Contacts of the strand formed by residues 337 - 348 (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 GLN 337 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259K LEU 3.5 0.2 - - - +
260K VAL* 3.3 7.4 - - - +
261K ASP 3.1 30.4 + - - +
262K ILE* 3.4 10.2 - - - +
263K VAL* 3.0 30.5 + - + +
308K VAL* 3.7 18.6 - - + -
309K THR 3.8 8.7 - - - +
310K TYR* 4.4 1.6 - - + -
326K THR* 2.5 28.2 + - - +
327K ALA 3.4 13.3 + - - -
328K PRO* 3.5 30.7 - - + +
330K ALA 5.5 0.2 + - - -
335K TRP 4.4 0.4 - - - -
336K LYS* 1.3 87.5 + - - +
338K THR* 1.3 65.1 + - - +
339K VAL* 4.2 0.4 - - - -
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Residues in contact with THR 338 (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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189K TYR* 4.8 0.5 - - - +
190K CYS* 3.4 34.5 + - + +
258K PRO* 3.9 22.9 - - + -
259K LEU 3.3 4.5 - - - +
260K VAL* 4.5 10.8 - - + +
308K VAL* 3.2 4.6 - - - -
309K THR* 2.9 48.5 + - - -
335K TRP 5.1 1.9 + - - -
337K GLN* 1.3 79.3 + - - +
339K VAL* 1.3 64.8 + - - +
340K PHE* 3.6 11.9 - - + -
393K MET* 4.2 10.5 - - - -
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Residues in contact with VAL 339 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226K ILE* 4.6 6.3 - - + -
228K ASP* 4.7 2.0 - - - +
258K PRO* 3.2 7.6 - - - +
259K LEU* 2.8 48.5 + - + +
261K ASP* 4.6 8.7 - - + +
263K VAL* 3.9 28.0 - - + -
306K ALA* 3.7 24.0 - - + -
307K LEU 3.5 4.0 - - - +
308K VAL* 4.1 7.2 - - + -
338K THR* 1.3 77.5 - - - +
340K PHE* 1.3 61.9 + - - +
341K TYR* 3.9 26.4 + - + +
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Residues in contact with PHE 340 (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* 4.2 5.2 - - - -
258K PRO* 3.7 21.1 - - + -
306K ALA* 3.2 3.2 - - - +
307K LEU* 2.7 48.4 + - + +
309K THR* 3.7 34.8 - - + -
338K THR* 3.6 19.3 - - + -
339K VAL* 1.3 71.0 - - - +
341K TYR* 1.3 66.8 + - - +
342K LEU* 4.5 2.3 - - + +
358K ILE* 5.3 3.8 - - + -
372K PHE* 3.8 47.8 - + + -
374K VAL* 4.8 9.4 - - + -
391K TYR* 3.8 39.2 + + + -
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Residues in contact with TYR 341 (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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228K ASP* 2.7 29.4 + - + -
231K TYR* 3.6 19.6 + - - -
232K LYS* 3.6 41.3 + - + -
235K LYS* 4.7 1.1 - - + -
236K ILE* 4.0 20.0 - - + -
254K ALA 5.9 0.9 - - - -
255K MET* 3.8 32.5 + - + +
257K GLU 5.5 2.5 - - - -
258K PRO* 5.7 0.4 - - - +
259K LEU* 3.9 34.0 - - + +
305K HIS* 4.1 2.9 - - + -
306K ALA* 4.0 13.0 - - + -
339K VAL* 3.9 19.8 + - + +
340K PHE* 1.3 72.1 - - - +
342K LEU* 1.3 56.8 + - - +
389K ASN* 4.4 0.3 + - - -
391K TYR* 2.4 37.5 + - - -
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Residues in contact with LEU 342 (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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232K LYS* 2.7 34.5 + - - -
255K MET* 3.7 4.1 - - - +
304K VAL* 4.2 10.8 - - + +
305K HIS 3.0 28.1 + - - +
306K ALA* 4.1 6.1 - - - +
307K LEU* 4.7 9.4 - - + -
340K PHE 4.5 3.6 - - - +
341K TYR* 1.3 77.3 - - - +
