - + +
342F LEU* 4.7 8.9 - - + +
354F ILE* 5.1 2.5 - - + -
358F ILE* 6.3 1.3 - - + -
374F VAL* 3.8 33.0 - - + -
376F LEU* 4.3 19.7 - - + -
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Residues in contact with VAL 308 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223F VAL* 3.3 4.6 - - - +
224F VAL* 2.9 43.0 + - + +
226F ILE* 3.6 39.5 - - + -
263F VAL* 4.1 8.5 - - + -
307F LEU* 1.3 80.2 - - - +
309F THR* 1.3 69.5 + - - +
310F TYR* 5.1 1.5 - - + -
328F PRO* 4.8 8.5 - - + -
337F GLN* 3.6 30.3 - - + -
338F THR 3.2 10.3 - - - +
339F VAL* 4.1 13.7 - - + -
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Residues in contact with THR 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F CYS* 3.4 20.6 - - - +
221F LEU* 4.2 7.9 - - + -
222F TYR 3.0 9.6 - - - +
223F VAL* 3.6 26.0 - - + -
275F ILE* 4.7 9.6 - - + -
308F VAL* 1.3 79.3 - - - +
310F TYR* 1.3 63.6 + - - +
337F GLN* 3.8 4.2 - - - +
338F THR* 2.9 45.7 + - - -
340F PHE* 3.8 18.2 - - + -
358F ILE* 4.9 5.2 - - + -
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Residues in contact with TYR 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F CYS* 6.5 0.4 - - - +
221F LEU* 3.6 6.7 - - - +
222F TYR* 2.8 68.3 + + + +
224F VAL* 4.2 25.8 - - + -
272F ALA* 3.2 21.5 - - - +
308F VAL* 5.1 1.8 - - + -
309F THR* 1.3 77.0 - - - +
311F PHE* 1.3 61.9 + - - +
312F ASN* 4.0 14.8 - - - -
325F SER* 4.4 0.2 - - - -
326F THR* 3.5 15.3 - - - +
327F ALA* 3.5 39.0 - - + -
328F PRO* 3.8 19.3 - - + -
329F ASP* 5.8 1.1 - - - -
336F LYS 5.4 0.7 - - - -
337F GLN* 4.4 2.2 - - + -
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Residues in contact with PHE 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187F MET* 4.1 9.0 - - + -
188F GLY 3.7 6.7 - - - -
190F CYS* 4.3 5.8 - - - -
191F LEU* 3.4 47.6 - - + -
220F ALA 3.1 18.8 - - - +
221F LEU* 4.1 9.9 - - + -
222F TYR* 4.9 0.2 - - - -
310F TYR* 1.3 77.2 - - - +
312F ASN* 1.3 63.0 + - - +
313F ILE* 3.7 32.8 - - + -
324F PHE* 4.5 2.9 - + - -
326F THR* 2.8 53.1 + - + +
335F TRP* 3.5 44.4 - + + -
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Residues in contact with ASN 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218F ARG* 5.8 3.8 + - - +
219F ALA* 3.4 5.0 - - - -
220F ALA* 3.0 32.8 + - + +
222F TYR* 3.3 26.3 + - + -
310F TYR* 4.0 10.4 - - - -
311F PHE* 1.3 78.9 + - - +
313F ILE* 1.3 67.6 + - - +
324F PHE 3.3 7.6 - - - +
325F SER* 2.5 37.9 + - - +
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Residues in contact with ILE 313 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186F TRP* 4.9 1.8 - - + -
187F MET* 3.9 29.6 - - + -
191F LEU* 4.3 0.2 - - + -
216F PRO* 3.5 31.4 - - + -
218F ARG 3.5 2.5 - - - +
219F ALA* 3.6 26.9 - - + -
311F PHE* 3.7 23.3 - - + -
312F ASN* 1.3 79.4 - - - +
314F GLU* 1.3 64.4 + - - +
315F PHE* 4.0 12.3 - - + -
321F LYS* 4.8 2.1 + - - -
323F GLY* 3.0 23.6 - - - -
324F PHE* 2.9 37.6 + - + +
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Residues in contact with GLU 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216F PRO* 3.3 3.1 - - - +
217F ASP* 3.2 8.2 + - - +
218F ARG* 2.9 67.4 + - + +
313F ILE* 1.3 75.1 - - - +
315F PHE* 1.3 73.9 + - - +
316F THR* 3.7 17.9 - - + +
321F LYS* 3.9 29.7 + - + +
322F MET 3.5 13.2 - - - +
323F 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