Contacts of the helix formed by residues 313 - 324 (chain A) in PDB entry 3QN3
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 ASN 313 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A LYS 4.5 9.9 + - - -
100A ASN 5.5 4.4 + - - -
310A PHE* 2.9 18.2 + - - +
311A VAL* 3.8 7.9 - - + +
312A THR* 1.3 76.1 - - - +
314A GLU* 1.3 59.0 + - - +
315A ASP* 2.9 28.3 + - - +
316A ILE* 3.1 28.1 + - + +
317A LEU* 2.8 31.8 + - - +
336A ILE* 3.8 19.8 - - + +
345A THR* 4.0 1.1 - - - +
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Residues in contact with GLU 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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313A ASN* 1.3 73.8 + - - +
315A ASP* 1.3 57.0 + - - +
317A LEU* 3.4 2.6 + - - -
318A ARG* 2.8 53.9 + - - +
336A ILE* 4.9 2.0 - - - +
341A GLN 5.6 0.4 - - - +
344A ARG* 2.8 72.3 + - + +
345A THR* 3.4 15.9 + - - +
348A LEU* 3.2 29.3 - - + +
351A ARG* 5.0 2.4 + - - -
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Residues in contact with ASP 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ASN* 2.9 18.0 + - - +
314A GLU* 1.3 72.7 - - - +
316A ILE* 1.3 66.1 + - + +
318A ARG* 3.3 24.0 + - - +
319A GLU* 3.2 26.7 + - - +
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Residues in contact with ILE 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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46A LYS* 3.6 36.6 - - + +
309A LEU 3.3 25.8 - - - +
310A PHE* 3.9 11.2 - - + +
311A VAL* 3.7 17.9 - - + -
313A ASN* 3.1 23.5 + - + +
315A ASP* 1.3 75.3 - - + +
317A LEU* 1.3 63.7 + - - +
319A GLU* 3.4 8.1 + - + +
320A GLY* 3.1 17.5 + - - -
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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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310A PHE* 3.7 40.5 - - + -
313A ASN 2.8 18.0 + - - +
314A GLU 3.7 3.6 - - - +
316A ILE* 1.3 77.6 - - - +
318A ARG* 1.3 63.0 + - - +
320A GLY* 3.1 1.7 + - - -
321A ILE* 2.9 30.3 + - + +
329A VAL* 4.3 7.0 - - + -
345A THR* 3.7 37.0 - - + +
348A LEU* 4.0 11.2 - - + -
349A ALA* 3.8 18.8 - - + +
354A TYR* 3.9 23.3 - - + -
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Residues in contact with ARG 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 GLU* 2.8 53.2 + - - +
315A ASP* 3.5 29.3 + - - +
316A ILE 3.2 0.4 - - - -
317A LEU* 1.3 74.0 - - - +
319A GLU* 1.3 67.4 + - - +
321A ILE* 3.3 7.6 + - - +
322A ILE* 3.0 41.8 + - + +
344A ARG* 4.6 5.1 - - - +
348A LEU* 3.9 30.6 - - + +
351A ARG* 4.8 5.3 - - - +
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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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315A ASP 3.2 11.7 + - - +
316A ILE* 3.7 9.2 - - + +
318A ARG* 1.3 82.0 - - - +
320A GLY* 1.3 51.8 + - - +
322A ILE* 3.2 22.3 + - - +
323A LYS* 2.8 60.4 + - + +
325A MET* 5.8 0.2 - - - -
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Residues in contact with GLY 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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310A PHE* 3.9 19.3 - - - -
316A ILE 3.1 7.5 + - - -
317A LEU 3.1 7.0 + - - -
319A GLU* 1.3 75.4 - - - +
321A ILE* 1.3 55.3 + - - +
323A LYS 3.3 1.2 + - - -
324A LYS 2.8 24.4 + - - -
325A MET* 2.9 28.2 + - - -
354A TYR* 3.8 6.5 - - - -
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Residues in contact with ILE 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 LEU* 2.9 29.7 + - + +
318A ARG* 3.5 7.6 - - + +
320A GLY* 1.3 74.4 - - - +
322A ILE* 1.3 69.6 + - + +
324A LYS* 3.1 16.8 + - - +
348A LEU* 3.8 30.5 - - + +
349A ALA* 4.8 0.4 - - - -
352A ASN* 3.8 38.6 - - + +
354A TYR* 3.5 36.5 + - + -
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Residues in contact with ILE 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 ARG* 3.0 31.1 + - + +
319A GLU* 3.5 27.8 - - - +
321A ILE* 1.3 84.0 - - + +
323A LYS* 1.3 79.5 + - - +
324A LYS* 3.4 7.4 + - - +
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Residues in contact with LYS 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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292A ILE* 3.5 24.7 - - + +
319A GLU* 2.8 38.0 + - + +
322A ILE* 1.3 92.0 - - - +
324A LYS* 1.3 71.5 + - - +
325A MET* 3.4 30.7 + - + -
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Residues in contact with LYS 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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292A ILE* 4.1 12.8 - - + +
295A THR* 3.4 24.5 - - + -
296A GLU* 6.0 4.8 - - + +
320A GLY 2.8 7.9 + - - -
321A ILE 3.1 13.3 + - - +
322A ILE 4.2 5.8 - - - +
323A LYS* 1.3 81.9 - - - +
325A MET* 1.3 57.0 + - - +
326A ALA 4.1 0.2 - - - -
354A TYR* 4.3 4.7 - - - -
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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