Contacts of the strand formed by residues 279 - 286 (chain B) in PDB entry 5DX1
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 LEU 279 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250B GLN* 3.9 8.1 + - - -
251B VAL* 3.7 13.9 - - + +
252B ASP 3.7 5.6 - - - +
253B ILE 4.1 0.4 - - - +
254B ILE* 3.8 16.8 - - + -
275B ALA 3.9 1.2 + - - -
276B LYS* 3.1 35.9 + - + +
277B LYS 4.8 0.2 - - - +
278B TYR* 1.3 79.3 - - - +
280B LYS* 1.3 72.4 + - - +
281B PRO* 3.8 2.9 - - - +
283B GLY* 3.6 35.9 - - - +
284B ASN 3.6 13.0 - - - +
285B MET* 4.0 23.1 - - + -
360B LEU* 4.7 3.6 - - + -
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Residues in contact with LYS 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B ILE* 5.6 2.4 - - + +
250B GLN* 3.5 30.7 - - + +
251B VAL 3.0 27.5 + - - +
252B ASP* 2.5 32.4 + - - +
278B TYR 3.6 0.6 + - - -
279B LEU* 1.3 78.7 - - - +
281B PRO* 1.3 74.0 - - + +
282B SER 3.2 0.5 + - - -
283B GLY* 2.7 24.9 + - - +
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Residues in contact with PRO 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B GLN* 6.1 0.7 - - + +
279B LEU 4.1 3.6 - - - +
280B LYS* 1.3 93.5 - - + +
282B SER* 1.3 70.7 + - - +
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Residues in contact with SER 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B LYS 3.2 0.6 + - - -
281B PRO* 1.3 74.7 - - - +
283B GLY* 1.3 64.6 + - - +
284B ASN* 3.9 1.2 + - - +
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Residues in contact with GLY 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B ASP* 3.1 19.5 - - - -
279B LEU* 3.6 20.0 - - - +
280B LYS* 2.7 25.2 + - - +
281B PRO 3.2 1.6 + - - -
282B SER* 1.3 77.2 - - - +
284B ASN* 1.3 60.3 + - - -
360B LEU* 3.7 10.9 - - - +
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Residues in contact with ASN 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B ASP* 4.8 9.5 + - + +
252B ASP 3.0 8.1 + - - +
253B ILE* 3.3 19.1 - - + +
254B ILE 3.1 21.7 + - - -
279B LEU* 3.6 2.9 - - - +
282B SER 3.9 1.1 + - - +
283B GLY* 1.3 74.7 - - - -
285B MET* 1.3 83.5 + - - +
286B PHE* 3.7 15.1 - - - -
288B THR* 4.0 14.2 - - - +
360B LEU* 4.1 9.7 - - - +
396B ILE 3.1 23.9 + - - +
397B GLY* 4.4 4.2 - - - -
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Residues in contact with MET 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B ILE* 3.5 13.2 - - + -
272B TYR* 3.4 50.7 - - + +
273B LEU* 4.5 1.8 - - + -
276B LYS* 3.3 29.4 - - + -
279B LEU* 4.0 11.0 - - + -
284B ASN* 1.3 85.3 + - - +
286B PHE* 1.3 63.2 + - - +
287B PRO 3.2 8.0 - - - +
288B THR* 2.8 31.3 + - - -
359B PHE* 3.0 36.1 - - + +
360B LEU* 3.9 12.2 - - + +
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Residues in contact with PHE 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B TYR* 4.6 1.0 - - - -
175B ALA 3.5 24.5 - - - -
176B ILE* 4.3 8.1 - - + -
179B ASN* 3.9 13.5 - - + -
182B ASP* 4.5 2.5 - - - -
183B PHE* 3.9 26.5 - + - -
253B ILE* 4.0 9.9 - - + -
254B ILE 2.8 12.7 + - - +
255B ILE* 3.3 14.0 - - + +
256B SER 3.1 23.4 + - - +
272B TYR* 3.0 3.0 + - - -
284B ASN* 3.7 22.0 - - - -
285B MET* 1.3 84.6 - - - +
287B PRO* 1.3 60.7 - - - +
288B THR* 4.1 2.7 - - - -
395B PHE* 3.7 29.4 - + + -
396B ILE 3.7 17.3 - - - -
397B GLY* 3.8 17.3 - - - -
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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