Contacts of the helix formed by residues 374 - 390 (chain C) in PDB entry 2QMR
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 374 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270C GLU* 6.1 0.2 - - - +
274C LEU* 3.7 16.8 - - - +
314C ASP* 3.1 34.6 + - - +
370C ILE* 3.8 19.2 - - - +
371C SER 4.6 3.2 + - - +
372C ASP 4.0 4.8 + - - -
373C TRP* 1.3 76.5 - - - +
375C LEU* 1.3 64.8 + - - +
376C ARG* 3.5 8.1 + - - +
377C LYS* 3.1 27.1 + - - +
378C CYS* 3.0 22.9 + - - +
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Residues in contact with LEU 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C THR* 4.6 10.8 - - + +
270C GLU* 3.8 28.8 + - - +
273C ALA* 4.2 17.5 - - + -
274C LEU* 4.0 27.7 - - + +
277C CYS* 3.7 28.3 - - + -
307C GLY* 4.3 17.7 - - - +
374C ASN* 1.3 75.9 - - - +
376C ARG* 1.3 54.8 + - - +
378C CYS* 3.2 1.1 + - - +
379C SER* 2.8 46.4 + - - +
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Residues in contact with ARG 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C GLY 3.4 16.5 + - - +
308C MET* 3.0 25.3 + - - +
309C LYS 4.3 5.2 - - - +
310C TYR* 3.3 44.1 + - - -
314C ASP* 4.5 7.0 - - - +
370C ILE* 5.4 5.6 - - - +
374C ASN* 3.3 12.2 + - - +
375C LEU* 1.3 79.1 - - - +
377C LYS* 1.3 65.7 + - + +
379C SER* 3.7 1.6 - - - -
380C ALA* 2.9 30.9 + - + +
415C GLU* 2.4 38.8 + - - -
419C LEU* 3.3 33.9 - - + +
457C ILE* 4.7 5.5 - - - +
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Residues in contact with LYS 377 (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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370C ILE* 3.5 35.1 - - - +
372C ASP* 3.1 38.4 + - - +
373C TRP* 3.9 25.9 - - + -
374C ASN* 3.1 18.3 + - - +
376C ARG* 1.3 84.7 - - + +
378C CYS* 1.3 57.9 + - - +
380C ALA* 3.7 6.3 - - - +
381C ALA* 2.8 30.5 + - - +
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Residues in contact with CYS 378 (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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274C LEU* 3.8 10.1 - - + -
277C CYS* 3.5 23.6 - - - -
278C GLU* 3.7 32.5 - - - -
281C LEU* 4.0 8.4 - - - +
373C TRP* 3.6 25.7 - - + -
374C ASN 3.0 17.4 + - - +
375C LEU 3.7 3.6 - - - +
377C LYS* 1.3 74.9 - - - +
379C SER* 1.3 60.2 + - - +
381C ALA* 3.2 2.8 + - - +
382C ALA* 2.8 28.2 + - - +
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Residues in contact with SER 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C THR* 5.6 0.7 - - - +
277C CYS* 3.5 17.7 - - - -
304C LEU* 3.4 35.9 - - - +
307C GLY* 3.8 15.3 - - - -
308C MET* 3.3 13.1 - - - +
375C LEU* 2.8 25.3 + - - +
376C ARG 3.7 3.6 - - - -
378C CYS* 1.3 75.4 - - - +
380C ALA* 1.3 56.8 + - - -
382C ALA* 3.2 3.3 + - - +
383C LEU 2.9 26.5 + - - -
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Residues in contact with ALA 380 (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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308C MET* 3.8 19.8 - - - +
376C ARG* 2.9 19.4 + - + +
377C LYS* 3.7 7.4 - - - +
379C SER* 1.3 76.4 - - - +
381C ALA* 1.3 60.8 + - - +
383C LEU* 3.5 1.7 + - - +
