Contacts of the helix formed by residues 338 - 352 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ASP* 3.5 36.7 - - + +
93C LEU* 4.2 15.3 - - + -
102C TYR* 3.2 15.0 - - + +
110C THR* 4.5 0.7 - - - -
111C LEU* 3.9 7.7 - - - +
114C SER* 3.8 4.0 - - - -
336C ILE* 3.7 2.8 - - - +
337C GLY* 1.3 81.3 - - - +
339C ILE* 1.3 59.3 - - - +
340C THR 3.7 0.9 + - - -
341C GLN* 2.6 47.6 + - - +
342C THR* 2.8 30.0 + - - -
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Residues in contact with ILE 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C GLN* 4.3 13.0 - - + +
90C ASP* 4.2 0.2 - - - +
111C LEU* 3.6 12.6 - - + -
114C SER* 3.0 15.5 + - - +
115C MET* 3.1 42.8 - - + +
118C ALA* 5.5 0.7 - - + -
133C LEU* 4.3 15.0 - - + -
333C PRO* 5.2 1.8 - - + -
338C THR* 1.3 70.0 - - - +
340C THR* 1.3 60.4 + - - +
342C THR* 3.3 5.1 + - - -
343C MET* 2.9 50.3 + - + +
369C PHE* 3.7 17.5 - - + -
373C PHE* 3.6 27.6 - - + -
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Residues in contact with THR 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C GLN* 3.5 15.4 + - - +
87C THR* 3.7 31.8 + - + +
90C ASP* 2.5 38.3 + - + +
91C ASP* 4.9 7.6 - - - +
339C ILE* 1.3 76.6 - - - +
341C GLN* 1.3 65.3 + - + +
343C MET* 3.0 14.8 + - + +
344C ARG* 2.9 36.7 + - + +
347C ARG* 5.3 5.2 - - - +
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Residues in contact with GLN 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ASP* 4.9 2.3 + - + +
91C ASP* 5.8 3.4 - - - +
94C ARG* 4.1 22.9 + - - +
102C TYR* 2.7 42.8 + - - -
314C GLU* 5.4 0.7 - - - +
336C ILE* 3.9 28.4 - - + +
338C THR* 2.6 35.3 + - - +
340C THR* 1.3 75.9 - - + +
342C THR* 1.3 62.2 + - - +
344C ARG* 3.3 16.6 + - - +
345C THR* 3.2 25.0 + - - -
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Residues in contact with THR 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C THR* 4.8 1.6 - - + -
331C ILE* 3.3 33.0 - - + -
333C PRO* 3.4 19.5 - - + +
336C ILE* 3.3 16.7 - - - +
338C THR 2.8 20.4 + - - -
339C ILE 3.4 7.9 - - - -
340C THR 3.2 0.2 - - - -
341C GLN* 1.3 75.9 - - - +
343C MET* 1.3 62.1 + - - +
345C THR* 3.1 7.4 + - - -
346C VAL* 3.0 23.7 + - + +
358C MET* 4.8 0.9 - - + -
373C PHE* 3.6 27.6 - - + -
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Residues in contact with MET 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ALA* 4.3 18.8 - - + +
137B ASN* 3.8 37.0 - - - +
86C GLN* 4.6 3.4 - - + -
87C THR* 5.9 1.1 - - - +
133C LEU* 4.7 5.8 - - + +
339C ILE* 2.9 45.5 + - + +
340C THR* 3.0 20.6 + - + +
342C THR* 1.3 72.5 - - - +
344C ARG* 1.3 52.6 + - - +
346C VAL* 3.3 7.4 + - - +
347C ARG* 2.8 54.7 + - - +
373C PHE* 3.7 21.3 - - + -
377C LEU* 3.9 10.1 - - + -
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Residues in contact with ARG 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B GLU* 3.2 35.6 + - - +
410B LEU* 6.0 1.0 - - - +
413B LYS* 6.0 4.0 - - - +
91C ASP* 5.9 2.2 - - - -
314C GLU* 2.7 48.4 + - - +
318C ARG* 4.6 3.8 - - - +
340C THR* 2.9 28.1 + - + +
341C GLN* 3.6 17.9 - - - +
343C MET* 1.3 71.5 - - - +
345C THR* 1.3 65.7 + - - +
347C ARG* 3.8 20.0 - - - +
348C LEU* 3.0 25.6 + - - +
351C ARG* 5.0 2.8 + - - +
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Residues in contact with THR 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C THR* 2.8 39.1 + - - +
313C ASN 4.5 0.9 - - - +
314C GLU* 3.3 24.5 + - - +
317C LEU* 3.6 21.1 - - + +
329C VAL* 4.7 3.1 - - + -
331C ILE* 3.9 20.4 - - + -
336C ILE* 4.9 1.2 - - - +
