Contacts of the helix formed by residues 310 - 321 (chain A) in PDB entry 2R8J
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 GLY 310 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303A THR* 5.0 0.5 + - - -
308A LEU 3.1 3.1 - - - +
309A GLY* 1.3 81.2 - - - +
311A VAL* 1.3 66.1 + - - -
312A LEU 3.2 2.5 - - - -
313A GLY* 3.0 9.4 + - - -
314A LYS* 3.1 21.4 + - - +
11Q G 3.4 22.0 + - - -
12Q A 4.0 3.6 + - - -
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Residues in contact with VAL 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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310A GLY* 1.3 67.6 - - - -
312A LEU* 1.3 69.3 + - - +
313A GLY 2.9 2.0 - - - -
314A LYS* 3.2 12.4 + - + +
315A GLU* 2.9 25.8 + - - +
361A ASN* 3.5 25.5 + - - +
10Q T 3.6 34.8 - - - +
11Q G 3.0 17.1 + - - +
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Residues in contact with LEU 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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307A THR* 3.7 22.4 - - - +
308A LEU* 4.3 9.2 - - + -
311A VAL* 1.3 81.5 - - - +
313A GLY* 1.3 59.2 + - - +
315A GLU* 3.8 2.9 - - - +
316A LEU* 3.1 46.5 + - + +
361A ASN* 3.8 40.8 - - + +
362A ILE* 4.4 13.5 - - + -
370A LEU* 6.0 4.0 - - + -
373A LYS* 6.0 1.8 - - - +
10Q T 5.2 0.2 - - - +
11Q G 3.2 14.5 + - - +
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Residues in contact with GLY 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ILE* 5.0 2.7 - - - +
303A THR* 4.9 5.4 - - - -
308A LEU* 3.1 32.9 + - - -
310A GLY 3.0 5.9 + - - -
311A VAL 2.9 0.8 - - - -
312A LEU* 1.3 77.5 - - - +
314A LYS* 1.3 57.9 + - - +
315A GLU 2.9 10.0 + - - -
316A LEU* 3.1 15.6 + - - +
317A ILE* 3.2 20.5 + - - +
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Residues in contact with LYS 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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303A THR* 5.2 5.3 + - - +
309A GLY 5.8 2.5 - - - -
310A GLY 3.1 14.4 + - - +
311A VAL* 3.2 13.4 + - + +
313A GLY* 1.3 73.7 - - - +
315A GLU* 1.3 58.7 + - - +
317A ILE* 3.8 15.4 - - + +
318A ASP* 3.6 19.4 + - - +
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Residues in contact with GLU 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 VAL 2.9 17.5 + - - +
312A LEU* 3.8 5.8 - - - +
313A GLY 2.9 0.2 + - - -
314A LYS* 1.3 75.1 - - - +
316A LEU* 1.3 54.0 + - - +
317A ILE 2.8 5.4 + - - -
318A ASP* 2.9 5.8 + - + +
319A VAL* 2.7 50.5 + - + +
355A TYR* 5.4 1.9 - - - -
359A THR 4.6 1.6 - - - +
360A SER* 3.4 14.4 + - - -
361A ASN* 3.1 36.6 + - - +
362A ILE* 3.0 35.8 - - - +
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Residues in contact with LEU 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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302A ILE* 3.6 29.2 - - + -
308A LEU* 4.0 23.6 - - + -
312A LEU* 3.1 24.4 + - + +
313A GLY* 3.1 4.3 + - - +
315A GLU* 1.3 77.2 - - - +
317A ILE* 1.3 56.2 + - - +
319A VAL* 3.8 6.1 - - + -
320A LEU* 3.0 42.0 + - + +
322A LEU* 3.7 2.4 - - - +
346A LEU* 5.4 1.3 - - + -
362A ILE* 4.1 18.2 - - + -
370A LEU* 4.0 34.8 - - + -
374A LEU* 4.3 14.6 - - + -
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Residues in contact with ILE 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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302A ILE* 4.0 25.4 - - + -
303A THR* 4.7 12.8 - - + -
313A GLY 3.2 17.9 - - - +
314A LYS* 3.8 17.7 - - + +
315A GLU 2.8 1.6 + - - -
316A LEU* 1.3 74.9 - - - +
318A ASP* 1.3 57.5 + - - +
319A VAL 3.0 3.8 - - - -
321A ASP* 3.0 11.4 + - - -
322A LEU* 3.0 53.4 + - + +
323A PRO 4.0 7.9 - - - +
324A HIS* 3.9 26.7 - - + +
327A SER* 6.5 0.2 - - - -
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Residues in contact with ASP 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 LYS 3.6 10.7 + - - +
315A GLU* 2.9 8.1 + - + +
317A ILE* 1.3 81.0 - - - +
319A VAL* 1.3 63.1 + - + +
321A ASP* 3.9 9.1 - - - +
349A LYS* 5.0 2.9 + - - -
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Residues in contact with VAL 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 GLU* 2.7 50.0 + - + +
316A LEU* 4.0 7.2 - - + +
318A ASP* 1.3 78.3 - - + +
320A LEU* 1.3 60.1 + - + +
321A ASP* 2.7 25.0 - - - +
345A PHE* 4.8 1.4 - - - -
346A LEU* 4.4 19.1 - - + -
349A LYS* 3.5 37.6 - - + +
350A VAL* 6.2 2.5 - - + -
355A TYR* 6.5 0.9 - - + -
362A ILE* 4.8 9.4 - - + -
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Residues in contact with LEU 320 (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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316A LEU* 3.0 28.5 + - + +
319A VAL* 1.3 76.8 - - + +
321A ASP* 1.3 71.4 + - - +
322A LEU* 3.3 30.7 + - + +
330A HIS* 5.7 1.6 - - - -
331A ILE* 4.7 5.8 - - + -
335A TRP* 4.2 15.6 - - + -
342A LEU* 4.4 12.3 - - + -
345A PHE* 4.0 29.8 - - + -
346A LEU* 3.4 33.7 - - + -
374A LEU* 3.8 28.5 - - + -
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Residues in contact with ASP 321 (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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317A ILE 3.0 6.7 + - - -
318A ASP* 3.9 7.6 - - - +
319A VAL 2.7 30.1 - - - +
320A LEU* 1.3 80.6 - - - +
322A LEU* 1.3 65.0 + - - +
323A PRO* 4.1 2.1 - - - +
330A HIS* 4.8 9.0 + - - -
345A PHE* 5.6 6.4 - - + -
349A LYS* 3.6 17.3 + - - -
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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