Contacts of the helix formed by residues 309 - 320 (chain B) in PDB entry 2GRU
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 ASP 309 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307B LYS 4.2 0.8 + - - -
308B SER* 1.3 78.4 - - - +
310B PRO* 1.3 76.1 - - + +
311B ASP* 3.0 19.5 + - - +
312B SER* 3.2 42.2 + - - -
313B ILE* 3.4 10.6 + - - +
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Residues in contact with PRO 310 (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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308B SER 4.3 2.9 - - - +
309B ASP* 1.3 86.7 - - + +
311B ASP* 1.3 63.9 + - - +
313B ILE* 3.5 5.7 + - + +
314B PHE* 2.9 31.0 + - - +
361B LYS* 5.0 3.1 - - + +
364B ILE* 3.7 23.3 - - + +
365B ARG* 3.6 51.4 - - + +
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Residues in contact with ASP 311 (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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309B ASP* 3.0 16.5 + - - +
310B PRO* 1.3 79.2 - - - +
312B SER* 1.3 59.6 + - - +
314B PHE* 3.9 4.4 - - - +
315B HIS* 3.0 30.7 + - - +
361B LYS* 3.2 31.6 + - - +
365B ARG* 3.3 23.4 + - - -
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Residues in contact with SER 312 (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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255B ALA* 3.4 21.7 + - - +
308B SER* 4.5 2.9 - - - -
309B ASP* 3.2 29.5 + - - -
311B ASP* 1.3 78.7 - - - +
313B ILE* 1.3 62.0 + - - +
315B HIS* 3.4 5.7 + - - +
316B TYR* 3.1 38.6 + - - -
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Residues in contact with ILE 313 (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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248B ILE* 4.3 5.2 - - + -
251B ALA* 3.7 7.9 - - + +
252B ILE* 3.9 32.5 - - + +
255B ALA* 4.0 17.3 - - + -
272B TYR* 5.4 2.5 - - + +
306B LEU* 4.1 18.6 - - + -
308B SER* 3.3 27.8 - - - +
309B ASP 3.4 8.9 + - - +
310B PRO* 3.7 8.1 - - + +
311B ASP 3.4 0.4 - - - -
312B SER* 1.3 78.1 + - - +
314B PHE* 1.3 62.0 - - - +
316B TYR* 3.4 0.9 + - - +
317B LEU* 3.2 20.0 + - + +
364B ILE* 3.9 37.0 - - + -
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Residues in contact with PHE 314 (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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310B PRO 2.9 18.4 + - - +
311B ASP 4.0 2.7 - - - +
312B SER 3.4 0.4 - - - -
313B ILE* 1.3 77.4 - - - +
315B HIS* 1.3 64.1 + - - +
317B LEU* 3.3 24.0 - - + +
318B ILE* 3.1 46.8 + - + +
333B LEU* 5.0 0.9 - - + -
357B LYS* 3.2 48.0 - - + -
360B ILE* 3.9 11.9 - - + -
361B LYS* 3.7 54.5 - - + -
364B ILE* 4.3 4.5 - - + -
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Residues in contact with HIS 315 (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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311B ASP 3.0 18.1 + - - +
312B SER* 3.8 6.1 - - - +
313B ILE 3.3 0.2 - - - -
314B PHE* 1.3 76.5 - - - +
316B TYR* 1.3 63.0 + - + +
317B LEU 3.4 0.2 + - - -
318B ILE* 3.4 19.0 + - + +
319B HIS* 3.1 63.1 + + - -
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Residues in contact with TYR 316 (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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251B ALA* 3.9 17.8 - - + +
254B LEU* 3.8 39.2 + - + +
255B ALA* 3.6 29.6 - - + -
257B GLN* 4.7 12.2 + - - +
312B SER* 3.1 30.9 + - - -
313B ILE 3.4 5.8 + - - +
315B HIS* 1.3 78.7 - - + +
317B LEU* 1.3 56.5 + - - +
319B HIS* 3.4 7.5 + - + +
320B ASP* 3.0 30.0 + - - +
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Residues in contact with LEU 317 (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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247B THR* 3.4 44.6 - - + +
248B ILE* 4.3 7.2 - - + -
251B ALA* 3.7 8.5 - - + +
313B ILE* 3.2 11.9 + - + +
314B PHE* 3.3 23.3 - - + +
316B TYR* 1.3 76.2 - - - +
318B ILE* 1.3 62.1 + - - +
319B HIS 3.4 0.5 + - - -
320B ASP* 3.4 21.3 + - + +
333B LEU* 3.8 24.9 - - + +
360B ILE* 3.4 33.7 - - + -
364B ILE* 4.3 8.1 - - + -
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Residues in contact with ILE 318 (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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314B PHE* 3.1 47.8 + - + +
315B HIS* 3.4 32.5 - - + +
317B LEU* 1.3 76.5 - - + +
319B HIS* 1.3 68.6 + - + +
320B ASP 3.5 2.4 - - - +
333B LEU* 5.0 9.4 - - + -
357B LYS* 4.7 24.0 - - + +
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Residues in contact with HIS 319 (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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315B HIS* 3.1 58.1 + + - +
316B TYR* 3.7 9.9 - - + +
317B LEU 3.2 0.4 - - - -
318B ILE* 1.3 92.0 - - + +
320B ASP* 1.3 61.7 + - - +
321B ASN* 3.6 3.3 + - - +
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Residues in contact with ASP 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B THR* 4.5 10.6 - - - +
250B HIS* 4.0 27.5 + - - +
251B ALA* 5.2 3.1 + - + +
254B LEU* 5.9 5.8 - - + -
316B TYR 3.0 16.5 + - - +
317B LEU* 3.4 17.5 + - + +
318B ILE 4.8 1.9 - - - +
319B HIS* 1.3 76.1 - - - +
321B ASN* 1.3 73.5 + - - +
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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