Contacts of the helix formed by residues 338 - 352 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B ASP* 3.5 31.5 - - - +
93B LEU* 4.1 17.9 - - + -
102B TYR* 3.3 23.8 - - + +
110B THR* 4.3 0.9 - - - -
111B LEU* 3.9 9.8 - - - +
114B SER* 3.7 4.9 - - - +
336B ILE* 3.7 4.2 + - - +
337B GLY* 1.3 82.8 - - - +
339B ILE* 1.3 62.3 + - - +
340B THR 3.7 0.3 + - - -
341B GLN* 2.8 33.0 + - - +
342B THR* 2.9 27.5 + - - -
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Residues in contact with ILE 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B GLN* 4.2 15.7 - - + +
90B ASP* 4.1 0.2 - - - +
111B LEU* 3.7 12.3 - - + -
114B SER* 3.0 16.1 + - - +
115B MET* 3.3 39.0 - - + +
118B ALA* 5.4 0.7 - - + -
133B LEU* 4.2 15.9 - - + -
333B PRO* 5.0 2.5 - - + -
338B THR* 1.3 70.5 - - - +
340B THR* 1.3 62.3 + - - +
342B THR* 3.3 3.9 + - - -
343B MET* 2.9 43.8 + - + +
369B PHE* 3.8 24.0 - - + -
373B PHE* 3.8 24.6 - - + -
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Residues in contact with THR 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B GLN* 3.3 15.4 + - - +
87B THR* 3.6 29.4 + - + +
90B ASP* 2.4 42.1 + - + +
91B ASP* 4.9 7.4 - - - +
338B THR 3.3 0.2 - - - -
339B ILE* 1.3 77.6 - - - +
341B GLN* 1.3 59.7 + - + +
343B MET* 3.1 16.2 + - + +
344B ARG* 2.9 41.0 + - + +
347B ARG* 5.5 3.8 - - - +
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Residues in contact with GLN 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ASP* 4.9 2.3 + - + -
91B ASP* 5.9 2.0 - - - +
94B ARG* 4.0 26.2 + - - +
102B TYR* 2.8 39.9 + - - -
314B GLU* 5.4 0.7 - - - +
336B ILE* 4.0 26.9 + - + +
338B THR* 2.8 33.7 + - - +
340B THR* 1.3 80.0 - - + +
342B THR* 1.3 62.1 + - - +
344B ARG* 3.4 17.2 + - - +
345B THR* 3.2 24.6 + - - -
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Residues in contact with THR 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B THR* 4.6 2.0 - - + -
331B ILE* 3.3 33.4 - - + -
333B PRO* 3.4 18.9 - - + +
336B ILE* 3.3 17.3 - - - +
338B THR 2.9 16.8 + - - -
339B ILE 3.5 8.3 - - - -
340B THR 3.2 0.2 - - - -
341B GLN* 1.3 76.9 - - - +
343B MET* 1.3 56.7 + - - +
345B THR* 3.1 8.5 + - - -
346B VAL* 2.9 29.1 + - + +
358B MET* 4.9 1.1 - - + -
373B PHE* 3.7 25.4 - - + -
377B LEU* 5.3 0.2 - - + -
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Residues in contact with MET 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B GLN* 5.1 2.9 - - + -
87B THR* 5.6 2.2 - - - +
133B LEU* 4.4 7.9 - - - +
339B ILE* 2.9 23.6 + - + +
340B THR* 3.1 28.2 + - + +
342B THR* 1.3 75.9 - - - +
344B ARG* 1.3 51.3 + - - +
346B VAL* 3.3 7.4 + - - +
347B ARG* 2.8 54.2 + - - +
373B PHE* 3.7 26.0 - - + -
377B LEU* 3.9 12.6 - - + -
136C ALA* 3.7 31.2 - - + +
137C ASN* 3.8 23.3 - - - +
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Residues in contact with ARG 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ASP* 6.2 0.2 - - - -
314B GLU* 2.7 49.4 + - + +
318B ARG* 5.7 0.4 - - - +
340B THR* 2.9 31.0 + - + +
341B GLN* 3.5 17.7 - - - +
342B THR 3.3 0.2 - - - -
343B MET* 1.3 72.3 - - - +
345B THR* 1.3 65.7 + - - +
347B ARG* 3.3 19.0 + - - +
348B LEU* 3.0 25.1 + - - +
351B ARG* 5.3 4.6 + - - +
408C GLU* 3.0 40.1 + - - +
410C LEU* 5.7 1.2 - - - +
413C LYS* 6.0 2.4 - - - +
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Residues in contact with THR 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B THR* 2.8 39.7 + - - +
313B ASN 4.5 0.7 - - - +
314B GLU* 3.2 26.0 + - - +
317B LEU* 3.6 21.6 - - + +
329B VAL* 4.8 2.9 - - + -
331B ILE* 4.1 17.3 - - + -
336B ILE* 4.9 0.9 - - - +
