Contacts of the strand formed by residues 302 - 314 (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 ASP 302 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227M GLU* 3.7 11.5 - - - +
269M VAL* 3.9 23.3 - - + -
300M ARG* 3.0 41.8 + - + +
301M ASN* 1.3 74.9 - - - +
303M TYR* 1.3 81.1 + - - +
347M THR 4.2 0.2 - - - -
348M VAL* 3.0 22.1 + - - +
319O HIS* 3.1 21.3 + - - -
320O LYS* 2.7 33.1 + - - +
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Residues in contact with TYR 303 (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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227M GLU* 3.0 31.1 + - + +
269M VAL* 4.1 0.9 - - - +
302M ASP* 1.3 89.9 + - - +
304M VAL* 1.3 62.7 + - - +
305M HIS* 3.8 22.2 - + + -
345M TYR* 3.8 26.5 - + + -
346M LEU 3.3 6.7 - - - +
347M THR* 3.9 24.0 - - + -
105O HIS* 2.6 45.9 + - + +
106O ASN* 3.1 13.3 + - - -
319O HIS* 3.7 10.5 - - - +
320O LYS* 4.0 37.0 + - + -
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Residues in contact with VAL 304 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225M ALA* 3.8 21.1 - - + -
226M ILE 3.3 3.8 - - - +
269M VAL* 3.9 28.0 - - + -
298M ILE* 5.2 0.2 - - + -
303M TYR* 1.3 75.6 - - - +
305M HIS* 1.3 61.6 + - - +
306M ALA 3.6 21.3 - - - +
307M LEU* 5.0 1.6 - - + -
342M LEU* 4.0 15.1 - - + +
345M TYR* 3.3 3.4 - - - -
346M LEU* 2.8 55.9 + - + -
348M VAL* 4.0 13.9 - - + -
354M ILE* 4.6 6.7 - - + -
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Residues in contact with HIS 305 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226M ILE 2.8 5.3 + - - -
227M GLU* 3.8 10.0 - - + -
228M ASP* 3.3 33.2 + - + +
229M ARG* 3.0 40.2 - - + +
232M LYS* 4.2 21.2 - - + +
303M TYR* 3.8 26.7 + + + -
304M VAL* 1.3 74.8 - - - +
306M ALA* 1.3 62.2 + - + +
341M TYR* 3.9 5.5 - - + -
342M LEU* 3.0 31.0 + - - +
345M TYR* 3.6 34.0 - + + +
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Residues in contact with ALA 306 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225M ALA* 3.4 4.3 - - - -
226M ILE* 3.0 37.3 + - + -
304M VAL* 3.6 8.6 - - - +
305M HIS* 1.3 83.3 - - + +
307M LEU* 1.3 66.3 + - - +
339M VAL* 3.8 24.5 - - + -
340M PHE 3.3 17.3 - - - +
341M TYR* 4.0 9.2 - - + -
342M LEU* 4.0 4.9 - - - -
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Residues in contact with LEU 307 (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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223M VAL* 4.7 14.8 - - + -
224M VAL 3.4 7.4 - - - +
225M ALA* 3.8 18.2 - - + -
294M PHE* 4.0 18.8 - - + -
296M LEU* 4.1 11.7 - - + -
304M VAL* 5.0 3.8 - - + -
306M ALA* 1.3 79.5 - - - +
308M VAL* 1.3 67.4 + - - +
339M VAL* 3.6 0.2 - - - -
340M PHE* 2.7 46.4 + - + +
342M LEU* 4.7 8.1 - - + -
354M ILE* 5.1 2.2 - - + -
358M ILE* 6.4 1.6 - - + -
374M VAL* 3.9 31.6 - - + -
376M LEU* 4.3 19.5 - - + -
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Residues in contact with VAL 308 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222M TYR 3.8 0.2 - - - +
223M VAL* 3.4 2.7 - - - -
224M VAL* 2.8 48.3 + - + +
226M ILE* 3.6 39.7 - - + -
263M VAL* 4.1 7.6 - - + -
307M LEU* 1.3 81.4 - - - +
