Contacts of the helix formed by residues 309 - 319 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307A LYS 4.0 0.8 + - - -
308A SER* 1.3 77.2 - - - +
310A PRO* 1.3 74.0 - - + +
311A ASP* 3.4 15.1 + - - +
312A SER* 2.9 46.1 + - - -
313A ILE* 3.3 13.1 + - - +
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Residues in contact with PRO 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A SER 4.3 2.7 - - - +
309A ASP* 1.3 88.1 - - + +
311A ASP* 1.3 60.0 + - - +
313A ILE* 3.2 6.5 + - + +
314A PHE* 3.0 50.4 + - + -
364A ILE* 4.0 16.8 - - + +
365A ARG* 4.0 42.2 - - + +
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Residues in contact with ASP 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A ASP* 3.2 12.1 + - - +
310A PRO* 1.3 79.3 - - - +
312A SER* 1.3 56.6 + - - +
314A PHE* 3.4 25.1 + - + +
315A HIS* 2.9 28.5 + - - +
365A ARG* 4.3 9.1 + - - -
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Residues in contact with SER 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A ALA* 4.2 11.7 - - - -
308A SER* 4.6 3.8 - - - -
309A ASP* 2.9 33.6 + - - -
311A ASP* 1.3 72.9 - - - +
313A ILE* 1.3 64.8 + - - +
315A HIS* 3.4 7.2 + - - +
316A TYR* 3.1 38.2 + - - -
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Residues in contact with ILE 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A ILE* 4.6 1.1 - - + -
251A ALA* 3.5 19.1 - - + +
252A ILE* 3.8 36.1 - - + +
255A ALA* 3.7 22.0 - - + -
256A GLU* 5.3 0.9 - - - +
272A TYR* 6.4 0.4 - - + -
308A SER* 3.7 15.7 - - - +
309A ASP 3.3 17.2 + - - +
310A PRO* 3.2 6.5 + - + +
312A SER* 1.3 75.3 - - - +
314A PHE* 1.3 61.6 + - - +
316A TYR 3.4 1.9 + - - -
317A LEU* 3.3 17.7 + - - +
364A ILE* 4.0 39.7 - - + +
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Residues in contact with PHE 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A PRO* 3.0 30.1 + - + -
311A ASP* 3.6 26.9 - - + +
313A ILE* 1.3 71.5 - - - +
315A HIS* 1.3 67.6 + - - +
317A LEU* 3.1 19.7 + - + +
318A ILE* 3.1 23.1 + - + +
360A ILE* 5.4 0.9 - - + -
361A LYS* 3.5 51.6 - - + -
364A ILE* 3.5 31.0 - - + -
365A ARG* 3.5 30.3 - - - -
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Residues in contact with HIS 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A ASP 2.9 15.1 + - - +
312A SER* 3.5 10.9 - - - +
313A ILE 3.3 0.2 - - - -
314A PHE* 1.3 77.6 - - - +
316A TYR* 1.3 94.2 + + - +
318A ILE* 3.5 7.1 + - - -
319A HIS* 3.1 55.5 + + + +
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Residues in contact with TYR 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ALA* 3.8 22.5 - - - +
254A LEU* 3.5 39.5 + - + +
255A ALA* 3.8 27.6 - - + -
257A GLN* 5.0 8.2 - - + +
312A SER* 3.1 31.0 + - - +
313A ILE 4.0 1.3 - - - +
314A PHE 3.3 0.2 - - - -
315A HIS* 1.3 102.7 - + - +
317A LEU* 1.3 58.5 + - - +
319A HIS* 3.8 3.3 + - + -
320A ASP* 3.2 30.0 + - - +
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Residues in contact with LEU 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A THR* 3.3 37.9 - - + +
248A ILE* 4.3 7.0 - - + +
251A ALA* 3.7 9.8 - - + +
313A ILE 3.3 12.5 + - - +
314A PHE* 3.1 13.4 + - + +
316A TYR* 1.3 79.0 - - - +
318A ILE* 1.3 61.1 + - + +
319A HIS 3.7 0.2 + - - -
320A ASP* 3.9 11.7 + - + +
326A ILE* 3.9 19.4 - - + +
327A LYS* 4.6 1.0 + - - -
333A LEU* 3.7 25.5 - - + +
360A ILE* 3.9 16.6 - - + -
364A ILE* 3.9 27.6 - - + -
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Residues in contact with ILE 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A PHE* 3.1 21.3 + - + +
315A HIS* 3.8 4.7 - - + +
317A LEU* 1.3 78.2 - - + +
319A HIS* 1.3 84.9 + - + +
320A ASP 3.4 1.3 - - - -
327A LYS* 2.8 38.7 + - + +
333A LEU* 4.6 17.0 - - + -
357A LYS* 4.4 23.3 - - + +
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Residues in contact with HIS 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A HIS* 3.1 46.8 + + + +
316A TYR* 3.9 5.2 - - + +
317A LEU 3.4 0.2 - - - -
318A ILE* 1.3 102.0 - - + +
320A ASP* 1.3 56.6 + - - -
321A ASN* 4.0 13.0 + - - +
327A LYS* 4.5 1.6 - - - -
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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