Contacts of the strand formed by residues 286 - 298 (chain A) in PDB entry 1LKF
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 LYS 286 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A VAL* 3.9 16.4 - - + -
21A THR* 4.7 3.4 - - - -
40A PHE* 4.1 1.7 - - - -
281A ASP* 2.8 40.8 + - + +
284A ASN* 3.2 28.2 - - + +
285A HIS* 1.3 79.6 - - - +
287A VAL* 1.3 68.3 + - - +
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Residues in contact with VAL 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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4A ILE* 3.5 35.3 - - + +
21A THR* 4.3 8.2 - - + +
23A ALA* 4.2 9.9 - - + -
38A PHE* 3.7 55.2 - - + -
40A PHE* 4.4 4.0 - - + -
278A TYR* 4.3 11.2 - - + -
279A GLU 3.3 7.4 - - - +
280A ILE* 4.3 12.8 - - + -
286A LYS* 1.3 83.7 - - - +
288A LYS* 1.3 63.2 + - - +
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Residues in contact with LYS 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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4A ILE* 4.0 3.6 - - - -
278A TYR* 3.3 5.1 - - - -
279A GLU* 2.8 56.3 + - + +
287A VAL* 1.3 76.2 - - - +
289A LEU* 1.3 71.7 + - - +
290A LEU* 3.3 26.0 + - + +
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Residues in contact with LEU 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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1A GLU* 5.2 7.6 - - - +
2A GLY 5.2 9.4 - - - +
4A ILE* 3.7 12.3 - - + +
24A THR 5.8 0.9 - - - +
25A ALA* 5.0 2.2 - - + -
276A SER* 4.4 0.7 - - - -
277A THR 3.5 10.1 - - - +
278A TYR* 3.6 38.7 - - + +
288A LYS* 1.3 84.0 - - - +
290A LEU* 1.3 60.1 - - - +
291A ASP 3.5 26.2 - - - +
292A THR* 3.9 21.5 - - + -
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Residues in contact with LEU 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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240A LYS* 3.6 37.5 - - + -
277A THR* 2.8 17.4 + - + +
278A TYR 4.2 1.3 - - - -
279A GLU* 3.8 28.3 - - + +
288A LYS* 3.8 44.4 - - + +
289A LEU* 1.3 74.8 - - - +
291A ASP* 1.3 65.0 + - + +
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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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275A LYS* 5.6 3.1 - - - -
276A SER* 3.4 0.3 - - - -
277A THR* 2.8 43.3 + - + +
289A LEU* 3.5 6.1 - - - +
290A LEU* 1.3 84.7 - - + +
292A THR* 1.3 86.6 + - - +
293A LYS* 4.3 10.0 - - - +
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Residues in contact with THR 292 (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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1A GLU* 4.1 12.5 + - - +
25A ALA* 4.4 5.6 - - + -
274A PHE* 4.1 26.7 - - + -
275A LYS 3.3 8.7 - - - +
276A SER* 4.4 1.1 - - - -
289A LEU* 3.9 27.4 - - + -
291A ASP* 1.3 93.0 + - - +
293A LYS* 1.3 62.8 + - - +
294A GLU* 6.0 0.2 - - - -
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Residues in contact with LYS 293 (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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273A THR* 3.6 1.4 - - - +
274A PHE* 3.6 4.4 - - - -
275A LYS* 2.9 49.5 + - + +
291A ASP* 4.3 10.3 - - - +
292A THR* 1.3 78.2 - - - +
294A GLU* 1.3 66.0 + - - +
295A THR* 3.4 29.4 + - + +
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Residues in contact with GLU 294 (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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26A ASP 4.8 0.7 - - - +
27A SER* 2.8 33.3 + - - +
28A ASP 4.6 0.5 + - - -
29A LYS* 3.9 27.6 + - - +
30A PHE* 3.6 15.7 - - + -
273A THR 3.4 4.9 - - - -
274A PHE* 3.9 19.1 - - + -
293A LYS* 1.3 78.3 - - - +
295A THR* 1.3 66.3 + - - +
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Residues in contact with THR 295 (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 PHE* 3.3 5.2 - - - -
273A THR* 2.8 55.8 + - - +
293A LYS* 3.4 37.5 + - + +
294A GLU* 1.3 81.5 - - - +
296A GLU* 1.3 64.7 + - - +
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Residues in contact with GLU 296 (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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29A LYS* 3.4 27.3 + - - +
30A PHE* 3.4 28.3 - - + -
271A THR* 3.3 6.5 - - - +
272A ARG* 3.6 21.2 + - - +
295A THR* 1.3 76.0 - - - +
297A ASN* 1.3 64.2 + - - +
298A ASN* 3.0 24.9 + - - +
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Residues in contact with ASN 297 (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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268A ASN 5.2 0.9 - - - +
269A PHE 5.4 0.5 - - - +
270A LYS* 3.3 2.1 - - - -
271A THR* 2.8 53.0 + - - +
272A ARG* 3.0 8.7 + - - -
296A GLU* 1.3 76.1 + - - +
298A ASN* 1.3 66.8 + - - +
299A LYS* 4.1 23.7 - - - +
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Residues in contact with ASN 298 (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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269A PHE 3.9 4.5 - - - -
270A LYS* 3.4 17.9 - - + +
272A ARG* 2.9 26.8 + - - +
296A GLU* 3.0 30.3 + - - +
297A ASN* 1.3 83.1 + - - +
299A LYS* 1.3 66.8 + - - +
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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