341B GLN 3.2 9.6 + - - -
342B THR 3.1 9.0 + - - -
344B ARG* 1.3 78.4 - - - +
346B VAL* 1.3 63.7 + - - +
348B LEU* 3.4 0.8 + - - -
349B ALA* 3.1 21.3 + - - +
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Residues in contact with VAL 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B ILE* 3.6 36.6 - - + -
342B THR 2.9 19.1 + - - +
343B MET 3.8 4.3 - - - +
345B THR* 1.3 77.4 - - - +
347B ARG* 1.4 57.5 + - + +
349B ALA* 3.1 2.4 + - - +
350B GLN* 2.9 57.8 + - - +
356B CYS* 3.8 15.3 - - + -
358B MET* 5.1 2.0 - - + -
377B LEU* 3.9 34.1 - - + -
379B THR* 4.8 1.6 - - + -
137C ASN* 6.3 0.7 - - - +
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Residues in contact with ARG 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B THR* 5.2 4.0 + - - +
343B MET* 2.8 45.6 + - - +
344B ARG* 3.9 27.7 - - - +
345B THR 3.3 0.2 - - - -
346B VAL* 1.4 74.4 - - + +
348B LEU* 1.3 57.9 + - - +
350B GLN* 3.3 7.7 + - - +
351B ARG* 2.9 50.4 + - + +
136C ALA 4.8 1.0 + - - -
137C ASN* 2.9 52.5 + - - +
139C SER* 3.7 17.7 + - - -
140C ILE* 4.4 6.7 - - - +
378C ASN* 3.7 26.7 - - + +
408C GLU* 3.2 24.5 + - - -
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Residues in contact with LEU 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLU* 3.2 41.1 - - + +
317B LEU* 4.0 10.1 - - + -
318B ARG* 3.7 29.4 - - + +
321B ILE* 3.7 9.4 - - + +
344B ARG 3.0 16.6 + - - +
345B THR 3.7 4.3 - - - +
347B ARG* 1.3 79.0 - - - +
349B ALA* 1.3 60.9 + - - +
351B ARG* 3.7 13.7 - - - +
352B ASN* 2.8 39.9 + - - +
414C LEU* 3.4 33.4 - - + +
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Residues in contact with ALA 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B LEU* 3.7 15.7 - - + -
321B ILE* 4.7 2.5 - - - -
329B VAL* 3.8 4.9 - - + -
345B THR 3.1 13.9 + - - +
346B VAL 3.1 0.2 + - - -
348B LEU* 1.3 77.2 - - - +
350B GLN* 1.3 58.7 + - - +
352B ASN 3.0 14.0 + - - -
354B TYR* 2.9 44.0 + - + -
356B CYS* 3.6 27.1 - - - -
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Residues in contact with GLN 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346B VAL* 2.9 38.1 + - + +
347B ARG* 4.0 7.7 - - - +
349B ALA* 1.3 76.8 - - - +
351B ARG* 1.3 58.3 + - - +
352B ASN 3.2 0.6 + - - -
353B ASN* 3.9 6.8 + - - +
354B TYR 4.1 6.7 - - - +
355B LYS* 6.0 0.2 - - - -
356B CYS* 4.1 13.3 - - - +
377B LEU* 3.2 27.1 + - - +
378B ASN 3.7 12.5 + - - -
379B THR* 4.0 9.3 + - - +
137C ASN* 5.5 5.0 + - - -
350C GLN* 4.1 21.2 - - + +
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Residues in contact with ARG 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLU* 5.1 6.1 + - - -
318B ARG* 5.6 0.6 - - - +
344B ARG* 5.3 2.8 + - - +
347B ARG* 2.9 47.6 + - + +
348B LEU* 3.7 17.9 - - - +
350B GLN* 1.3 74.4 - - - +
352B ASN* 1.3 70.3 + - - +
353B ASN 3.7 0.9 - - - -
140C ILE* 4.2 15.8 - - - +
355C LYS* 3.1 30.4 + - - +
378C ASN 5.8 4.0 - - - +
408C GLU* 5.0 3.0 + - - -
410C LEU* 3.5 40.4 - - - +
414C LEU* 2.8 38.9 + - - +
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Residues in contact with ASN 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B ILE* 3.9 30.7 - - + +
348B LEU* 2.8 34.7 + - - +
349B ALA 3.0 3.7 + - - +
351B ARG* 1.3 83.6 - - - +
353B ASN* 1.3 70.5 + - - +
354B TYR* 3.2 15.5 - - - -
353C ASN* 4.5 2.2 - - - -
355C LYS* 5.2 0.2 - - - +
414C LEU* 3.2 43.7 + - - +
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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
------------------------------------------------------------
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