Contacts of the strand formed by residues 302 - 314 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227K GLU* 3.8 14.0 - - - +
269K VAL* 3.5 21.5 - - + +
300K ARG* 2.9 46.3 + - + +
301K ASN* 1.3 76.6 - - - +
303K TYR* 1.3 80.9 + - - +
348K VAL* 3.0 32.6 + - - +
319M HIS* 3.4 10.7 + - - -
320M LYS* 3.2 26.8 + - - +
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Residues in contact with TYR 303 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227K GLU* 3.2 26.7 + - + +
269K VAL* 4.1 0.3 - - - +
302K ASP* 1.3 88.0 + - - +
304K VAL* 1.3 66.0 + - - +
305K HIS* 4.0 20.2 - + + -
345K TYR* 3.7 27.8 - + + -
346K LEU 3.2 6.5 - - - +
347K THR* 3.8 29.2 - - + -
105M HIS* 2.5 46.9 + + + +
106M ASN* 3.2 12.5 + - - -
319M HIS* 3.7 16.1 - - - +
320M LYS* 4.4 25.2 + - + +
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Residues in contact with VAL 304 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225K ALA* 3.9 24.7 - - + -
226K ILE 3.3 11.4 - - - +
269K VAL* 3.8 28.9 - - + -
298K ILE* 5.2 0.2 - - + -
303K TYR* 1.3 77.9 - - - +
305K HIS* 1.3 63.2 + - - +
306K ALA 3.9 9.6 - - - +
307K LEU* 5.2 1.6 - - + -
342K LEU* 4.2 8.0 - - + +
345K TYR* 3.3 3.9 - - - -
346K LEU* 2.8 60.6 + - + -
348K VAL* 4.1 13.0 - - + -
354K ILE* 4.6 5.8 - - + -
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Residues in contact with HIS 305 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226K ILE 2.9 4.9 + - - -
227K GLU* 3.8 9.1 - - + +
228K ASP* 3.2 34.7 + - + +
229K ARG* 3.0 42.6 - - + +
232K LYS* 4.1 23.9 + - + +
303K TYR* 4.0 24.0 - + + -
304K VAL* 1.3 74.4 - - - +
306K ALA* 1.3 60.8 + - + +
341K TYR* 4.1 4.0 - - + -
342K LEU* 3.0 34.3 + - - +
345K TYR* 3.6 32.3 - + + +
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Residues in contact with ALA 306 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225K ALA* 3.4 5.7 - - - +
226K ILE* 2.9 38.7 + - + +
228K ASP* 5.3 0.2 - - + -
304K VAL* 3.7 3.8 - - - +
305K HIS* 1.3 82.2 - - + +
307K LEU* 1.3 65.8 + - - +
339K VAL* 3.7 25.8 - - + -
340K PHE 3.2 17.0 - - - +
341K TYR* 4.0 10.1 - - + -
342K LEU* 4.1 5.4 - - - -
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Residues in contact with LEU 307 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223K VAL* 4.7 15.5 - - + -
224K VAL 3.4 3.6 - - - +
225K ALA* 4.0 18.8 - - + -
294K PHE* 4.1 18.4 - - + -
296K LEU* 4.1 14.4 - - + -
304K VAL* 5.2 2.9 - - + -
306K ALA* 1.3 81.5 - - - +
308K VAL* 1.3 59.6 + - - +
309K THR 4.4 0.2 - - - -
339K VAL* 3.5 2.3 - - - -
340K PHE* 2.7 49.7 + - + +
342K LEU* 4.7 8.5 - - + -
354K ILE* 5.2 3.4 - - + -
358K ILE* 6.4 1.1 - - + -
374K VAL* 3.8 32.8 - - + -
376K LEU* 4.3 19.3 - - + -
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Residues in contact with VAL 308 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222K TYR 4.0 0.2 - - - +
223K VAL* 3.4 2.4 - - - -
224K VAL* 2.7 43.1 + - + +
226K ILE* 3.5 44.0 - - + -
263K VAL* 4.2 7.4 - - + -
307K LEU* 1.3 79.9 - - - +
