Contacts of the strand formed by residues 353 - 362 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295H CYS* 4.1 11.0 - - - -
296H LEU 3.3 10.5 - - - +
297H GLN* 3.5 25.5 - - - +
298H ILE* 4.1 1.1 - - - -
351H GLY 3.9 7.4 - - - +
352H GLU* 1.3 85.0 - - - +
354H ILE* 1.3 62.5 + - - +
355H TYR* 2.7 48.0 + - + -
377H ASP 4.4 1.6 - - - +
378H PHE* 3.1 22.0 - - - -
379H LYS 4.9 2.1 + - - +
273M CYS* 3.1 33.0 - - - +
274M LEU 4.3 5.6 + - - +
293M ALA 4.8 0.5 - - - +
295M CYS 4.2 3.8 - - - +
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Residues in contact with ILE 354 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225H ALA* 4.1 26.2 - - + -
270H THR* 4.7 0.9 - - + -
294H PHE* 3.8 12.0 - - + +
295H CYS* 3.1 5.7 - - - -
296H LEU* 2.8 50.5 + - + +
298H ILE* 3.7 21.3 - - + -
304H VAL* 4.6 7.9 - - + -
307H LEU* 5.1 2.5 - - + -
346H LEU* 4.2 16.4 - - + -
348H VAL* 5.2 0.4 - - + -
353H GLU* 1.3 75.3 - - - +
355H TYR* 1.3 66.4 + - - +
376H LEU* 3.7 36.6 - - + -
377H ASP 4.0 4.3 - - - +
378H PHE* 3.8 12.1 - - + -
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Residues in contact with TYR 355 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294H PHE* 3.5 6.3 - - - -
295H CYS* 3.6 18.4 - - + -
353H GLU* 2.7 44.7 + - + -
354H ILE* 1.3 83.2 - - - +
356H GLY* 1.3 59.4 + - - +
376H LEU* 3.6 3.1 - - - +
377H ASP* 2.8 46.3 + - + +
378H PHE* 6.1 0.4 - - - -
293M ALA* 3.4 24.9 + - + -
294M PHE* 3.0 31.7 + - - -
295M CYS* 3.2 12.2 + - + -
355M TYR* 4.5 14.1 - + - -
356M GLY 5.5 0.2 - - - -
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Residues in contact with GLY 356 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293H ALA* 3.4 5.0 - - - +
294H PHE* 2.7 47.4 + - - +
355H TYR* 1.3 77.6 - - - +
357H THR* 1.3 60.6 + - - +
375H ASP* 3.1 17.0 - - - -
376H LEU* 4.3 0.4 - - - -
377H ASP* 4.5 2.5 - - - -
355M TYR* 5.6 0.2 - - - -
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Residues in contact with THR 357 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291H THR* 4.1 22.0 - - + +
292H SER 3.3 7.9 - - - -
293H ALA* 4.2 13.5 - - + +
294H PHE* 3.5 5.5 - - - -
356H GLY* 1.3 79.9 - - - +
358H ILE* 1.3 61.1 + - - +
359H SER* 5.1 1.7 + - - -
373H THR 5.0 1.2 + - - -
374H VAL* 3.5 2.3 - - - -
375H ASP* 2.9 54.6 + - + +
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Residues in contact with ILE 358 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221H LEU* 5.9 1.1 - - + -
223H VAL* 4.9 7.6 - - + -
275H ILE* 3.9 37.9 - - + -
290H PHE* 4.1 4.7 - - + -
291H THR* 3.8 1.0 - - - -
292H SER* 2.9 31.7 + - - +
294H PHE* 3.5 24.2 - - + -
307H LEU* 6.4 1.8 - - + -
309H THR* 4.9 11.7 - - + -
340H PHE* 5.2 3.4 - - + -
357H THR* 1.3 75.1 - - - +
359H SER* 1.3 68.7 + - - +
360H MET* 5.3 4.0 - - + -
372H PHE* 4.2 22.9 - - + -
373H THR 3.4 5.8 - - - +
374H VAL* 4.3 19.5 - - + -
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Residues in contact with SER 359 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290H PHE 3.1 9.4 - - - -
291H THR* 3.0 32.8 + - - +
357H THR* 5.1 2.1 + - - -
358H ILE* 1.3 77.1 + - - +
360H MET* 1.3 61.9 + - - +
361H LYS* 6.2 2.0 - - - -
372H PHE* 3.3 6.6 - - - +
373H THR* 3.0 45.9 + - - +
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Residues in contact with MET 360 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190H CYS 5.1 2.5 - - - +
192H PHE* 3.5 44.6 - - + -
221H LEU* 4.8 7.4 - - - -
288H LEU 3.5 22.0 - - - +
289H SER* 3.3 4.5 - - - -
290H PHE* 3.0 50.5 + - + -
358H ILE* 5.3 3.4 - - + -
359H SER* 1.3 75.9 - - - +
361H LYS* 1.3 65.6 + - - +
362H PRO* 6.1 0.2 - - + -
370H LEU* 3.8 18.8 - - + -
371H ASP 3.1 13.5 - - - +
372H PHE* 3.6 33.2 - - + -
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Residues in contact with LYS 361 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289H SER* 3.7 15.0 - - - +
290H PHE 5.6 0.7 - - - +
359H SER* 6.2 2.0 - - - -
360H MET* 1.3 78.0 - - - +
362H PRO* 1.3 82.1 - - + +
363H ASN* 5.7 0.4 - - - +
364H ALA* 5.7 4.9 - - - +
370H LEU* 3.6 11.4 - - - +
371H ASP* 3.1 49.5 + - + +
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Residues in contact with PRO 362 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195H SER* 4.2 14.4 - - - +
198H ASN* 5.2 6.7 - - - +
288H LEU* 4.8 7.4 - - + +
289H SER* 3.2 21.3 - - - +
360H MET* 6.1 0.2 - - + -
361H LYS* 1.3 100.5 - - - +
363H ASN* 1.3 66.4 + - - +
364H ALA* 3.6 1.7 + - - -
367H VAL* 3.7 32.5 - - + +
369H ASP 3.7 7.4 - - - +
370H LEU* 4.7 5.2 - - + -
371H ASP* 5.0 0.2 - - - -
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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