Contacts of the strand formed by residues 284 - 291 (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 PHE 284 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ASN* 6.2 0.4 - - - +
241A MET* 5.1 3.6 - - + -
243A ILE* 6.3 1.1 - - + -
281A LEU* 4.4 7.0 - - + -
282A PRO* 3.2 26.0 - - + -
283A LYS* 1.3 75.4 - - - +
285A LYS* 1.3 63.0 + - - +
286A ILE* 3.9 31.0 - - + -
333A ILE* 4.3 8.5 - - + -
334A GLU* 3.9 0.5 - - - +
335A VAL* 2.8 66.1 + - + +
367A PHE* 3.8 33.7 - + - -
369A PHE* 4.2 20.9 - + + -
383A CYS* 4.2 15.7 - - + -
386A PRO* 4.5 12.8 - - + +
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Residues in contact with LYS 285 (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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42A ASN* 5.3 3.3 + - - -
284A PHE* 1.3 78.0 - - - +
286A ILE* 1.3 64.8 + - - +
287A GLU 4.3 0.2 + - - -
332A PHE* 3.9 19.5 - - + -
333A ILE 3.0 12.6 - - - +
334A GLU* 2.9 36.7 + - - -
386A PRO 5.4 1.0 + - - -
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Residues in contact with ILE 286 (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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42A ASN* 3.9 23.8 - - + +
43A VAL 3.9 14.4 - - - +
44A VAL* 3.7 22.5 - - + +
284A PHE* 3.9 20.2 - - + -
285A LYS* 1.3 77.5 - - - +
287A GLU* 1.3 64.1 + - - +
288A THR* 3.7 9.2 - - - +
331A ALA 3.6 1.0 - - - +
332A PHE* 3.3 3.5 - - - -
333A ILE* 2.7 40.5 + - + +
369A PHE* 3.5 36.3 - - + -
382A VAL 3.8 13.0 - - - +
383A CYS* 4.2 7.0 - - + -
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Residues in contact with GLU 287 (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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42A ASN 5.7 0.3 - - - +
156A ARG 4.7 3.5 - - - +
157A ILE* 4.6 8.0 - - - +
158A LYS 5.3 0.5 + - - -
285A LYS 4.3 0.6 + - - -
286A ILE* 1.3 77.8 - - - +
288A THR* 1.3 63.9 + - - +
289A THR* 5.6 0.2 - - - +
330A LYS* 3.8 34.8 + - - -
331A ALA 3.1 8.3 - - - +
332A PHE* 3.7 35.3 - - + +
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Residues in contact with THR 288 (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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34A VAL* 5.2 1.1 - - + -
38A ASN* 5.3 3.8 - - - +
42A ASN 4.4 1.9 + - - +
43A VAL* 3.6 29.3 - - + -
44A VAL* 3.0 39.1 + - - +
286A ILE* 3.7 2.6 - - - +
287A GLU* 1.3 78.1 + - - +
289A THR* 1.3 67.7 + - - +
290A THR* 3.9 17.2 + - - +
329A GLN* 3.8 1.2 - - - +
330A LYS* 3.4 4.5 - - - +
331A ALA* 2.8 41.0 + - - +
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Residues in contact with THR 289 (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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160A LEU 4.6 8.7 - - - +
287A GLU* 5.6 0.2 - - - +
288A THR* 1.3 75.4 - - - +
290A THR* 1.3 64.2 + - - +
291A ASP 4.1 1.0 + - - -
328A ILE* 3.9 25.1 - - + -
329A GLN 3.5 3.8 - - - +
330A LYS* 3.5 26.8 - - + +
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Residues in contact with THR 290 (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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30A MET* 4.9 2.5 - - + -
34A VAL* 4.2 20.4 - - + +
44A VAL 4.8 3.5 + - - -
45A LEU* 5.1 1.6 - - - +
288A THR* 3.9 15.6 - - - +
289A THR* 1.3 75.9 + - - +
291A ASP* 1.3 64.0 + - - +
292A LEU* 3.0 16.4 + - + -
295A VAL* 3.5 29.6 - - + -
328A ILE* 3.7 6.5 - - - +
329A GLN* 2.7 52.4 + - - -
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Residues in contact with ASP 291 (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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289A THR 4.1 1.6 + - - -
290A THR* 1.3 72.4 - - - +
292A LEU* 1.3 63.2 + - - +
293A LYS* 3.0 28.0 + - - +
294A GLU* 2.9 38.4 + - + +
295A VAL* 3.1 14.8 + - - +
327A ALA 3.7 6.6 + - - +
328A ILE* 5.1 4.0 - - - +
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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