Contacts of the strand formed by residues 337 - 348 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B LEU 3.5 0.2 - - - +
260B VAL* 3.3 7.6 - - - +
261B ASP 3.0 31.4 + - - +
262B ILE* 3.5 11.9 - - - +
263B VAL* 2.9 35.4 + - + +
308B VAL* 3.7 17.0 - - + -
309B THR 3.8 9.0 - - - +
310B TYR* 4.5 0.9 - - + -
326B THR 2.5 27.3 + - - +
327B ALA 3.2 15.0 + - - -
328B PRO* 3.9 28.6 - - + +
333B THR* 5.6 0.6 + - - +
335B TRP 4.4 0.7 - - - -
336B LYS* 1.3 86.9 + - - +
338B THR* 1.3 64.9 + - - +
339B VAL* 4.2 0.9 - - - -
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Residues in contact with THR 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B TYR* 4.3 3.5 - - - +
190B CYS* 3.3 36.8 + - + -
258B PRO* 3.9 16.4 - - + -
259B LEU 3.4 4.5 - - - +
260B VAL* 4.6 7.3 - - + +
308B VAL* 3.3 4.0 - - - -
309B THR* 2.9 43.6 + - - -
335B TRP 5.1 1.7 + - - -
337B GLN* 1.3 79.3 + - - +
339B VAL* 1.3 62.3 + - - +
340B PHE* 3.6 21.1 - - + -
393B MET* 4.2 9.9 - - - -
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Residues in contact with VAL 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ILE* 4.6 5.8 - - + -
228B ASP* 4.8 2.2 - - - +
258B PRO* 3.1 6.8 - - - +
259B LEU* 2.8 53.2 + - + +
261B ASP* 4.7 9.0 - - + +
263B VAL* 3.9 27.8 - - + -
306B ALA* 3.8 22.4 - - + -
307B LEU 3.5 4.5 - - - +
308B VAL* 4.1 7.4 - - + -
338B THR* 1.3 77.6 - - - +
340B PHE* 1.3 63.5 + - - +
341B TYR* 4.0 27.7 + - + +
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Residues in contact with PHE 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B CYS* 4.0 7.0 - - - -
258B PRO* 3.6 17.3 - - + -
306B ALA* 3.3 3.3 - - - +
307B LEU* 2.8 46.5 + - + +
309B THR* 3.8 22.9 - - + -
338B THR* 3.6 31.4 - - + -
339B VAL* 1.3 73.9 - - - +
341B TYR* 1.3 66.0 + - - +
342B LEU* 4.6 2.1 - - - +
358B ILE* 5.3 2.5 - - + -
372B PHE* 3.8 44.4 - + - -
374B VAL* 4.8 9.4 - - + -
391B TYR* 3.8 39.6 + + + +
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Residues in contact with TYR 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ASP* 2.8 30.2 + - + -
231B TYR* 3.5 20.3 + - - -
232B LYS* 3.7 36.9 + - + -
235B LYS* 4.7 1.8 - - + -
236B ILE* 3.9 20.9 - - + -
254B ALA 5.9 0.9 - - - -
255B MET* 3.9 32.0 + - + +
257B GLU 5.5 2.7 - - - -
258B PRO* 5.7 0.6 - - - +
259B LEU* 4.0 32.9 - - + +
305B HIS* 4.0 6.5 - - + -
306B ALA* 3.9 18.4 - - + -
339B VAL* 4.0 13.6 + - + +
340B PHE* 1.3 71.2 - - - +
342B LEU* 1.3 57.0 + - - +
389B ASN* 4.5 0.7 + - - -
391B TYR* 2.5 35.8 + - - -
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Residues in contact with LEU 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B LYS* 2.7 33.6 + - - -
255B MET* 3.6 5.6 - - - +
304B VAL* 4.1 21.3 - - + +
305B HIS 3.1 27.7 + - - +
306B ALA* 4.1 5.6 - - - +
307B LEU* 4.8 10.1 - - + -
340B PHE 4.6 3.4 - - - +
341B TYR* 1.3 73.5 - - - +
343B GLU* 1.3 55.6 + - - +
344B ASP 3.5 10.8 - - - +
346B LEU* 4.2 25.8 - - + -
374B VAL* 5.8 2.9 - - + -
376B LEU* 4.3 24.0 - - + -
389B ASN* 4.1 18.2 - - - +
391B TYR* 4.2 7.2 - - - +
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Residues in contact with GLU 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B LYS* 2.8 17.5 + - - -
237B HIS* 5.0 5.0 - - - -
255B MET* 3.8 22.0 - - + +
256B LYS* 5.6 12.1 - - - -
342B LEU* 1.3 71.9 - - - +
344B ASP* 1.3 72.2 + - - +
387B VAL* 4.3 9.7 - - + +
389B ASN* 3.3 28.9 - - - +
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Residues in contact with ASP 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B LYS* 4.4 1.8 - - - +
342B LEU* 3.5 23.7 - - - +
343B GLU* 1.3 86.9 - - - +
345B TYR* 1.3 70.6 + - + +
346B LEU* 3.9 4.9 + - + +
385B THR* 5.7 6.6 - - + +
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Residues in contact with TYR 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B LYS* 4.6 4.1 - - - +
303B TYR* 3.7 33.5 - + - -
304B VAL 3.2 13.9 - - - +
305B HIS* 3.6 37.2 - + + +
344B ASP* 1.3 81.7 - - + +
346B LEU* 1.3 64.9 + - - +
347B THR* 4.0 10.7 + - - -
383B CYS* 5.0 2.4 - - - -
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Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B TYR* 3.4 7.3 - - - +
304B VAL* 2.7 48.0 + - + +
342B LEU* 4.2 16.4 - - + -
344B ASP* 4.3 4.7 - - + +
345B TYR* 1.3 79.4 - - - +
347B THR* 1.3 61.6 + - - +
348B VAL* 3.8 13.8 + - + -
354B ILE* 4.2 28.3 - - + -
376B LEU* 4.1 23.3 - - + -
378B PHE* 4.3 18.6 - - + -
383B CYS* 4.1 8.1 - - - -
385B THR* 4.0 20.6 - - + +
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Residues in contact with THR 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ASP 4.1 4.0 - - - +
303B TYR* 3.9 31.2 - - + +
345B TYR* 4.0 11.1 + - - -
346B LEU* 1.3 71.6 + - - +
348B VAL* 1.3 63.8 + - - +
352B GLU* 4.1 1.9 - - - +
378B PHE* 3.8 5.7 - - - -
382B LEU* 3.8 40.2 - - + +
383B CYS* 3.3 26.8 - - - +
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Residues in contact with VAL 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B VAL* 4.1 4.9 - - + -
298B ILE* 3.6 35.7 - - + -
301B ASN* 3.4 4.0 + - - +
302B ASP 3.1 47.3 + - - +
304B VAL* 4.0 18.4 - - + +
346B LEU* 3.8 23.6 - - + -
347B THR* 1.3 79.8 - - - +
349B ARG* 1.3 63.6 + - - +
352B GLU* 3.8 3.1 - - - -
378B PHE* 3.6 23.6 - - + -
382B LEU* 5.5 1.2 - - - +
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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