309K THR* 1.3 66.4 + - - +
310K TYR* 4.3 2.6 + - + -
328K PRO* 4.8 9.6 - - + -
337K GLN* 3.7 33.4 - - + -
338K THR 3.2 6.3 - - - +
339K VAL* 4.1 13.2 - - + -
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Residues in contact with THR 309 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190K CYS* 3.3 22.0 - - - +
221K LEU* 4.2 7.2 - - + -
222K TYR 3.1 9.4 - - - +
223K VAL* 3.6 26.2 - - + -
275K ILE* 4.7 9.6 - - + -
308K VAL* 1.3 75.3 - - - +
310K TYR* 1.3 60.5 + - - +
337K GLN* 3.8 4.7 - - - +
338K THR* 2.9 46.3 + - - -
340K PHE* 3.7 19.4 - - + -
358K ILE* 4.9 4.7 - - + -
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Residues in contact with TYR 310 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190K CYS* 6.3 0.2 - - - +
221K LEU* 3.5 5.6 - - - +
222K TYR* 2.8 63.5 + + + +
224K VAL* 4.3 22.7 - - + -
272K ALA* 3.4 20.4 - - - +
308K VAL* 4.9 5.6 - - + -
309K THR* 1.3 74.8 - - - +
311K PHE* 1.3 66.2 + - - +
312K ASN* 3.8 18.6 - - - -
326K THR* 3.6 24.7 - - - +
327K ALA* 3.5 28.5 - - + -
328K PRO* 3.9 18.8 - - + -
329K ASP* 5.8 1.1 - - - -
336K LYS 5.3 0.7 - - - -
337K GLN* 4.4 2.7 - - + -
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Residues in contact with PHE 311 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187K MET* 4.1 8.1 - - + -
188K GLY 3.6 8.3 - - - -
190K CYS* 4.3 7.0 - - - -
191K LEU* 3.4 48.7 - - + -
220K ALA 3.0 17.5 - - - +
221K LEU* 4.0 9.9 - - + -
310K TYR* 1.3 78.5 - - - +
312K ASN* 1.3 63.8 + - - +
313K ILE* 3.8 28.5 - - + -
324K PHE* 4.5 2.0 - + - -
325K SER* 3.9 0.2 - - - -
326K THR* 3.1 48.8 + - + +
335K TRP* 3.5 44.6 - + + -
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Residues in contact with ASN 312 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218K ARG* 5.6 4.2 + - - +
219K ALA* 3.3 4.2 - - - -
220K ALA* 2.8 36.3 + - + +
222K TYR* 3.3 27.4 + - + -
310K TYR* 3.8 12.3 - - - -
311K PHE* 1.3 77.9 - - - +
313K ILE* 1.3 66.5 + - - +
324K PHE 3.4 8.1 - - - +
325K SER* 2.9 34.5 + - - -
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Residues in contact with ILE 313 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186K TRP* 4.9 1.1 - - + -
187K MET* 3.8 31.4 - - + -
191K LEU* 4.3 0.2 - - + -
216K PRO* 3.4 31.6 - - + -
218K ARG* 3.7 3.1 - - - +
219K ALA* 3.7 26.0 - - + -
311K PHE* 3.8 18.4 - - + -
312K ASN* 1.3 78.5 - - - +
314K GLU* 1.3 64.6 + - - +
315K PHE* 4.1 4.9 - - + -
321K LYS* 4.7 2.9 + - - -
323K GLY* 3.1 2.6 - - - -
324K PHE* 2.9 68.1 + - + +
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Residues in contact with GLU 314 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216K PRO* 3.3 4.0 - - - +
217K ASP* 3.3 21.5 + - - +
218K ARG* 2.8 51.5 + - + +
313K ILE* 1.3 75.2 - - - +
315K PHE* 1.3 74.7 + - - +
316K THR* 3.7 15.4 - - + +
321K LYS* 3.9 31.1 + - + +
322K MET 3.4 12.6 - - - +
323K GLY* 4.1 0.2 - - - -
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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