Contacts of the helix formed by residues 338 - 352 (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 THR 338 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ASP* 3.5 37.1 - - + +
93A LEU* 4.3 14.1 - - + -
102A TYR* 3.3 14.1 - - + +
110A THR* 4.4 1.1 - - - -
111A LEU* 3.8 10.1 - - - +
114A SER* 3.7 4.5 - - - +
336A ILE* 3.8 2.7 - - - +
337A GLY* 1.3 79.6 - - - +
339A ILE* 1.3 59.0 - - - +
341A GLN* 2.7 45.1 + - - +
342A THR* 2.9 30.0 + - - -
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Residues in contact with ILE 339 (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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86A GLN* 4.1 7.4 - - + +
90A ASP* 3.8 2.7 - - - +
111A LEU* 4.2 7.6 - - + -
114A SER* 2.9 35.1 + - - +
115A MET* 3.6 13.9 - - + -
118A ALA* 5.1 0.9 - - + -
133A LEU* 4.1 14.8 - - + -
333A PRO* 5.1 2.5 - - + -
338A THR* 1.3 68.4 - - - +
340A THR* 1.3 63.3 + - - +
342A THR* 3.1 6.8 + - - -
343A MET* 2.8 44.4 + - + +
369A PHE* 3.5 35.7 - - + -
373A PHE* 3.6 27.1 - - + -
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Residues in contact with THR 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLN* 3.6 15.6 + - - +
87A THR* 3.7 32.0 + - + +
90A ASP* 2.5 36.9 + - + +
91A ASP* 4.8 7.2 - - - +
338A THR 3.4 0.2 - - - -
339A ILE* 1.3 74.8 - - - +
341A GLN* 1.3 59.9 + - + +
343A MET* 3.0 17.3 + - + +
344A ARG* 2.8 44.8 + - + +
347A ARG* 5.4 4.3 - - - +
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Residues in contact with GLN 341 (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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90A ASP* 4.7 2.6 + - + -
91A ASP* 5.9 2.5 - - - +
94A ARG* 4.1 20.7 + - - +
102A TYR* 2.6 41.7 + - - -
314A GLU* 5.4 0.3 - - - +
336A ILE* 4.0 26.7 - - + +
338A THR* 2.7 36.1 + - - +
340A THR* 1.3 75.6 - - + +
342A THR* 1.3 64.0 + - - +
344A ARG* 3.4 15.9 + - - +
345A THR* 3.2 23.6 + - - -
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Residues in contact with THR 342 (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 THR* 4.7 1.8 - - + -
331A ILE* 3.3 33.2 - - + -
333A PRO* 3.4 19.5 - - + +
336A ILE* 3.3 17.2 - - - +
338A THR 2.9 16.6 + - - -
339A ILE 3.1 7.6 + - - -
341A GLN* 1.3 76.1 - - - +
343A MET* 1.3 63.2 + - - +
345A THR* 3.1 8.7 + - - -
346A VAL* 3.0 23.1 + - + +
358A MET* 4.8 0.4 - - + -
373A PHE* 3.8 26.0 - - + -
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Residues in contact with MET 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLN* 5.0 7.0 - - + -
87A THR* 5.7 1.8 - - - +
133A LEU* 4.7 18.6 - - + +
339A ILE* 2.8 31.2 + - + +
340A THR* 3.0 32.5 + - + +
342A THR* 1.3 71.3 - - - +
344A ARG* 1.3 57.6 + - - +
346A VAL* 3.3 7.7 + - - +
347A ARG* 2.8 55.8 + - + +
373A PHE* 3.8 21.3 - - + -
377A LEU* 3.9 21.0 - - + +
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Residues in contact with ARG 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ASP* 6.0 1.6 - - - -
314A GLU* 2.8 49.1 + - - +
318A ARG* 4.6 5.1 - - - +
340A THR* 2.8 31.3 + - + +
341A GLN* 3.6 18.8 - - - +
343A MET* 1.3 71.9 - - - +
345A THR* 1.3 62.9 + - - +
347A ARG* 3.4 27.8 + - - +
348A LEU* 3.0 25.1 + - - +
351A ARG* 5.1 3.8 + - - +
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Residues in contact with THR 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A THR* 2.8 39.8 + - - +
