Contacts of the strand formed by residues 370 - 379 (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 LEU 370 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189L TYR 4.9 2.0 - - - +
190L CYS* 5.0 2.2 - - + +
192L PHE* 4.1 14.6 - - + +
193L TYR* 3.8 38.6 - - + +
195L SER* 4.5 10.8 - - - +
360L MET* 3.8 25.8 - - + -
361L LYS 3.6 13.5 - - - +
362L PRO* 4.6 2.0 - - + -
368L ARG 4.4 1.1 - - - +
369L ASP* 1.3 80.5 - - - +
371L ASP* 1.3 65.0 + - - +
372L PHE* 3.8 32.2 - - + -
391L TYR 3.8 0.3 - - - +
392L LYS* 3.3 5.2 - - - +
393L MET* 2.8 41.9 + - + +
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Residues in contact with ASP 371 (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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360L MET* 3.1 26.5 - - - +
361L LYS* 3.1 34.1 + - + +
363L ASN* 3.2 42.4 + - - +
364L ALA 4.7 0.7 + - - -
369L ASP* 4.3 0.9 - - - +
370L LEU* 1.3 76.7 - - - +
372L PHE* 1.3 63.0 + - - +
391L TYR 3.5 4.5 - - - +
392L LYS* 3.5 22.9 + - + +
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Residues in contact with PHE 372 (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* 3.7 26.0 - - + -
221L LEU* 6.1 0.4 - - + -
340L PHE* 3.9 26.7 - + + -
358L ILE* 4.2 19.3 - - + -
359L SER 3.2 8.3 - - - -
360L MET* 3.7 30.5 - - + -
370L LEU* 3.8 35.2 - - + -
371L ASP* 1.3 79.6 - - - +
373L THR* 1.3 68.7 + - - +
374L VAL* 5.0 1.6 - - + -
390L ASP* 3.5 5.7 - - - +
391L TYR* 2.7 51.3 + - + +
393L MET* 4.0 18.8 - - + -
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Residues in contact with THR 373 (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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357L THR* 3.7 1.4 + - - +
358L ILE* 3.4 2.8 - - - -
359L SER* 3.0 42.1 + - - +
372L PHE* 1.3 73.2 + - - +
374L VAL* 1.3 62.9 + - - +
375L ASP* 3.4 26.8 + - - +
388L SER* 3.7 10.3 - - - +
389L ASN 3.2 6.1 - - - +
390L ASP* 3.0 20.1 + - - +
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Residues in contact with VAL 374 (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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294L PHE* 4.4 6.7 - - + -
307L LEU* 3.7 29.6 - - + -
340L PHE* 4.8 10.3 - - + -
342L LEU* 5.7 3.4 - - + -
357L THR 3.4 6.7 - - - +
358L ILE* 4.3 21.3 - - + -
372L PHE* 5.0 3.1 - - + -
373L THR* 1.3 75.9 - - - +
375L ASP* 1.3 71.7 + - - +
376L LEU* 4.0 7.8 + - + +
387L VAL 4.0 0.9 - - - +
388L SER* 3.6 0.9 - - - -
389L ASN* 2.9 35.4 + - + +
391L TYR* 3.9 28.9 - - + +
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Residues in contact with ASP 375 (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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294L PHE* 3.9 3.6 - - - -
356L GLY* 3.0 5.7 - - - -
357L THR* 2.8 50.9 + - + +
373L THR* 3.4 14.3 + - - +
374L VAL* 1.3 74.1 - - - +
376L LEU* 1.3 60.0 + - - +
377L ASP* 5.1 3.4 - - - +
387L VAL 3.3 5.2 - - - +
388L SER* 2.5 34.0 + - - -
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Residues in contact with LEU 376 (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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294L PHE* 4.8 2.0 - - + -
307L LEU* 4.3 23.3 - - + -
342L LEU* 4.3 29.4 - - + -
346L LEU* 4.0 24.2 - - + -
354L ILE* 3.7 26.5 - - + -
355L TYR 3.6 3.4 - - - +
356L GLY* 4.3 0.2 - - - -
374L VAL* 4.6 7.4 - - + +
375L ASP* 1.3 76.5 - - - +
377L ASP* 1.3 72.9 + - - +
378L PHE* 4.4 3.1 - - + +
385L THR* 4.5 10.3 - - - +
386L SER* 3.3 2.9 - - - -
387L VAL* 2.9 46.1 + - + +
389L ASN* 6.1 1.8 - - - +
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Residues in contact with ASP 377 (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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353L GLU 4.2 0.5 - - - +
354L ILE* 3.8 1.7 - - - +
355L TYR* 2.7 49.9 + - + +
356L GLY* 4.6 0.8 - - - -
375L ASP* 5.1 2.9 - - - +
376L LEU* 1.3 83.1 + - - +
378L PHE* 1.3 63.0 + - - +
385L THR 3.6 2.2 - - - -
386L SER* 3.4 26.5 + - - -
387L VAL 4.4 1.6 + - - +
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Residues in contact with PHE 378 (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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298L ILE* 4.1 3.8 - - + -
346L LEU* 4.4 12.6 - - + -
347L THR 3.9 7.2 - - - -
348L VAL* 3.7 22.4 - - + -
352L GLU* 3.3 39.0 - - + -
353L GLU 3.2 28.3 - - - -
354L ILE* 3.9 9.0 - - + -
355L TYR* 6.0 0.4 - - - -
376L LEU* 4.3 12.5 - - + +
377L ASP* 1.3 75.7 - - - +
379L LYS* 1.3 61.2 + - - +
380L GLY* 3.4 20.6 - - - -
383L CYS* 3.7 32.3 - - - -
384L GLU* 3.2 6.6 - - - +
385L THR* 2.9 34.5 + - - +
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Residues in contact with LYS 379 (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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352L GLU* 5.5 1.7 - - - +
353L GLU 4.8 2.6 + - - -
355L TYR* 6.3 0.2 - - - -
378L PHE* 1.3 75.9 - - - +
380L GLY* 1.3 63.6 + - - +
383L CYS 4.2 2.2 - - - -
384L GLU* 3.3 35.9 - - + +
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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