Contacts of the strand formed by residues 370 - 379 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189O TYR 4.8 2.0 - - - +
190O CYS 5.0 1.8 - - - +
192O PHE* 4.0 15.0 - - + +
193O TYR* 3.7 38.4 - - + +
195O SER* 4.6 9.9 - - - +
360O MET* 3.8 25.6 - - + -
361O LYS 3.6 13.7 - - - +
362O PRO* 4.6 2.2 - - + -
368O ARG 4.6 0.9 - - - +
369O ASP* 1.3 81.6 - - - +
371O ASP* 1.3 64.2 + - - +
372O PHE* 3.7 33.4 - - + -
392O LYS* 3.4 4.5 - - - -
393O MET* 3.0 39.1 + - + +
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Residues in contact with ASP 371 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360O MET* 3.1 26.9 - - - +
361O LYS* 3.1 35.5 + - + +
363O ASN* 3.3 40.4 + - - +
364O ALA 4.8 0.9 + - - -
369O ASP* 4.3 0.9 + - - +
370O LEU* 1.3 75.5 - - - +
372O PHE* 1.3 62.6 + - - +
391O TYR 3.7 4.5 - - - +
392O LYS* 3.4 24.6 + - - +
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Residues in contact with PHE 372 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190O CYS* 4.0 20.2 - - + -
221O LEU* 6.1 0.4 - - + -
340O PHE* 3.9 27.4 - + + -
358O ILE* 4.2 17.5 - - + -
359O SER 3.3 8.5 - - - -
360O MET* 3.6 31.6 - - + -
370O LEU* 3.7 41.7 - - + -
371O ASP* 1.3 79.1 - - - +
373O THR* 1.3 71.1 + - - +
374O VAL* 5.0 1.8 - - + -
390O ASP* 3.6 5.7 - - - +
391O TYR* 3.0 48.4 + - + +
393O MET* 3.9 18.6 - - + -
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Residues in contact with THR 373 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357O THR* 4.0 0.9 + - - +
358O ILE* 3.4 2.4 - - - -
359O SER* 3.0 41.8 + - - +
372O PHE* 1.3 76.7 + - - +
374O VAL* 1.3 63.0 + - - +
375O ASP* 3.7 24.7 + - - +
388O SER* 4.0 8.3 - - - +
389O ASN 3.3 6.7 - - - +
390O ASP* 2.8 24.2 + - - +
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Residues in contact with VAL 374 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294O PHE* 4.4 6.1 - - + -
307O LEU* 3.8 30.1 - - + -
340O PHE* 4.7 10.3 - - + -
342O LEU* 5.7 3.1 - - + -
357O THR 3.5 6.5 - - - +
358O ILE* 4.3 22.4 - - + -
372O PHE* 5.0 2.0 - - + -
373O THR* 1.3 76.8 - - - +
375O ASP* 1.3 72.9 + - - +
376O LEU* 3.9 7.4 + - + +
387O VAL 3.9 1.0 - - - +
388O SER* 3.7 0.7 - - - -
389O ASN* 2.9 33.3 + - + +
391O TYR* 3.9 28.3 - - + +
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Residues in contact with ASP 375 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294O PHE* 3.8 2.9 - - - -
356O GLY* 3.0 23.3 - - - -
357O THR* 2.8 34.3 + - + +
373O THR* 3.7 11.9 + - - +
374O VAL* 1.3 74.0 - - - +
376O LEU* 1.3 60.7 + - - +
377O ASP* 5.2 3.8 - - - +
387O VAL 3.3 4.3 - - - +
388O SER* 2.7 35.2 + - - -
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Residues in contact with LEU 376 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294O PHE* 4.7 2.2 - - + -
307O LEU* 4.3 27.8 - - + -
342O LEU* 4.3 24.0 - - + -
346O LEU* 4.1 23.3 - - + -
354O ILE* 3.6 27.4 - - + -
355O TYR 3.5 3.4 - - - +
374O VAL* 4.5 7.6 - - + +
375O ASP* 1.3 77.3 - - - +
377O ASP* 1.3 70.1 + - - +
378O PHE* 4.4 3.6 - - + +
385O THR* 4.6 10.5 - - - +
386O SER* 3.2 2.3 - - - -
387O VAL* 2.8 48.4 + - + +
389O ASN* 6.3 0.9 - - - +
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Residues in contact with ASP 377 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353O GLU 4.4 0.7 - - - +
354O ILE* 3.9 1.4 - - - +
355O TYR* 2.7 48.8 + - + +
356O GLY* 4.6 0.8 - - - -
375O ASP* 5.2 2.8 - - - +
376O LEU* 1.3 78.8 + - - +
378O PHE* 1.3 62.5 + - - +
385O THR 3.6 2.9 - - - -
386O SER* 3.4 29.0 + - - -
387O VAL 4.5 0.9 + - - +
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Residues in contact with PHE 378 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298O ILE* 4.1 4.0 - - + -
346O LEU* 4.4 12.1 - - + -
347O THR 3.9 6.5 - - - -
348O VAL* 3.6 26.2 - - + -
352O GLU* 3.6 30.7 - - + -
353O GLU 3.1 36.1 - - - -
354O ILE* 3.8 9.4 - - + -
355O TYR* 5.9 0.7 - - - -
376O LEU* 4.4 11.9 - - + -
377O ASP* 1.3 76.0 - - - +
379O LYS* 1.3 61.2 - - - +
380O GLY* 3.5 19.1 - - - -
383O CYS* 3.7 34.3 - - - -
384O GLU* 3.2 7.0 - - - +
385O THR* 2.9 34.8 + - - +
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Residues in contact with LYS 379 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291J THR 5.9 1.0 + - - -
352O GLU* 5.6 1.0 - - - +
353O GLU 4.8 2.6 + - - -
355O TYR* 6.4 0.2 - - - -
378O PHE* 1.3 77.2 - - - +
380O GLY* 1.3 63.1 + - - +
383O CYS 4.1 2.7 - - - -
384O GLU* 3.3 35.2 - - + +
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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