343K GLU* 1.3 55.3 + - - +
344K ASP 3.5 11.8 - - - +
346K LEU* 4.1 35.0 - - + -
374K VAL* 5.8 2.2 - - + -
376K LEU* 4.3 24.7 - - + -
389K ASN* 3.9 20.0 - - - +
391K TYR* 4.2 4.0 - - - +
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Residues in contact with GLU 343 (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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232K LYS* 3.0 15.4 + - - -
237K HIS* 5.1 5.2 - - - -
255K MET* 3.7 21.6 - - + +
256K LYS* 5.8 10.1 - - - -
342K LEU* 1.3 72.8 - - - +
344K ASP* 1.3 73.2 + - - +
387K VAL* 4.3 10.1 - - + +
389K ASN* 3.6 25.8 - - - +
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Residues in contact with ASP 344 (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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232K LYS* 4.5 1.8 - - - +
305K HIS 5.7 0.2 - - - -
342K LEU* 3.5 21.2 - - - +
343K GLU* 1.3 88.1 - - - +
345K TYR* 1.3 68.3 + - + +
346K LEU* 3.9 8.8 + - + +
385K THR* 6.2 3.6 - - + -
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Residues in contact with TYR 345 (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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232K LYS* 4.8 3.6 - - - +
303K TYR* 3.7 36.1 - + - -
304K VAL 3.3 14.1 - - - +
305K HIS* 3.6 37.0 - + + +
344K ASP* 1.3 79.8 - - + +
346K LEU* 1.3 64.5 + - - +
347K THR* 3.9 11.0 + - - -
383K CYS* 4.9 2.8 - - - -
104M TYR 2.9 27.7 + - - -
105M HIS* 4.0 8.9 - + - -
107M LYS* 3.4 20.0 + - + +
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Residues in contact with LEU 346 (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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303K TYR* 3.2 8.3 - - - +
304K VAL* 2.8 39.8 + - + +
342K LEU* 4.1 22.2 - - + -
344K ASP* 4.1 10.3 - - + +
345K TYR* 1.3 77.9 - - - +
347K THR* 1.3 60.1 + - - +
348K VAL* 3.8 15.0 + - + -
354K ILE* 4.1 29.2 - - + -
376K LEU* 4.1 18.8 - - + -
378K PHE* 4.4 17.3 - - + -
383K CYS* 4.1 6.5 - - - -
385K THR* 4.1 20.4 - - + +
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Residues in contact with THR 347 (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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302K ASP 4.1 1.8 - - - -
303K TYR* 3.8 29.1 - - + -
345K TYR* 3.9 10.8 + - - -
346K LEU* 1.3 73.1 - - - +
348K VAL* 1.3 63.4 + - - +
352K GLU* 4.2 1.6 - - - +
378K PHE* 3.8 13.2 - - - -
382K LEU* 3.9 38.5 - - + +
383K CYS* 3.5 17.9 - - - +
108M HIS* 4.2 15.2 + - + +
319M HIS* 3.9 16.8 - - + +
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Residues in contact with VAL 348 (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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269K VAL* 4.1 11.0 - - + -
298K ILE* 3.6 34.8 - - + -
301K ASN* 3.3 0.3 - - - -
302K ASP 3.0 52.1 + - - +
303K TYR 4.5 0.2 - - - +
304K VAL* 4.1 9.4 - - + -
346K LEU* 3.8 23.8 - - + -
347K THR* 1.3 78.9 - - - +
349K ARG* 1.3 61.7 + - - +
352K GLU* 3.8 2.7 - - - -
354K ILE* 5.3 0.4 - - + -
378K PHE* 3.6 24.7 - - + -
319M HIS* 3.2 7.4 - - - -
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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