Contacts of the strand formed by residues 300 - 307 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264G VAL* 4.0 0.3 - - - -
265G ASP 3.8 8.7 + - - -
266G VAL* 2.8 47.1 + - + +
267G SER 4.1 9.0 - - - -
268G GLN* 4.2 18.2 - - + -
271G PRO* 3.9 28.0 - - + -
292G ARG* 3.7 28.3 - - + -
293G GLU* 3.4 22.9 - - - -
294G GLU* 3.6 37.0 + - + +
295G GLN* 5.1 0.7 - - - -
299G THR* 1.3 77.7 + - - +
301G ARG* 1.3 58.7 + - - +
302G VAL* 6.4 0.7 - - + -
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Residues in contact with ARG 301 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243G PHE* 6.0 0.8 - - - -
262G VAL* 4.0 26.3 - - + +
263G VAL 3.4 13.7 - - - +
264G VAL* 3.8 22.5 - - + +
292G ARG* 3.7 1.2 - - - -
293G GLU* 2.9 36.1 + - - +
295G GLN* 3.4 41.2 + - + +
300G TYR* 1.3 74.4 - - - +
302G VAL* 1.3 66.2 + - - +
303G VAL* 3.6 20.0 - - + +
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Residues in contact with VAL 302 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262G VAL* 3.6 2.6 - - - +
263G VAL* 3.1 53.0 + - + +
266G VAL* 5.3 3.6 - - + -
272G GLU 4.4 8.3 - - - +
273G VAL* 4.1 20.6 - - + -
275G PHE* 3.9 21.6 - - + -
289G THR* 4.5 0.9 - - + -
290G LYS 3.1 27.4 - - - +
291G PRO 4.1 1.6 - - - -
292G ARG* 4.0 19.7 - - + +
293G GLU* 5.9 0.2 - - - -
300G TYR* 6.4 0.9 - - + -
301G ARG* 1.3 75.9 - - - +
303G VAL* 1.3 65.3 + - - +
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Residues in contact with VAL 303 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260G THR* 3.6 30.5 - - + -
261G CYS 3.5 4.3 - - - +
262G VAL* 3.7 13.7 - - + -
275G PHE* 4.2 2.9 - - - -
289G THR* 3.7 2.4 - - - +
290G LYS* 2.8 58.1 + - + +
291G PRO 5.2 0.6 + - - -
301G ARG* 3.6 29.8 - - - +
302G VAL* 1.3 83.9 - - - +
304G SER* 1.4 59.8 + - - +
305G VAL* 4.1 11.7 - - + -
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Residues in contact with SER 304 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260G THR* 3.6 1.4 - - - -
261G CYS 2.7 38.1 + - - -
275G PHE* 3.5 30.8 - - - -
277G TRP* 2.8 29.8 + - - -
287G ALA* 3.8 4.3 - - - +
289G THR* 2.8 27.3 + - - +
303G VAL* 1.4 73.0 - - - +
305G VAL* 1.3 60.5 + - - +
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Residues in contact with VAL 305 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258G GLU* 3.7 41.1 - - + +
259G VAL 3.6 3.6 - - - +
260G THR* 3.9 21.5 - - + +
286G ASN 4.8 0.2 - - - +
287G ALA* 3.6 2.6 - - - -
288G LYS* 3.0 42.9 + - + +
290G LYS* 3.9 29.6 - - - +
303G VAL* 4.1 2.7 - - + -
304G SER* 1.3 78.5 + - - +
306G LEU* 1.3 61.9 + - - +
307G THR* 4.0 4.4 + - - +
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Residues in contact with LEU 306 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258G GLU* 3.4 1.7 - - - -
259G VAL* 2.8 37.8 + - + +
277G TRP* 3.6 43.8 - - + -
278G TYR 5.5 0.7 - - - +
279G VAL* 4.2 5.8 - - + -
284G VAL* 3.9 21.5 - - + -
286G ASN* 3.5 32.1 - - - +
287G ALA* 3.9 15.7 - - + +
305G VAL* 1.3 72.8 - - - +
307G THR* 1.3 80.1 + - - +
308G VAL* 3.8 3.6 - - + +
319G TYR* 4.0 22.2 - - + -
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Residues in contact with THR 307 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256G THR* 3.6 30.7 - - + +
257G PRO* 3.7 6.7 - - + +
258G GLU* 4.2 10.5 - - + +
286G ASN* 4.3 16.8 + - - -
288G LYS* 5.8 5.0 - - - +
305G VAL* 4.0 5.1 + - - +
306G LEU* 1.3 91.0 - - - +
308G VAL* 1.3 70.3 + - - +
319G TYR* 5.2 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