341C GLN 3.2 10.4 + - - -
342C THR 3.1 9.0 + - - -
344C ARG* 1.3 78.4 - - - +
346C VAL* 1.3 65.1 + - - +
348C LEU* 3.7 0.8 - - - +
349C ALA* 3.1 21.1 + - - +
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Residues in contact with VAL 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C ILE* 3.7 37.2 - - + -
342C THR 3.0 15.4 + - - +
343C MET 3.7 7.2 - - - +
345C THR* 1.3 77.2 - - - +
347C ARG* 1.3 59.1 + - + +
349C ALA* 3.2 2.4 + - - +
350C GLN* 2.9 57.6 + - - +
356C CYS* 3.8 15.3 - - + -
358C MET* 4.9 2.5 - - + -
377C LEU* 3.9 32.8 - - + -
379C THR* 4.8 1.8 - - + -
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Residues in contact with ARG 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ALA 4.8 1.2 + - - -
137B ASN* 2.8 53.1 + - - +
139B SER* 3.5 17.7 + - - -
140B ILE* 4.5 6.6 - - - +
378B ASN* 3.7 26.5 - - + +
408B GLU* 3.2 24.9 + - - -
87C THR* 5.9 1.0 + - - -
340C THR* 5.2 5.5 + - - +
343C MET* 2.8 40.7 + - - +
344C ARG* 3.8 26.7 - - - +
345C THR 3.4 0.2 - - - -
346C VAL* 1.3 73.9 - - + +
348C LEU* 1.3 64.1 + - - +
350C GLN* 3.3 9.0 + - - +
351C ARG* 2.9 45.3 + - + +
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Residues in contact with LEU 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B LEU* 3.5 38.8 - - + +
314C GLU* 3.2 40.2 - - + +
317C LEU* 3.8 12.6 - - + -
318C ARG* 3.7 28.7 - - + +
321C ILE* 3.8 9.0 - - + -
344C ARG 3.0 17.9 + - - +
345C THR 3.7 2.9 - - - +
347C ARG* 1.3 78.4 - - - +
349C ALA* 1.3 62.2 + - - +
351C ARG* 3.5 14.2 - - - +
352C ASN* 2.8 33.8 + - - +
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Residues in contact with ALA 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C LEU* 3.9 15.7 - - + -
321C ILE* 4.8 2.5 - - - -
329C VAL* 3.9 9.6 - - + -
345C THR 3.1 12.8 + - - +
346C VAL 3.4 8.5 - - - +
348C LEU* 1.3 77.3 - - - +
350C GLN* 1.3 57.1 + - - +
352C ASN* 2.9 18.7 + - - -
353C ASN 3.4 0.2 + - - -
354C TYR* 3.1 32.1 + - + +
356C CYS* 3.5 22.9 - - - -
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Residues in contact with GLN 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ASN* 5.5 3.8 + - - -
350B GLN* 4.1 19.7 - - + +
353B ASN* 5.9 1.9 - - - -
355B LYS* 5.3 0.7 + - - -
346C VAL* 2.9 39.7 + - + +
347C ARG* 4.1 8.2 - - - +
349C ALA* 1.3 74.9 - - - +
351C ARG* 1.4 59.6 + - - +
352C ASN 3.4 0.2 + - - -
353C ASN* 3.9 7.5 + - - +
354C TYR 4.0 8.7 - - - +
355C LYS* 6.1 0.2 - - - -
356C CYS* 4.2 11.0 - - - +
377C LEU* 3.2 26.6 + - - +
378C ASN 3.7 11.9 + - - -
379C THR* 4.1 9.5 + - - +
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Residues in contact with ARG 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ILE* 4.1 16.8 - - - +
355B LYS* 2.7 33.0 + - + +
378B ASN 5.8 4.0 - - - +
408B GLU* 4.8 3.6 + - - -
410B LEU* 3.3 38.0 - - - +
414B LEU* 2.8 37.5 + - - +
314C GLU* 5.0 5.9 + - - -
318C ARG* 4.9 2.2 - - - +
344C ARG* 5.0 2.0 + - - +
347C ARG* 2.9 37.2 + - + +
348C LEU* 3.5 26.1 - - - +
349C ALA 3.2 0.2 + - - -
350C GLN* 1.4 75.7 - - - +
352C ASN* 1.3 70.6 + - - +
353C ASN 3.6 0.4 - - - -
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Residues in contact with ASN 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B ASN* 4.5 2.7 - - - -
414B LEU* 3.0 49.9 + - - +
321C ILE* 3.7 32.3 - - + +
348C LEU* 2.8 32.4 + - - +
349C ALA 2.9 4.2 + - - +
351C ARG* 1.3 83.2 - - - +
353C ASN* 1.3 71.0 + - - +
354C TYR* 3.3 14.0 - - - -
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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