Contacts of the strand formed by residues 337 - 348 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260M VAL* 3.3 7.6 - - - +
261M ASP 3.1 29.2 + - - +
262M ILE* 3.4 9.6 - - - +
263M VAL* 2.8 35.2 + - + +
308M VAL* 3.7 18.8 - - + -
309M THR 3.9 8.7 - - - +
310M TYR* 4.5 2.0 - - + -
326M THR 2.5 28.4 + - - +
327M ALA 3.2 14.3 + - - -
328M PRO* 3.7 28.3 - - + +
335M TRP 4.1 1.1 - - - -
336M LYS* 1.3 85.8 + - - +
338M THR* 1.3 66.0 + - - +
339M VAL* 4.1 0.4 - - - -
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Residues in contact with THR 338 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189M TYR* 4.3 3.5 - - - +
190M CYS* 3.3 35.8 + - + -
258M PRO* 3.9 16.4 - - + -
259M LEU 3.3 5.2 - - - +
260M VAL* 4.6 7.4 - - + +
308M VAL* 3.3 5.4 - - - -
309M THR* 3.0 41.5 + - - -
335M TRP 4.8 1.9 + - - -
337M GLN* 1.3 80.6 + - - +
339M VAL* 1.3 63.6 + - - +
340M PHE* 3.7 20.8 - - + -
393M MET* 4.2 9.0 - - - -
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Residues in contact with VAL 339 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226M ILE* 4.6 5.4 - - + -
228M ASP* 4.7 3.1 - - - +
258M PRO* 3.2 7.8 - - - +
259M LEU* 2.7 48.8 + - + +
261M ASP* 4.5 10.3 - - + +
263M VAL* 3.9 27.6 - - + -
306M ALA* 3.8 22.4 - - + -
307M LEU 3.6 3.8 - - - +
308M VAL* 4.2 7.2 - - + -
338M THR* 1.3 77.4 - - - +
340M PHE* 1.3 63.4 + - - +
341M TYR* 4.0 26.9 + - + +
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Residues in contact with PHE 340 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190M CYS* 4.2 2.5 - - - -
258M PRO* 3.5 18.2 - - + -
306M ALA* 3.3 2.6 - - - +
307M LEU* 2.7 49.8 + - + +
309M THR* 3.8 26.7 - - + -
338M THR* 3.7 32.1 - - + -
339M VAL* 1.3 73.7 - - - +
341M TYR* 1.3 65.9 + - - +
342M LEU* 4.5 2.4 - - - +
358M ILE* 5.4 3.4 - - + -
372M PHE* 3.8 46.7 - + + -
374M VAL* 4.9 9.4 - - + -
391M TYR* 3.7 40.0 + + + +
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Residues in contact with TYR 341 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228M ASP* 2.8 33.9 + - + -
231M TYR* 3.5 20.0 - - - -
232M LYS* 3.5 43.3 + - + -
235M LYS* 4.7 1.8 - - + -
236M ILE* 3.9 20.6 - - + -
254M ALA 6.0 0.4 - - - -
255M MET* 3.6 32.9 + - + +
257M GLU 5.5 2.7 + - - -
258M PRO* 5.8 0.8 - - - +
259M LEU* 3.9 32.5 - - + +
305M HIS* 3.9 9.9 - - + -
306M ALA* 4.0 7.4 - - + -
339M VAL* 4.0 12.4 + - + +
340M PHE* 1.3 72.3 - - - +
342M LEU* 1.3 57.2 + - - +
389M ASN* 4.5 0.5 + - - -
391M TYR* 2.4 37.1 + - - -
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Residues in contact with LEU 342 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232M LYS* 2.8 34.0 + - - -
255M MET* 3.6 4.5 - - - +
304M VAL* 4.0 33.4 - - + +
305M HIS 3.0 17.1 + - - +
306M ALA* 4.0 7.0 - - - +
307M LEU* 4.7 9.6 - - + -
340M PHE* 4.5 3.6 - - + +
341M TYR* 1.3 79.5 - - - +
343M GLU* 1.3 54.9 + - - +
344M ASP 3.4 14.5 - - - +
346M LEU* 4.2 18.6 - - + -
374M VAL* 5.7 3.4 - - + -
376M LEU* 4.4 24.5 - - + -
389M ASN* 4.1 17.3 - - - +
391M TYR* 4.1 4.5 - - - +
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Residues in contact with GLU 343 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232M LYS* 3.0 16.3 + - - -
237M HIS* 5.1 4.9 - - - -
255M MET* 3.8 20.4 - - + +
256M LYS* 5.8 10.3 - - - -
342M LEU* 1.3 71.7 - - - +
344M ASP* 1.3 71.7 + - - +
387M VAL* 4.3 9.4 - - + +
389M ASN* 3.5 27.8 - - - +
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Residues in contact with ASP 344 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232M LYS* 4.6 1.3 - - - -
342M LEU* 3.4 24.5 - - - +
343M GLU* 1.3 88.5 - - - +
345M TYR* 1.3 68.6 + - + +
346M LEU* 4.0 5.9 + - + +
385M THR* 5.8 6.9 - - + +
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Residues in contact with TYR 345 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232M LYS* 4.7 4.0 - - - +
303M TYR* 3.8 33.7 - + + -
304M VAL 3.3 10.8 - - - +
305M HIS* 3.6 40.6 - + + +
344M ASP* 1.3 82.2 - - + +
346M LEU* 1.3 64.8 + - - +
347M THR* 3.9 11.7 + - - -
383M CYS* 5.1 2.6 - - - -
104O TYR 2.7 28.6 + - - -
105O HIS* 3.6 16.0 - + - -
107O LYS* 3.7 16.7 + - + +
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Residues in contact with LEU 346 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303M TYR* 3.3 8.0 - - - +
304M VAL* 2.8 39.3 + - + +
342M LEU* 4.2 19.1 - - + -
344M ASP* 4.3 9.4 - - + +
345M TYR* 1.3 78.8 - - - +
347M THR* 1.3 61.5 + - - +
348M VAL* 3.7 13.8 + - + +
354M ILE* 4.2 27.4 - - + -
376M LEU* 4.1 24.2 - - + -
378M PHE* 4.4 18.2 - - + -
383M CYS* 4.2 6.3 - - - -
385M THR* 4.0 21.8 - - + +
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Residues in contact with THR 347 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302M ASP 4.2 1.8 - - - -
303M TYR* 3.9 20.8 - - + -
345M TYR* 3.9 11.3 + - - -
346M LEU* 1.3 72.0 - - - +
348M VAL* 1.3 58.7 + - - +
352M GLU* 4.2 1.4 - - - +
378M PHE* 3.7 16.1 - - - -
382M LEU* 3.9 29.5 - - + +
383M CYS* 3.6 18.9 + - - +
105O HIS 5.1 0.3 + - - -
108O HIS* 4.1 19.0 + - + +
319O HIS* 3.5 32.3 - - + +
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Residues in contact with VAL 348 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269M VAL* 4.1 3.6 - - + -
298M ILE* 3.7 36.1 - - + -
301M ASN* 3.4 0.7 - - - -
302M ASP 3.0 49.0 + - - +
304M VAL* 4.0 17.9 - - + -
346M LEU* 3.7 24.5 - - + +
347M THR* 1.3 78.6 - - - +
349M ARG* 1.3 62.5 + - - +
352M GLU* 3.8 3.1 - - - -
354M ILE* 5.2 0.7 - - + -
378M PHE* 3.6 21.3 - - + -
319O HIS* 3.1 8.6 - - - -
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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