Contacts of the strand formed by residues 353 - 362 (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 GLU 353 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295B CYS* 4.1 10.2 - - - -
296B LEU 3.3 9.6 - - - +
297B GLN* 3.6 24.0 - - - +
298B ILE* 4.1 0.7 - - - -
351B GLY 3.8 9.0 - - - +
352B GLU* 1.3 85.2 - - - +
354B ILE* 1.3 61.5 + - - +
355B TYR* 2.6 48.1 + - + -
378B PHE* 3.0 23.6 - - - -
379B LYS 4.7 2.3 + - - -
273G CYS* 3.1 31.6 - - - +
274G LEU 4.4 6.0 + - - +
293G ALA 4.6 0.5 - - - +
295G CYS 4.1 4.7 - - - +
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Residues in contact with ILE 354 (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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225B ALA* 4.0 26.9 - - + -
270B THR* 4.7 0.4 - - + -
294B PHE* 3.8 11.6 - - + +
295B CYS* 3.2 5.8 - - - -
296B LEU* 2.8 49.9 + - + +
298B ILE* 3.8 21.1 - - + -
304B VAL* 4.6 7.4 - - + -
307B LEU* 5.1 2.7 - - + -
346B LEU* 4.2 17.0 - - + -
348B VAL* 5.3 0.2 - - + -
353B GLU* 1.3 73.8 - - - +
355B TYR* 1.3 65.2 + - - +
376B LEU* 3.7 37.5 - - + -
377B ASP 4.0 3.6 - - - +
378B PHE* 3.9 11.9 - - + -
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Residues in contact with TYR 355 (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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294B PHE* 3.5 7.9 - - - -
295B CYS* 3.5 17.0 - - - -
353B GLU* 2.6 45.1 + - + -
354B ILE* 1.3 80.1 - - - +
356B GLY* 1.3 58.8 + - - +
376B LEU* 3.7 2.8 - - - +
377B ASP* 2.9 44.3 + - + +
293G ALA* 3.4 25.6 - - + -
294G PHE* 3.0 32.8 + - - -
295G CYS* 3.2 10.8 + - + -
355G TYR* 4.3 18.2 - + - -
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Residues in contact with GLY 356 (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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293B ALA* 3.3 5.4 - - - +
294B PHE* 2.6 49.6 + - - +
355B TYR* 1.3 77.4 - - - +
357B THR* 1.3 60.5 + - - +
375B ASP* 3.1 15.3 - - - -
376B LEU* 4.4 0.4 - - - -
377B ASP* 4.7 1.8 - - - -
355G TYR* 5.5 0.2 - - - -
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Residues in contact with THR 357 (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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291B THR* 4.0 21.5 - - + +
292B SER 3.3 8.7 - - - -
293B ALA* 4.3 13.2 - - + +
294B PHE* 3.6 2.5 - - - -
356B GLY* 1.3 79.6 - - - +
358B ILE* 1.3 63.0 + - - +
359B SER* 4.9 3.1 + - - -
373B THR* 3.8 1.1 + - - +
374B VAL* 3.5 2.3 - - - -
375B ASP* 2.8 53.3 + - + +
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Residues in contact with ILE 358 (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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221B LEU* 5.8 1.1 - - + -
223B VAL* 4.9 12.1 - - + -
275B ILE* 3.9 38.8 - - + -
290B PHE* 4.2 4.7 - - + -
291B THR* 3.9 0.2 - - - -
292B SER* 2.9 31.0 + - - +
294B PHE* 3.6 23.6 - - + -
307B LEU* 6.3 1.1 - - + -
309B THR* 4.9 8.1 - - + -
340B PHE* 5.3 3.1 - - + -
357B THR* 1.3 74.9 - - - +
359B SER* 1.3 68.1 + - - +
360B MET* 5.3 3.6 - - + -
372B PHE* 4.3 22.7 - - + -
373B THR 3.4 4.3 - - - -
374B VAL* 4.2 20.6 - - + -
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Residues in contact with SER 359 (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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290B PHE 3.0 16.6 - - - -
291B THR* 3.1 27.2 + - - +
357B THR* 4.9 2.6 + - - -
358B ILE* 1.3 75.9 + - - +
360B MET* 1.3 61.9 + - - +
361B LYS* 6.3 1.3 - - - -
372B PHE* 3.3 8.1 - - - +
373B THR* 3.0 46.3 + - - +
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Residues in contact with MET 360 (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 5.1 1.6 - - - +
192B PHE* 3.4 46.4 - - + -
221B LEU* 4.9 7.6 - - - -
288B LEU 3.5 21.1 - - - +
289B SER* 3.3 4.3 - - - -
290B PHE* 2.9 51.7 + - + -
358B ILE* 5.3 3.4 - - + -
359B SER* 1.3 77.2 - - - +
361B LYS* 1.3 64.7 - - - +
362B PRO* 6.1 0.2 - - + -
370B LEU* 3.9 19.1 - - + -
371B ASP 3.1 14.1 - - - +
372B PHE* 3.7 32.3 - - + -
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Residues in contact with LYS 361 (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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289B SER* 3.8 14.6 - - - +
290B PHE 5.6 0.2 - - - +
359B SER* 5.9 1.8 - - - -
360B MET* 1.3 77.5 - - - +
362B PRO* 1.3 85.2 - - + +
363B ASN* 5.7 0.2 - - - +
364B ALA* 5.6 5.8 - - - +
370B LEU* 3.7 10.1 - - - +
371B ASP* 3.1 45.4 + - + +
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Residues in contact with PRO 362 (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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195B SER* 4.1 14.1 - - - +
198B ASN* 5.1 7.6 - - - +
288B LEU* 4.5 11.2 - - + +
289B SER* 3.3 17.5 - - - +
360B MET* 6.1 0.4 - - + -
361B LYS* 1.3 99.9 - - + +
363B ASN* 1.3 65.0 + - - +
364B ALA* 3.6 1.6 + - - -
367B VAL* 3.7 34.1 - - + +
369B ASP 3.7 7.4 - - - +
370B LEU* 4.7 5.2 - - + -
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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