Contacts of the strand formed by residues 273 - 282 (chain A) in PDB entry 1SEK
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 TYR 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A ARG* 3.4 3.3 - - - -
219A TYR* 2.9 74.8 + + - -
220A ALA* 4.5 3.8 - - - -
221A ASP 5.5 0.7 - - - -
271A ARG 3.9 10.5 - - - +
272A LEU* 1.3 74.9 - - - +
274A ASN* 1.3 76.5 + - - +
275A THR* 3.7 24.3 + - + +
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Residues in contact with ASN 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A VAL 3.6 6.7 - - - +
218A ARG* 3.6 39.9 - - - +
273A TYR* 1.3 81.4 - - - +
275A THR* 1.3 65.9 + - - +
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Residues in contact with THR 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ASP* 3.4 8.2 - - - +
217A VAL* 2.9 31.4 + - + +
219A TYR* 3.7 30.3 - - + -
273A TYR* 3.7 20.6 + - + +
274A ASN* 1.3 77.0 - - - +
276A GLU* 1.3 76.0 + - - +
277A VAL* 4.2 12.7 - - + +
359A PRO* 5.4 3.3 - - - +
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Residues in contact with GLU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A LYS* 3.5 28.7 - - - +
215A LYS* 3.5 10.1 + - - +
216A ASP* 3.1 36.3 + - - +
275A THR* 1.3 83.3 + - - +
277A VAL* 1.3 68.0 + - - +
356A HIS* 3.3 30.0 - - + +
358A VAL* 4.2 6.6 - - + +
359A PRO* 3.5 15.8 - - - +
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Residues in contact with VAL 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A LYS* 3.3 2.8 - - - +
215A LYS 2.9 30.6 + - - +
217A VAL* 3.8 15.7 - - + -
219A TYR* 4.9 7.4 - - + -
230A ILE* 5.6 0.2 - - + -
275A THR* 4.2 17.3 - - + -
276A GLU* 1.3 82.7 - - - +
278A GLU* 1.3 59.7 + - - +
279A ILE* 3.4 32.2 + - + -
358A VAL* 3.8 8.5 - - - -
359A PRO* 3.4 22.4 - - + +
361A VAL* 3.9 22.9 - - + -
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Residues in contact with GLU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ARG* 5.6 1.2 - - - -
212A ILE* 3.2 25.3 - - + +
213A GLY* 3.6 15.3 + - - -
214A LYS* 3.7 25.1 + - - +
277A VAL* 1.3 71.6 - - - +
279A ILE* 1.3 58.7 + - - +
280A TYR* 3.3 35.5 - - + +
358A VAL* 3.8 7.8 - - + +
359A PRO 2.7 15.7 + - - +
360A LYS* 4.2 8.1 - - + -
361A VAL 2.8 28.3 + - - -
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Residues in contact with ILE 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A PHE* 3.4 33.0 - - + -
211A MET 3.4 0.2 - - - +
212A ILE* 3.4 6.4 - - - +
213A GLY 2.8 33.1 + - - +
215A LYS* 5.1 4.3 - - + -
217A VAL* 4.1 10.3 - - + -
230A ILE* 3.8 28.3 - - + -
232A MET* 4.6 13.0 - - + -
277A VAL* 3.4 27.7 + - + +
278A GLU* 1.3 73.1 - - - +
280A TYR* 1.3 64.2 + - - +
281A LEU* 4.1 12.6 - - + -
361A VAL* 3.5 17.9 - - + +
363A ILE* 5.0 8.7 - - + -
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Residues in contact with TYR 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A ARG* 3.6 34.5 - - - +
210A THR* 3.6 11.7 - - + +
211A MET 3.4 5.6 - - - -
212A ILE* 3.7 31.0 - - + +
278A GLU* 3.3 39.6 - - + +
279A ILE* 1.3 72.0 - - - +
281A LEU* 1.3 60.8 + - - +
282A PRO* 3.9 0.3 - - - +
360A LYS* 3.5 36.9 + - + +
361A VAL 2.9 21.2 + - - +
362A GLU* 3.4 23.8 - - + -
363A ILE* 2.9 31.1 + - - +
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Residues in contact with LEU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A TRP* 4.3 13.5 - - + -
188A PHE* 4.6 3.6 - - + -
210A THR* 3.5 3.6 - - - +
211A MET* 2.8 56.5 + - + +
232A MET* 4.0 26.2 - - + -
241A MET* 6.2 0.2 - - + -
243A ILE* 4.2 20.0 - - + -
279A ILE* 3.8 13.9 - - + -
280A TYR* 1.3 74.5 - - - +
282A PRO* 1.3 84.8 - - + +
284A PHE* 4.4 12.1 - - + -
335A VAL* 4.6 6.1 - - + -
363A ILE* 4.3 15.5 - - + -
367A PHE* 4.6 2.5 - - + -
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Residues in contact with PRO 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A PHE* 3.8 21.3 - - + -
208A VAL* 4.0 14.8 - - + -
209A PRO 3.4 15.0 - - - +
210A THR* 3.8 8.3 - - + +
211A MET* 4.0 0.7 - - - +
280A TYR 3.9 1.6 - - - +
281A LEU* 1.3 104.8 - - + +
283A LYS* 1.3 68.8 + - - +
284A PHE* 3.2 17.2 - - + -
363A ILE* 3.2 28.7 - - + +
367A PHE* 4.7 3.8 - - + -
386A PRO* 4.0 10.1 - - + -
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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