Contacts of the helix formed by residues 310 - 322 (chain A) in PDB entry 3DAG
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 310 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306A GLU 3.7 8.4 + - - +
308A ALA 4.1 1.6 + - - -
309A LEU* 1.3 74.3 - - - +
311A PRO* 1.3 69.4 - - - +
312A ALA* 3.0 26.6 + - - +
313A ALA* 2.8 28.8 + - + +
314A LEU* 4.4 0.5 + - - +
342A VAL* 2.9 44.9 + - + +
344A GLU* 5.3 2.3 - - - +
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Residues in contact with PRO 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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306A GLU* 3.6 24.7 - - + -
309A LEU* 3.1 10.9 - - + +
310A ASP* 1.3 88.1 - - - +
312A ALA* 1.3 60.1 + - - +
313A ALA 3.0 1.1 + - - -
314A LEU* 3.3 20.1 + - + +
315A LEU 4.2 1.4 + - - -
337A LEU* 3.4 57.8 - - + +
340A HIS* 3.4 26.5 - - + +
342A VAL* 4.4 0.9 - - + -
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Residues in contact with ALA 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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310A ASP* 3.0 21.8 + - - +
311A PRO* 1.3 75.1 - - - +
313A ALA* 1.3 64.7 + - - +
314A LEU 3.1 0.2 - - - -
315A LEU* 3.1 37.6 + - + +
316A GLY 4.3 1.2 + - - -
337A LEU 4.5 1.3 + - - -
341A LYS* 3.7 23.6 - - + +
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Residues in contact with ALA 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LEU* 3.8 19.5 - - + -
310A ASP* 2.8 23.9 + - + +
312A ALA* 1.3 79.1 - - - +
314A LEU* 1.3 59.8 + - + +
315A LEU 3.4 0.7 + - - -
316A GLY* 3.9 7.3 + - - -
317A THR* 3.9 13.3 + - - +
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Residues in contact with LEU 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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309A LEU* 4.3 27.8 - - + -
311A PRO* 3.3 13.6 + - + +
312A ALA 3.1 1.2 - - - -
313A ALA* 1.3 78.7 - - + +
315A LEU* 1.3 60.7 + - - +
316A GLY 3.2 0.7 - - - -
317A THR* 3.6 13.7 - - - +
318A ALA* 2.9 43.5 + - + +
334A LEU* 4.1 5.1 - - + +
337A LEU* 3.8 28.9 - - + -
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Residues in contact with LEU 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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312A ALA* 3.1 34.9 + - + +
314A LEU* 1.3 78.4 - - - +
316A GLY* 1.3 56.4 + - - +
319A ASP* 3.2 26.2 - - - +
334A LEU* 3.4 46.2 - - + +
337A LEU* 4.2 7.6 - - + -
338A GLU* 3.9 34.8 - - + +
341A LYS* 5.6 2.5 - - + -
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Residues in contact with GLY 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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312A ALA 4.3 1.8 + - - -
313A ALA 3.9 5.7 + - - -
314A LEU 3.2 1.0 - - - -
315A LEU* 1.3 76.4 - - - +
317A THR* 1.3 64.4 + - - +
319A ASP* 3.1 16.5 - - - +
320A SER* 6.1 0.2 - - - -
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Residues in contact with THR 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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313A ALA 3.9 9.4 + - - +
314A LEU* 3.3 24.4 + - - +
316A GLY* 1.3 83.7 - - - +
318A ALA* 1.3 67.4 + - - +
319A ASP* 3.2 4.2 + - - +
320A SER* 2.8 27.9 + - - -
321A MET* 4.5 2.1 + - - +
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Residues in contact with ALA 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 LEU* 2.9 30.1 + - + +
317A THR* 1.3 74.6 + - - +
319A ASP* 1.3 66.1 + - - +
320A SER 3.1 0.4 - - - -
321A MET* 3.0 19.2 + - + +
330A LEU* 3.3 30.6 - - + +
334A LEU* 3.9 19.5 - - + -
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Residues in contact with ASP 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 LEU 3.2 21.1 + - - +
316A GLY* 3.1 26.8 - - - +
317A THR 3.3 1.7 + - - +
318A ALA* 1.3 72.5 - - - +
320A SER* 1.3 65.4 + - - -
321A MET 3.2 1.0 + - - -
322A CYS* 3.2 20.8 + - - +
334A LEU* 3.9 17.6 - - + +
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Residues in contact with SER 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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317A THR 2.8 20.3 + - - -
319A ASP* 1.3 82.3 + - - +
321A MET* 1.3 65.9 + - - +
322A CYS 3.4 0.8 + - - -
323A PHE* 3.9 12.0 - - - -
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Residues in contact with MET 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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267A TYR* 3.9 28.7 - - + +
271A VAL* 4.5 10.3 - - + -
275A LEU* 4.8 8.3 - - + -
317A THR 4.9 0.9 - - - +
318A ALA* 3.0 18.1 + - + +
320A SER* 1.3 86.0 - - - +
322A CYS* 1.3 58.2 + - - +
323A PHE* 3.0 34.4 + - + -
326A LEU* 3.4 36.6 - - + +
330A LEU* 3.5 12.8 - - + +
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Residues in contact with CYS 322 (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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318A ALA 3.8 3.6 - - - -
319A ASP* 3.2 20.2 + - - +
320A SER 3.4 1.4 - - - -
321A MET* 1.3 72.7 - - - +
323A PHE* 1.3 59.3 + - - +
326A LEU 4.7 1.8 - - - -
327A ALA* 4.3 10.0 - - - +
330A LEU* 3.6 32.1 - - - -
331A PRO* 3.9 22.4 - - + -
334A LEU* 3.9 17.7 - - - -
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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