313A ASN 4.4 2.5 - - - +
314A GLU* 3.4 23.9 + - - +
317A LEU* 3.7 18.4 - - + +
329A VAL* 4.7 3.6 - - + -
331A ILE* 4.0 17.7 - - + -
336A ILE* 4.9 1.0 - - - +
341A GLN 3.2 9.7 + - - -
342A THR 3.1 9.5 + - - -
344A ARG* 1.3 77.5 - - - +
346A VAL* 1.3 65.4 + - - +
348A LEU* 3.3 2.9 + - - +
349A ALA* 3.1 21.8 + - - +
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Residues in contact with VAL 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ILE* 3.7 35.2 - - + -
342A THR 3.0 16.6 + - - +
343A MET* 3.8 5.8 - - - +
345A THR* 1.3 76.6 - - - +
347A ARG* 1.3 60.2 + - + +
349A ALA* 3.2 2.6 + - - +
350A GLN* 2.9 58.5 + - - +
356A CYS* 3.9 14.6 - - + -
358A MET* 4.8 2.0 - - + -
377A LEU* 3.8 36.8 - - + -
379A THR* 4.7 1.6 - - + -
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Residues in contact with ARG 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A THR* 5.1 4.9 + - - +
343A MET* 2.8 53.2 + - + +
344A ARG* 3.7 36.9 - - - +
346A VAL* 1.3 74.3 - - + +
348A LEU* 1.3 63.6 + - - +
350A GLN* 3.3 8.4 + - - +
351A ARG* 2.9 48.3 + - + +
377A LEU* 6.2 3.3 - - + +
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Residues in contact with LEU 348 (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* 3.2 40.4 - - + +
317A LEU* 4.0 11.0 - - + -
318A ARG* 3.8 37.9 - - + +
321A ILE* 3.8 10.1 - - + -
344A ARG 3.0 17.6 + - - +
345A THR 3.6 3.4 - - - +
347A ARG* 1.3 79.3 - - - +
349A ALA* 1.3 62.1 + - - +
351A ARG* 3.5 24.7 + - - +
352A ASN* 2.7 48.8 + - - +
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Residues in contact with ALA 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A LEU* 3.8 9.4 - - + +
321A ILE* 4.8 2.9 - - - -
329A VAL* 3.7 18.8 - - + -
345A THR 3.1 11.7 + - - +
346A VAL 3.5 2.5 - - - +
348A LEU* 1.3 75.2 - - - +
350A GLN* 1.3 60.1 + - - +
352A ASN 2.9 18.0 + - - -
353A ASN 3.4 0.2 + - - -
354A TYR* 3.0 33.1 + - + +
356A CYS* 3.4 27.8 - - - -
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Residues in contact with GLN 350 (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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346A VAL* 2.9 39.6 + - + +
347A ARG* 4.0 7.3 - - - +
349A ALA* 1.3 77.2 - - - +
351A ARG* 1.3 60.5 + - - +
352A ASN 3.3 0.5 + - - -
353A ASN* 3.9 7.3 + - - +
354A TYR 4.1 7.9 - - - +
355A LYS* 6.0 0.2 - - - -
356A CYS* 4.3 12.1 - - + +
377A LEU 3.2 25.6 + - - +
378A ASN* 3.9 11.5 + - - +
379A THR* 4.1 9.7 + - - +
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Residues in contact with ARG 351 (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* 5.0 3.0 + - - -
318A ARG* 4.8 7.5 - - - +
344A ARG* 5.1 3.6 + - - +
347A ARG* 2.9 41.2 + - + +
348A LEU* 3.6 34.9 - - - +
349A ALA 3.3 0.4 - - - -
350A GLN* 1.3 74.0 - - - +
352A ASN* 1.3 72.4 + - - +
353A ASN 3.6 1.3 + - - -
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Residues in contact with ASN 352 (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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321A ILE* 3.8 34.1 - - + +
348A LEU* 2.7 45.2 + - - +
349A ALA 2.9 3.1 + - - +
351A ARG* 1.3 91.6 - - - +
353A ASN* 1.3 71.5 + - - +
354A TYR* 3.2 16.2 - - + -
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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