Contacts of the strand formed by residues 337 - 348 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259L LEU 3.6 0.2 - - - +
260L VAL* 3.4 7.4 - - - +
261L ASP 3.1 30.1 + - - +
262L ILE* 3.3 11.5 - - - +
263L VAL* 2.8 36.6 + - + +
308L VAL* 3.6 17.9 - - + -
309L THR 3.9 7.2 - - - +
310L TYR* 4.5 2.0 - - + -
326L THR 2.5 28.9 + - - +
327L ALA 3.3 12.5 + - - -
328L PRO* 3.6 29.6 - - + +
335L TRP 4.4 0.9 - - - -
336L LYS* 1.3 85.8 - - - +
338L THR* 1.3 65.9 + - - +
339L VAL* 4.1 0.4 - - - -
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Residues in contact with THR 338 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189L TYR* 4.8 2.6 - - - +
190L CYS* 3.3 38.5 + - + -
258L PRO* 3.9 15.9 - - + -
259L LEU 3.4 5.2 - - - +
260L VAL* 4.6 7.6 - - + +
308L VAL* 3.2 5.7 - - - +
309L THR* 2.9 45.9 + - - -
335L TRP 5.0 1.7 + - - -
337L GLN* 1.3 79.8 + - - +
339L VAL* 1.3 62.8 + - - +
340L PHE* 3.7 19.9 - - + -
393L MET* 4.2 9.2 - - - -
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Residues in contact with VAL 339 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226L ILE* 4.6 6.5 - - + -
228L ASP* 4.8 1.8 - - - +
258L PRO* 3.1 7.8 - - - +
259L LEU* 2.7 51.7 + - + +
261L ASP* 4.6 10.1 - - + +
263L VAL* 3.9 27.4 - - + -
306L ALA* 3.8 23.6 - - + -
307L LEU 3.5 3.8 - - - +
308L VAL* 4.1 6.5 - - + -
338L THR* 1.3 77.2 - - - +
340L PHE* 1.3 62.3 + - - +
341L TYR* 4.0 24.5 + - + +
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Residues in contact with PHE 340 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190L CYS* 4.0 7.6 - - - -
258L PRO* 3.6 18.6 - - + -
306L ALA* 3.2 3.1 - - - +
307L LEU* 2.7 46.9 + - + +
309L THR* 3.8 26.7 - - + -
338L THR* 3.7 28.7 - - + -
339L VAL* 1.3 72.8 - - - +
341L TYR* 1.3 66.2 + - - +
342L LEU* 3.7 2.5 + - + +
358L ILE* 5.4 3.4 - - + -
372L PHE* 3.9 44.0 - + + -
374L VAL* 4.8 9.0 - - + -
391L TYR* 3.8 39.5 + + + +
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Residues in contact with TYR 341 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228L ASP* 2.7 30.8 + - + -
231L TYR* 3.5 18.7 - - - -
232L LYS* 3.6 40.6 + - + -
235L LYS* 4.6 2.0 - - + -
236L ILE* 3.9 21.3 - - + -
254L ALA 6.0 0.4 - - - -
255L MET* 3.8 32.2 + - + +
257L GLU 5.6 1.8 - - - -
258L PRO* 5.8 0.6 - - - +
259L LEU* 3.9 34.0 - - + +
305L HIS* 4.1 2.2 - - + -
306L ALA* 4.0 13.5 - - + -
339L VAL* 4.0 17.9 + - + +
340L PHE* 1.3 71.9 - - - +
342L LEU* 1.3 57.8 + - - +
389L ASN* 4.5 0.5 + - - -
391L TYR* 2.5 36.2 + - - -
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Residues in contact with LEU 342 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232L LYS* 2.9 23.4 + - - -
255L MET* 3.4 9.3 - - - +
304L VAL* 4.2 11.4 - - + +
305L HIS 3.0 27.5 + - - +
306L ALA* 4.1 5.6 - - - +
307L LEU* 4.7 9.4 - - + -
340L PHE* 4.5 4.0 - - + +
