Contacts of the strand formed by residues 290 - 297 (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 PHE 290 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192N PHE* 4.2 10.3 - + - -
221N LEU* 4.8 5.6 - - + -
275N ILE* 3.8 12.6 - - + -
276N LYS* 3.8 39.0 - - + +
287N GLU 3.5 15.9 - - - +
288N LEU* 3.4 16.4 - - - -
289N SER* 1.3 74.4 - - - +
291N THR* 1.3 66.9 + - - +
292N SER* 3.7 27.8 - - - -
358N ILE* 4.1 8.7 - - + -
359N SER* 3.1 5.7 - - - -
360N MET* 3.1 64.2 + - + +
361N LYS* 5.6 0.6 - - - +
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Residues in contact with THR 291 (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* 1.3 74.3 - - - +
292N SER* 1.3 67.4 + - - +
357N THR* 4.0 25.8 - - + +
358N ILE 3.9 0.9 - - - -
359N SER* 3.1 26.8 + - - +
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Residues in contact with SER 292 (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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275N ILE* 2.5 41.4 + - - -
290N PHE* 3.7 11.2 - - - -
291N THR* 1.3 81.8 - - - +
293N ALA* 1.3 64.2 + - - +
357N THR* 4.3 2.7 - - - -
358N ILE* 2.9 41.9 + - - +
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Residues in contact with ALA 293 (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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273N CYS* 4.4 3.1 - - - -
274N LEU 4.5 3.1 - - - +
275N ILE* 4.2 5.2 - - - +
292N SER* 1.3 81.1 + - - +
294N PHE* 1.3 63.0 + - - +
356N GLY 3.3 10.8 - - - +
357N THR* 4.2 10.0 - - + +
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Residues in contact with PHE 294 (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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223N VAL* 4.0 7.9 - - + -
273N CYS* 3.5 18.4 - - - -
275N ILE* 3.9 11.4 - - + -
293N ALA* 1.3 76.9 - - - +
295N CYS* 1.3 62.0 + - - +
296N LEU* 4.0 30.3 - - + -
307N LEU* 4.0 22.0 - - + -
354N ILE* 4.2 13.7 - - + -
355N TYR* 3.5 6.6 - - - +
356N GLY* 2.8 77.9 + - - +
357N THR 3.5 13.7 - - - -
358N ILE* 3.5 22.7 - - + -
374N VAL* 4.4 5.2 - - + -
375N ASP 3.9 4.5 - - - -
376N LEU* 4.7 5.6 - - + -
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Residues in contact with CYS 295 (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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271N ASN* 4.6 4.2 + - - +
273N CYS* 3.3 24.9 - - - +
294N PHE* 1.3 75.6 - - - +
296N LEU* 1.3 67.6 + - - +
297N GLN* 4.3 1.1 - - - -
353N GLU* 4.0 20.9 - - - -
354N ILE 3.1 10.5 - - - -
355N TYR* 3.7 36.6 - - + -
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Residues in contact with LEU 296 (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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223N VAL* 3.5 22.2 - - + +
224N VAL* 3.9 7.2 - - - +
225N ALA* 3.8 28.7 - - + +
270N THR* 3.8 13.2 - - + +
271N ASN* 3.4 24.5 - - - +
273N CYS* 3.7 10.8 - - + -
294N PHE* 4.0 25.8 - - + -
295N CYS* 1.3 84.7 - - - +
297N GLN* 1.3 61.2 + - - +
298N ILE* 3.7 3.5 + - - +
307N LEU* 4.1 8.5 - - + -
353N GLU* 3.4 4.6 - - - -
354N ILE* 2.8 45.4 + - + +
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Residues in contact with GLN 297 (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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270N THR* 3.1 18.6 - - - -
271N ASN* 2.8 27.0 + - - +
295N CYS* 4.3 1.0 - - - -
296N LEU* 1.3 71.1 - - - +
298N ILE* 1.3 65.6 + - - +
299N GLN* 3.0 32.3 + - - +
351N GLY* 4.8 9.9 - - - +
352N GLU 3.9 7.4 - - - +
353N GLU* 3.4 23.9 - - + +
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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