Contacts of the helix formed by residues 317 - 328 (chain A) in PDB entry 3A61
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 THR 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A GLU* 2.7 37.2 + - + +
315A TYR 3.5 4.3 + - - +
316A LEU* 1.3 77.7 - - - +
318A GLN* 1.3 69.0 + - - +
319A GLU* 3.0 31.7 - - + +
320A ALA 3.0 7.6 + - - -
321A ARG* 3.3 10.9 + - - +
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Residues in contact with GLN 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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317A THR* 1.3 72.8 - - - +
319A GLU* 1.3 63.3 + - - +
321A ARG* 2.7 51.5 + - - +
322A ASP* 2.7 32.9 + - + +
325A LYS* 5.4 5.4 + - - -
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Residues in contact with GLU 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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192A GLU* 5.0 1.1 - - - +
317A THR* 3.0 25.9 + - + +
318A GLN* 1.3 82.0 - - - +
320A ALA* 1.3 63.8 + - - +
322A ASP* 2.7 16.9 + - - +
323A LEU* 2.8 12.8 + - - +
349A HIS* 3.5 24.0 + - + -
350A PRO* 4.1 7.9 - - + +
351A PHE* 4.0 17.0 - - + -
353A ARG* 3.3 29.0 + - - +
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Residues in contact with ALA 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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192A GLU* 3.2 33.2 - - - +
283A MET* 4.3 4.4 - - + +
287A LEU* 4.3 13.2 - - + -
316A LEU* 4.1 10.1 - - + -
317A THR* 3.0 7.5 + - - +
319A GLU* 1.3 78.4 - - - +
321A ARG* 1.3 63.3 + - - +
323A LEU* 3.5 2.9 + - - +
324A LEU* 3.1 29.3 + - + +
351A PHE* 3.7 19.0 - - + -
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Residues in contact with ARG 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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312A LEU* 3.8 37.9 - - + +
313A PRO 3.3 26.3 + - - -
314A PRO* 3.7 13.3 + - - +
316A LEU* 3.2 34.3 + - + -
317A THR 3.3 6.5 - - - +
318A GLN* 2.7 35.5 + - - +
320A ALA* 1.3 69.6 - - - +
322A ASP* 1.3 65.2 + - - +
324A LEU* 3.3 3.4 + - - +
325A LYS* 2.9 37.6 + - - +
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Residues in contact with ASP 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 GLN* 2.7 26.4 + - + +
319A GLU* 2.7 13.6 + - - +
321A ARG* 1.3 78.3 - - - +
323A LEU* 1.3 62.6 + - - +
325A LYS* 3.3 9.0 + - - +
326A LYS* 2.9 49.0 + - - +
349A HIS* 3.5 15.4 + - + +
350A PRO* 5.8 1.7 - - - +
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Residues in contact with LEU 323 (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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199A LEU* 5.4 0.7 - - + -
279A LEU* 6.2 0.4 - - + -
283A MET* 3.3 33.2 - - + -
319A GLU 2.8 14.3 + - - +
320A ALA 3.6 8.3 - - - +
322A ASP* 1.3 70.9 - - - +
324A LEU* 1.3 51.3 + - - +
326A LYS* 2.7 9.2 + - - +
327A LEU* 2.6 55.3 + - + +
336A LEU* 4.2 11.9 - - + -
346A VAL* 4.7 4.0 - - + +
349A HIS* 3.1 39.3 + - + +
351A PHE* 3.7 18.2 - - + -
352A PHE* 4.1 18.2 - - + -
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Residues in contact with LEU 324 (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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280A GLY* 4.1 15.9 - - - +
283A MET* 4.2 11.0 - - + -
284A TYR* 3.4 44.9 - - + +
287A LEU* 5.6 2.7 - - + -
310A LEU* 4.2 2.5 - - + -
312A LEU* 4.0 12.6 - - + -
316A LEU* 3.9 22.4 - - + -
320A ALA 3.1 15.1 + - - +
321A ARG 3.5 7.2 - - - +
323A LEU* 1.3 78.2 - - - +
325A LYS* 1.3 57.9 + - - +
326A LYS 2.9 0.2 + - - -
327A LEU* 4.2 3.8 - - - +
328A LEU* 2.7 62.5 + - + +
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Residues in contact with LYS 325 (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 LEU* 3.9 21.4 - - + +
312A LEU* 3.7 26.9 - - + -
318A GLN* 5.4 5.3 + - - -
321A ARG* 2.9 31.8 + - - +
322A ASP* 3.7 7.9 - - - +
324A LEU* 1.3 74.3 - - - +
326A LYS* 1.3 57.6 + - + +
328A LEU 4.6 0.3 - - - -
329A LYS* 2.8 33.7 + - - +
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Residues in contact with LYS 326 (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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322A ASP* 2.9 34.8 + - - +
323A LEU 2.7 10.9 + - - +
325A LYS* 1.3 81.3 - - + +
327A LEU* 1.3 60.7 + - - +
329A LYS* 4.2 18.2 - - + +
334A SER 5.9 0.4 - - - +
335A ARG* 3.7 4.7 - - - -
336A LEU* 2.8 63.1 + - + +
349A HIS* 4.6 5.6 - - + -
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Residues in contact with LEU 327 (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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276A TRP* 4.1 11.7 - - + +
277A TRP* 3.8 4.0 - - - -
279A LEU* 3.9 19.5 - - + +
280A GLY* 3.4 36.3 - - - +
283A MET* 4.7 5.8 - - - -
323A LEU* 2.6 48.8 + - + +
324A LEU* 3.8 3.4 - - - +
326A LYS* 1.3 75.7 - - - +
328A LEU* 1.3 58.3 + - - +
329A LYS 3.0 2.5 + - - -
335A ARG* 2.9 33.7 - - - +
336A LEU* 4.1 11.2 - - + +
346A VAL* 4.1 27.8 - - + -
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Residues in contact with LEU 328 (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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277A TRP* 2.8 68.4 - - + +
280A GLY* 3.8 8.1 - - - -
281A ALA* 3.7 13.2 - - + +
284A TYR* 4.6 0.7 - - + -
292A PRO* 3.9 25.6 - - + -
293A PHE* 5.7 3.5 - - + -
308A CYS* 5.0 4.2 - - - +
310A LEU* 4.0 31.8 - - + +
324A LEU* 2.7 41.5 + - + +
325A LYS 4.6 1.1 - - - -
327A LEU* 1.3 70.5 - - - +
329A LYS* 1.3 59.5 + - - +
330A ARG 3.4 1.4 + - - -
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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