Contacts of the strand formed by residues 300 - 307 (chain B) in PDB entry 5DK3
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 300 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263B VAL 3.9 1.0 - - - +
264B VAL* 3.8 20.1 - - - +
265B ASP 3.9 1.2 + - - -
266B VAL* 2.8 34.8 + - + +
267B SER 3.8 16.2 - - - -
268B GLN* 4.0 20.9 - - + -
271B PRO* 4.3 19.3 - - + +
292B ARG* 4.3 13.7 - - + -
293B GLU* 3.3 27.6 - - - -
294B GLU* 3.3 43.0 + - + +
295B GLN 5.5 0.4 - - - -
299B THR* 1.4 78.6 + - - +
301B ARG* 1.3 59.2 + - - +
302B VAL* 4.3 5.8 - - + -
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Residues in contact with ARG 301 (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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262B VAL* 3.4 26.0 - - + +
263B VAL 3.5 10.8 - - - +
264B VAL* 4.0 14.9 - - + +
291B PRO 4.9 0.9 - - - +
292B ARG* 4.0 0.3 - - - -
293B GLU* 2.9 42.6 + - + +
295B GLN 4.6 12.8 - - - +
300B TYR* 1.3 73.7 - - - +
302B VAL* 1.4 62.7 + - - +
303B VAL* 3.4 30.2 + - + +
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Residues in contact with VAL 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B VAL* 3.7 0.5 - - - -
263B VAL* 3.1 33.6 + - + +
266B VAL* 5.0 4.3 - - + -
271B PRO 5.0 3.1 - - - +
273B VAL* 4.3 29.6 - - + +
275B PHE* 3.6 27.7 - - + -
289B THR* 4.7 5.2 - - + -
290B LYS 3.8 18.6 - - - +
291B PRO 5.6 0.4 - - - -
292B ARG* 4.0 25.4 - - + +
300B TYR* 4.9 7.6 - - + -
301B ARG* 1.4 79.2 - - - +
303B VAL* 1.4 63.0 + - - +
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Residues in contact with VAL 303 (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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260B THR* 3.8 26.5 - - + -
261B CYS 3.5 2.5 - - - +
262B VAL* 3.8 8.3 - - + -
275B PHE* 4.3 2.9 - - - -
289B THR* 3.7 1.4 - - - +
290B LYS* 2.8 66.5 + - + +
291B PRO 5.7 0.4 + - - -
301B ARG* 3.4 43.3 + - + +
302B VAL* 1.4 81.5 - - - +
304B SER* 1.3 60.3 + - - +
305B VAL* 4.5 1.6 - - + -
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Residues in contact with SER 304 (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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260B THR* 3.5 2.4 - - - +
261B CYS 2.7 38.5 + - - +
275B PHE* 3.6 34.4 - - - -
277B TRP* 2.8 30.9 + - - -
287B ALA* 4.0 3.5 - - - +
288B LYS 3.5 5.5 + - - -
289B THR* 3.5 16.2 + - - -
303B VAL* 1.3 72.6 - - - +
305B VAL* 1.3 61.6 + - - +
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Residues in contact with VAL 305 (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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258B GLU* 3.4 42.4 - - + +
259B VAL 3.6 2.7 - - - -
260B THR* 3.7 27.6 - - + +
277B TRP* 4.4 1.3 - - - -
287B ALA* 3.6 1.6 - - - -
288B LYS* 2.8 49.8 + - + +
290B LYS* 4.4 23.6 - - - +
303B VAL* 4.3 2.4 - - + -
304B SER* 1.3 75.0 - - - +
306B LEU* 1.4 58.7 + - - +
307B THR* 4.2 2.7 + - - +
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Residues in contact with LEU 306 (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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258B GLU* 3.3 3.3 - - - -
259B VAL* 2.7 41.1 + - + +
277B TRP* 3.8 34.9 - - + -
279B VAL* 4.2 5.8 - - + -
284B VAL* 3.9 22.2 - - + -
286B ASN* 3.6 34.5 - - - +
287B ALA* 3.7 20.2 - - + +
305B VAL* 1.4 72.0 - - - +
307B THR* 1.3 66.4 + - - +
308B VAL 3.6 0.2 + - - -
319B TYR* 3.8 32.8 - - + -
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Residues in contact with THR 307 (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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256B THR* 3.8 23.0 - - + +
257B PRO* 3.7 10.5 - - + +
258B GLU* 3.8 16.4 + - + +
286B ASN* 3.7 25.8 + - - +
287B ALA* 5.5 0.6 - - - +
305B VAL* 4.2 2.9 + - - +
306B LEU* 1.3 81.9 - - - +
308B VAL* 1.3 77.1 + - - +
309B LEU* 3.7 10.6 + - + +
319B TYR* 5.3 0.5 - - - -
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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