Contacts of the strand formed by residues 353 - 362 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273F CYS* 3.1 28.9 - - - +
274F LEU 4.6 5.3 - - - +
293F ALA 4.5 1.2 - - - +
295F CYS* 4.1 5.8 - - - +
295K CYS* 4.1 11.3 - - - -
296K LEU 3.4 11.0 - - - +
297K GLN* 3.5 24.0 - - - +
298K ILE* 4.0 1.1 - - - -
351K GLY 3.8 8.3 - - - +
352K GLU* 1.3 83.9 - - - +
354K ILE* 1.3 64.4 + - - +
355K TYR* 2.5 47.1 + - + -
378K PHE* 3.0 21.2 - - - -
379K LYS 4.7 2.4 + - - -
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Residues in contact with ILE 354 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225K ALA* 4.1 26.2 - - + -
270K THR* 4.7 0.7 - - + -
294K PHE* 3.8 11.6 - - + +
295K CYS* 3.2 6.6 - - - -
296K LEU* 2.9 40.7 + - + +
298K ILE* 3.8 21.3 - - + -
304K VAL* 4.6 7.0 - - + -
307K LEU* 5.2 2.2 - - + -
346K LEU* 4.1 17.5 - - + -
348K VAL* 5.3 0.4 - - + -
353K GLU* 1.3 76.0 - - - +
355K TYR* 1.3 65.3 + - - +
376K LEU* 3.7 36.6 - - + -
377K ASP 3.9 4.5 - - - +
378K PHE* 3.8 11.9 - - + -
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Residues in contact with TYR 355 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293F ALA* 3.4 25.5 - - + -
294F PHE* 3.0 32.7 + - - -
295F CYS* 3.3 10.4 + - + -
355F TYR* 4.3 17.7 - + - -
356F GLY 5.5 0.2 - - - -
294K PHE* 3.5 6.7 - - - -
295K CYS* 3.6 17.3 - - + -
353K GLU* 2.5 45.4 + - + -
354K ILE* 1.3 79.5 - - - +
356K GLY* 1.3 59.9 + - - +
376K LEU* 3.6 2.8 - - - -
377K ASP* 2.8 44.9 + - + +
378K PHE* 6.1 0.2 - - - -
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Residues in contact with GLY 356 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293K ALA* 3.4 5.4 - - - +
294K PHE* 2.9 42.3 + - - +
355K TYR* 1.3 77.8 - - - +
357K THR* 1.3 62.7 + - - +
375K ASP* 3.0 17.0 - - - -
376K LEU* 4.2 0.2 - - - -
377K ASP* 4.6 1.6 - - - -
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Residues in contact with THR 357 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291K THR* 4.0 22.4 - - + +
292K SER 3.4 7.4 - - - -
293K ALA* 4.3 13.5 - - + +
294K PHE* 3.7 1.9 - - - -
356K GLY* 1.3 79.7 - - - +
358K ILE* 1.3 63.7 + - - +
359K SER* 5.1 1.7 + - - -
373K THR* 3.7 1.8 + - - +
374K VAL* 3.4 2.3 - - - -
375K ASP* 2.9 54.1 + - + +
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Residues in contact with ILE 358 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221K LEU* 5.9 0.9 - - + -
223K VAL* 4.9 11.9 - - + -
275K ILE* 3.9 37.7 - - + -
290K PHE* 4.3 4.6 - - + -
291K THR* 4.8 0.7 - - - -
292K SER* 2.9 34.7 + - - +
294K PHE* 3.5 24.5 - - + -
307K LEU* 6.4 0.9 - - + -
309K THR* 4.9 7.4 - - + -
340K PHE* 5.3 4.0 - - + -
357K THR* 1.3 75.1 - - - +
359K SER* 1.3 67.6 - - - +
360K MET* 5.3 3.1 - - + -
372K PHE* 4.2 22.7 - - + -
373K THR 3.4 5.4 - - - +
374K VAL* 4.2 19.1 - - + -
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Residues in contact with SER 359 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290K PHE* 3.1 10.8 - - - -
291K THR* 3.1 32.2 + - - +
357K THR* 5.1 2.1 + - - -
358K ILE* 1.3 75.9 - - - +
360K MET* 1.3 62.8 + - - +
361K LYS* 6.3 1.3 - - - -
372K PHE* 3.1 7.4 - - - +
373K THR* 2.9 46.6 + - - +
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Residues in contact with MET 360 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190K CYS 5.1 1.8 - - - +
192K PHE* 3.5 45.8 - - + -
221K LEU* 4.9 7.0 - - - -
288K LEU* 3.7 18.0 - - + +
289K SER* 3.4 4.5 - - - -
290K PHE* 3.1 50.5 + - + +
358K ILE* 5.3 2.7 - - + -
359K SER* 1.3 77.6 - - - +
361K LYS* 1.3 67.0 + - - +
362K PRO* 6.1 0.4 - - + -
370K LEU* 3.8 18.8 - - + -
371K ASP 3.1 12.3 - - - +
372K PHE* 3.6 34.5 - - + -
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Residues in contact with LYS 361 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289K SER* 3.9 14.4 - - - +
290K PHE 5.7 0.2 - - - +
359K SER* 5.9 1.6 - - - -
360K MET* 1.3 78.6 - - - +
362K PRO* 1.4 81.5 + - + +
364K ALA* 5.6 6.2 - - - +
370K LEU* 3.5 11.0 - - - +
371K ASP* 3.0 49.8 + - + +
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Residues in contact with PRO 362 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195K SER* 4.3 12.1 - - - +
198K ASN* 5.2 7.2 - - - +
288K LEU* 4.7 9.6 - - + +
289K SER* 3.3 18.8 - - - +
360K MET* 6.1 0.4 - - + -
361K LYS* 1.4 100.6 - - + +
363K ASN* 1.3 65.5 + - - +
364K ALA* 3.6 1.9 + - - -
367K VAL* 3.7 33.2 - - + +
369K ASP 3.6 7.4 - - - +
370K LEU* 4.6 5.4 - - + -
371K ASP* 4.8 0.4 - - - -
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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