Contacts of the strand formed by residues 288 - 294 (chain G) in PDB entry 6DKS
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 288 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273G THR* 3.3 7.8 - - - +
274G VAL* 2.8 41.4 + - + +
276G LEU* 3.8 31.2 - - + +
285G LEU* 4.1 20.4 - - + -
286G PRO* 3.1 19.3 - - + +
287G ARG* 1.3 71.9 - - - +
289G ILE* 1.3 58.5 + - - +
290G ILE 4.0 0.4 - - - -
314G PHE* 3.7 44.2 - - + +
315G TYR 3.3 9.6 - - - +
316G LEU* 3.9 23.8 - - + -
317G LYS* 4.8 2.0 - - - -
324G LEU* 4.7 7.4 - - + -
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Residues in contact with ILE 289 (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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271G GLY 4.6 10.5 - - - +
272G GLN 3.5 10.1 - - - +
273G THR* 5.1 5.4 - - - +
288G LEU* 1.3 72.5 - - - +
290G ILE* 1.3 62.9 + - - +
291G ARG* 3.4 17.1 + - + +
313G ALA 3.6 0.9 - - - +
314G PHE* 4.7 1.1 - - - -
315G TYR* 2.8 54.5 + - + +
317G LYS* 5.1 5.6 - - + -
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Residues in contact with ILE 290 (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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248G ILE* 4.4 7.2 - - + -
268G ILE* 3.9 14.4 - - + -
269G HIS 3.7 20.2 - - - +
270G TYR* 3.4 12.8 - - + -
271G GLY* 2.8 32.1 + - - -
272G GLN 3.3 13.7 + - - +
274G VAL* 4.2 9.8 - - + +
288G LEU 4.0 2.0 + - - -
289G ILE* 1.3 70.7 - - - +
291G ARG* 1.3 57.1 + - - +
306G VAL* 3.9 20.6 - - + -
312G CYS* 3.7 27.4 - - - -
313G ALA 3.7 4.7 - - - +
314G PHE* 3.7 28.9 - - + -
356G ILE* 4.1 9.9 - - + -
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Residues in contact with ARG 291 (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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270G TYR* 3.5 10.1 - - - -
271G GLY* 4.9 10.4 - - - +
289G ILE* 3.4 11.5 + - - +
290G ILE* 1.3 77.0 - - - +
292G LYS* 1.3 63.7 + - - +
298G ALA* 4.9 8.1 - - + -
299G LEU 4.0 14.1 - - - +
300G LEU* 3.6 52.0 + - - +
302G ALA* 6.3 0.2 - - + -
312G CYS* 3.6 4.7 - - - -
313G ALA* 2.9 46.9 + - + +
315G TYR* 3.5 54.1 - - - +
346G GLU* 3.8 12.7 + - - -
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Residues in contact with LYS 292 (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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270G TYR* 3.4 32.3 - - + +
291G ARG* 1.3 71.4 - - - +
293G VAL* 1.3 60.0 + - - +
294G ASP 4.1 0.2 - - - -
298G ALA* 3.7 1.0 - - - -
299G LEU* 3.0 44.7 + - + +
302G ALA* 4.2 18.2 - - + -
311G LYS 4.0 2.7 - - - +
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Residues in contact with VAL 293 (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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9F G 5.4 0.5 + - - -
291G ARG 3.7 0.6 + - - -
292G LYS* 1.3 72.0 - - - +
294G ASP* 1.3 59.7 + - - +
295G LYS 4.1 3.4 + - - +
296G GLN* 6.3 0.4 - - - -
297G THR 3.6 11.0 - - - +
298G ALA* 4.4 2.0 - - + +
299G LEU* 5.0 0.2 - - - -
311G LYS* 3.1 40.5 + - + +
312G CYS 3.9 19.7 - - - +
313G ALA* 4.5 6.5 - - + -
353G SER* 4.8 11.7 - - - -
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Residues in contact with ASP 294 (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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292G LYS 4.0 0.4 + - - -
293G VAL* 1.3 70.4 - - - +
295G LYS* 1.4 58.3 + - - +
296G GLN 2.8 16.5 + - - -
297G THR* 2.8 28.1 + - - +
299G LEU* 3.8 22.7 - - + -
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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