Contacts of the strand formed by residues 353 - 362 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295N CYS* 4.0 12.1 - - - -
296N LEU 3.4 6.5 - - - +
297N GLN* 3.4 31.0 - - - +
298N ILE* 4.0 1.1 - - - -
351N GLY 4.0 7.4 - - - +
352N GLU* 1.3 85.5 - - - +
354N ILE* 1.3 61.3 + - - +
355N TYR* 2.9 42.8 + - + -
378N PHE* 2.9 24.2 - - - -
379N LYS 4.6 2.9 + - - -
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Residues in contact with ILE 354 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225N ALA* 4.1 26.0 - - + -
270N THR* 4.7 0.7 - - + -
294N PHE* 3.9 11.8 - - + +
295N CYS* 3.1 6.8 - - - -
296N LEU* 2.8 48.4 + - + +
298N ILE* 3.8 21.5 - - + -
304N VAL* 4.6 7.9 - - + -
307N LEU* 5.2 2.7 - - + -
346N LEU* 4.2 16.8 - - + -
348N VAL* 5.2 0.4 - - + -
353N GLU* 1.3 74.4 - - - +
355N TYR* 1.3 65.1 + - - +
376N LEU* 3.8 36.3 - - + -
377N ASP 3.9 4.9 - - - +
378N PHE* 3.8 11.9 - - + -
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Residues in contact with TYR 355 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294N PHE* 3.5 6.1 - - - -
295N CYS* 3.7 20.5 - - + -
353N GLU* 2.9 42.4 + - + -
354N ILE* 1.3 82.4 - - - +
356N GLY* 1.3 59.0 + - - +
376N LEU* 3.6 2.4 - - - -
377N ASP* 2.7 50.2 + - + +
378N PHE* 5.8 0.4 - - - -
379N LYS 6.2 0.7 - - - -
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Residues in contact with GLY 356 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293N ALA* 3.3 5.5 - - - +
294N PHE* 2.8 46.9 + - - +
355N TYR* 1.3 76.8 - - - +
357N THR* 1.3 60.8 + - - +
375N ASP* 3.0 16.4 - - - -
376N LEU* 4.3 0.2 - - - -
377N ASP* 4.6 1.8 - - - -
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Residues in contact with THR 357 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291N THR* 4.0 21.2 - - + +
292N SER 3.4 8.1 - - - -
293N ALA* 4.3 12.3 - - + +
294N PHE* 3.7 2.3 - - - -
356N GLY* 1.3 80.1 - - - +
358N ILE* 1.3 63.5 + - - +
359N SER* 4.9 3.3 + - - -
373N THR* 3.8 1.1 + - - +
374N VAL* 3.4 2.8 - - - -
375N ASP* 2.9 52.6 + - + +
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Residues in contact with ILE 358 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221N LEU* 5.9 0.9 - - + -
223N VAL* 4.9 7.2 - - + -
275N ILE* 3.9 38.8 - - + -
290N PHE* 4.1 4.5 - - + -
291N THR* 3.9 0.6 - - - -
292N SER* 2.9 34.2 + - - +
294N PHE* 3.5 24.9 - - + -
307N LEU* 6.4 0.7 - - + -
309N THR* 4.9 11.7 - - + -
340N PHE* 5.2 3.6 - - + -
357N THR* 1.3 74.3 - - - +
359N SER* 1.3 69.4 + - - +
360N MET* 5.3 4.3 - - + -
372N PHE* 4.3 22.9 - - + -
373N THR 3.4 7.0 - - - +
374N VAL* 4.3 17.7 - - + -
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Residues in contact with SER 359 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290N PHE 3.1 9.2 - - - -
291N THR* 3.1 32.4 + - - +
357N THR* 4.9 3.1 + - - -
358N ILE* 1.3 76.2 + - - +
360N MET* 1.3 63.1 + - - +
361N LYS* 5.9 1.3 - - - -
372N PHE* 3.2 6.9 - - - +
373N THR* 2.9 48.5 + - - +
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Residues in contact with MET 360 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190N CYS 5.1 1.6 - - - +
192N PHE* 3.5 45.5 - - + -
221N LEU* 5.0 6.7 - - - -
288N LEU* 3.6 18.2 - - + +
289N SER* 3.4 4.3 - - - -
290N PHE* 3.1 51.0 + - + -
358N ILE* 5.3 3.4 - - + -
359N SER* 1.3 76.3 - - - +
361N LYS* 1.3 67.8 + - - +
362N PRO* 6.0 0.7 - - + -
370N LEU* 3.8 19.1 - - + -
371N ASP 3.1 13.5 - - - +
372N PHE* 3.7 33.9 - - + -
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Residues in contact with LYS 361 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289N SER* 3.9 15.0 - - - +
290N PHE 5.6 0.2 - - - +
359N SER* 5.9 1.1 - - - -
360N MET* 1.3 77.7 - - - +
362N PRO* 1.3 81.1 + - + +
364N ALA* 5.8 4.9 - - - +
370N LEU* 3.6 10.3 - - - +
371N ASP* 2.9 50.6 + - + +
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Residues in contact with PRO 362 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195N SER* 4.2 13.2 - - - +
198N ASN* 5.1 6.7 - - - +
288N LEU* 4.7 10.5 - - + +
289N SER* 3.3 17.9 - - - +
360N MET* 6.0 0.7 - - + -
361N LYS* 1.3 100.3 - - + +
363N ASN* 1.3 64.4 + - - +
364N ALA* 3.6 1.7 + - - -
367N VAL* 3.6 33.2 - - + +
369N ASP 3.6 8.1 - - - +
370N LEU* 4.7 5.4 - - + -
371N ASP* 5.2 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