341L TYR* 1.3 78.4 - - - +
343L GLU* 1.3 60.2 + - - +
344L ASP 3.6 18.2 - - - +
346L LEU* 4.1 28.7 - - + -
374L VAL* 5.7 3.4 - - + -
376L LEU* 4.3 23.8 - - + -
389L ASN* 4.1 18.2 - - - +
391L TYR* 4.2 4.5 - - - +
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Residues in contact with GLU 343 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232L LYS* 3.0 17.2 + - - -
237L HIS* 5.1 4.3 - - - -
255L MET* 3.7 20.6 - - + +
256L LYS* 5.8 10.5 - - - -
342L LEU* 1.3 72.8 - - - +
344L ASP* 1.3 70.0 + - - +
387L VAL* 4.1 11.4 - - + +
389L ASN* 3.5 25.6 - - - +
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Residues in contact with ASP 344 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232L LYS* 4.5 2.5 - - - +
342L LEU* 3.6 19.3 - - - +
343L GLU* 1.3 86.9 - - - +
345L TYR* 1.3 70.6 + - + +
346L LEU* 3.8 9.0 + - + +
385L THR* 5.8 6.1 - - + +
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Residues in contact with TYR 345 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104J TYR 2.8 27.9 + - - -
105J HIS* 3.6 14.5 - + - -
107J LYS* 3.8 19.0 + - + +
232L LYS* 4.8 3.8 - - - +
303L TYR* 3.7 34.1 - + - -
304L VAL 3.2 15.5 - - - +
305L HIS* 3.6 37.7 - + + +
344L ASP* 1.3 82.7 - - + +
346L LEU* 1.3 63.1 + - - +
347L THR* 3.9 10.5 + - - -
383L CYS* 5.0 2.8 - - - -
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Residues in contact with LEU 346 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303L TYR* 3.3 6.6 - - - +
304L VAL* 2.8 39.2 + - + +
342L LEU* 4.1 19.5 - - + -
344L ASP* 4.0 10.3 - - + +
345L TYR* 1.3 78.9 - - - +
347L THR* 1.3 60.5 - - - +
348L VAL* 3.8 14.2 + - + -
354L ILE* 4.2 26.9 - - + -
376L LEU* 4.0 24.7 - - + -
378L PHE* 4.4 17.5 - - + -
383L CYS* 4.1 9.2 - - - -
385L THR* 4.0 20.4 - - + +
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Residues in contact with THR 347 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105J HIS 5.1 0.5 + - - -
108J HIS* 4.2 18.8 + - + +
319J HIS* 3.5 31.9 - - + +
302L ASP 4.0 2.0 - - - -
303L TYR* 3.8 21.2 - - + -
345L TYR* 3.9 11.8 + - - -
346L LEU* 1.3 71.6 - - - +
348L VAL* 1.3 59.7 + - - +
352L GLU* 4.3 1.9 - - - +
378L PHE* 3.9 12.1 - - - -
382L LEU* 3.9 29.7 - - + +
383L CYS* 3.5 16.2 - - - +
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Residues in contact with VAL 348 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319J HIS* 3.2 6.4 - - - -
269L VAL* 4.1 11.7 - - + -
298L ILE* 3.7 34.8 - - + -
301L ASN* 3.4 0.5 - - - -
302L ASP 2.9 53.4 + - - +
303L TYR* 4.8 0.2 - - - -
304L VAL* 4.1 11.4 - - + -
346L LEU* 3.8 24.5 - - + +
347L THR* 1.3 77.7 - - - +
349L ARG* 1.3 62.3 + - - +
352L GLU* 3.8 2.7 - - - -
354L ILE* 5.1 0.7 - - + -
378L PHE* 3.7 23.1 - - + -
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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