309M THR* 1.3 66.5 + - - +
310M TYR* 4.3 2.9 + - + -
328M PRO* 4.8 8.5 - - + -
337M GLN* 3.7 31.4 - - + -
338M THR 3.3 11.0 - - - +
339M VAL* 4.2 12.8 - - + -
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Residues in contact with THR 309 (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* 3.2 26.5 - - - +
221M LEU* 4.2 10.8 - - + -
222M TYR 3.0 16.4 - - - +
223M VAL* 3.6 21.1 - - + -
275M ILE* 4.7 9.2 - - + -
308M VAL* 1.3 73.5 - - - +
310M TYR* 1.3 61.4 + - - +
337M GLN* 3.9 5.2 - - - +
338M THR* 3.0 36.1 + - - -
340M PHE* 3.8 19.6 - - + -
358M ILE* 4.9 4.9 - - + -
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Residues in contact with TYR 310 (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* 6.4 0.2 - - - +
221M LEU* 3.3 7.2 - - - +
222M TYR* 2.8 61.9 + + + +
224M VAL* 4.2 22.4 - - + -
272M ALA* 3.2 22.3 - - - +
308M VAL* 4.8 5.8 - - + -
309M THR* 1.3 77.5 - - - +
311M PHE* 1.3 67.3 + - - +
312M ASN* 3.8 17.9 - - - -
326M THR* 3.5 15.5 - - - +
327M ALA* 3.5 37.7 - - + -
328M PRO* 3.9 17.5 - - + -
329M ASP* 5.6 1.3 - - - -
336M LYS 5.4 0.4 - - - -
337M GLN* 4.5 2.7 - - + -
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Residues in contact with PHE 311 (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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187M MET* 4.1 9.9 - - + -
188M GLY 3.6 6.5 - - - -
190M CYS* 4.4 5.8 - - - -
191M LEU* 3.5 41.3 - - + -
220M ALA 3.1 19.7 - - - +
221M LEU* 4.1 7.4 - - + -
310M TYR* 1.3 78.5 - - - +
312M ASN* 1.3 62.9 + - - +
313M ILE* 3.7 36.8 - - + -
324M PHE* 4.5 3.1 - + - -
325M SER* 3.7 0.2 - - - -
326M THR* 2.9 50.7 + - + +
335M TRP* 3.6 42.2 - + + -
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Residues in contact with ASN 312 (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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218M ARG* 5.8 4.8 + - - +
219M ALA* 3.4 3.5 - - - -
220M ALA* 2.9 34.0 + - + +
222M TYR* 3.4 27.7 + - + -
310M TYR* 3.8 11.2 - - - -
311M PHE* 1.3 78.9 + - - +
313M ILE* 1.3 67.9 + - - +
324M PHE 3.4 8.3 - - - +
325M SER* 2.8 35.6 + - - -
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Residues in contact with ILE 313 (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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186M TRP* 4.9 1.1 - - + -
187M MET* 3.8 31.4 - - + -
191M LEU* 4.3 0.2 - - + -
216M PRO* 3.5 31.0 - - + -
218M ARG* 3.5 3.6 - - - +
219M ALA* 3.6 26.5 - - + -
311M PHE* 3.7 22.7 - - + -
312M ASN* 1.3 78.8 - - - +
314M GLU* 1.3 64.5 + - - +
315M PHE* 4.1 11.9 - - + -
321M LYS* 4.7 2.3 + - - -
323M GLY* 3.0 22.6 - - - -
324M PHE* 2.9 37.7 + - + +
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Residues in contact with GLU 314 (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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216M PRO* 3.3 3.5 - - - +
217M ASP* 3.3 21.8 + - - +
218M ARG* 2.9 51.5 + - + +
313M ILE* 1.3 76.4 - - - +
315M PHE* 1.3 74.1 + - - +
316M THR* 3.7 18.9 - - + +
321M LYS* 3.8 29.6 + - - +
322M MET 3.4 13.7 - - - +
323M GLY* 4.1 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