384C ASP* 3.1 24.6 + - - +
419C LEU* 4.4 22.0 - - + -
423C ALA* 4.3 8.1 - - + +
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Residues in contact with ALA 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C LEU* 4.1 14.4 - - + -
373C TRP* 4.0 18.2 - - + -
377C LYS 2.8 21.7 + - - +
378C CYS 3.2 4.2 + - - +
380C ALA* 1.3 70.0 - - - +
382C ALA* 1.3 66.7 + - - +
384C ASP* 3.4 7.8 + - - +
385C VAL* 3.0 29.8 + - + +
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Residues in contact with ALA 382 (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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277C CYS 5.0 2.0 - - - +
280C TRP* 4.0 20.9 - - + -
281C LEU* 4.1 19.4 - - + +
284C ALA* 5.0 0.4 - - - +
304C LEU* 3.9 20.6 - - + -
378C CYS 2.8 16.5 + - - +
379C SER* 3.5 4.5 - - - +
381C ALA* 1.3 76.5 - - - +
383C LEU* 1.3 52.4 + - - +
385C VAL* 2.9 7.0 + - - +
386C LEU* 2.8 40.0 + - + +
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Residues in contact with LEU 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C ILE* 4.1 18.2 - - + -
304C LEU* 4.1 15.8 - - + +
305C VAL* 4.3 4.7 - - + -
308C MET* 3.1 37.5 - - + -
379C SER 2.9 9.6 + - - +
380C ALA 3.9 2.5 - - - +
382C ALA* 1.3 71.5 - - - +
384C ASP* 1.3 53.6 + - - +
386C LEU* 3.7 4.2 - - + +
387C ALA* 2.8 37.0 + - - +
394C LEU* 4.6 4.5 - - + -
398C ILE* 3.6 23.1 - - + -
420C VAL* 3.9 21.1 - - + -
423C ALA* 4.4 6.7 - - + -
424C ILE* 3.8 23.8 - - + -
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Residues in contact with ASP 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C ALA 3.1 18.6 + - - +
381C ALA* 3.5 8.1 - - - +
382C ALA 3.2 0.2 - - - -
383C LEU* 1.3 77.0 - - - +
385C VAL* 1.3 62.6 + - - +
387C ALA* 3.2 4.8 - - - +
388C ASN* 2.7 45.2 + - - -
423C ALA* 3.6 23.2 + - + +
426C GLU* 4.4 5.2 - - - +
464C ARG* 3.4 24.0 + - - -
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Residues in contact with VAL 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C LEU* 4.3 17.3 - - + -
284C ALA* 3.8 31.4 - - + +
285C GLU* 4.4 15.9 - - + +
381C ALA* 3.0 18.6 + - + +
382C ALA* 2.9 7.4 + - - +
384C ASP* 1.3 78.7 - - - +
386C LEU* 1.3 66.8 + - - +
388C ASN* 3.0 11.1 + - + +
389C VAL* 3.0 22.7 + - + +
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Residues in contact with LEU 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C TRP* 5.1 5.8 - - + +
284C ALA* 3.9 22.0 - - + -
289C CYS* 4.1 8.7 - - - -
293C LEU* 4.0 23.1 - - + -
297C LEU* 5.2 0.4 - - + -
300C LEU* 3.9 17.5 - - + -
301C ILE* 4.7 8.5 - - + -
304C LEU* 3.6 31.0 - - + -
382C ALA* 2.8 22.4 + - + +
383C LEU* 3.8 6.3 - - + +
385C VAL* 1.3 71.2 - - - +
387C ALA* 1.3 54.8 + - - +
389C VAL* 2.8 21.8 + - + +
390C TYR* 2.9 33.2 + - + +
394C LEU* 4.5 14.4 - - + -
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Residues in contact with ALA 387 (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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383C LEU 2.8 18.4 + - - +
384C ASP* 3.2 8.3 - - - +
386C LEU* 1.3 77.2 - - - +
388C ASN* 1.3 57.2 + - - +
390C TYR 2.7 16.1 - - - +
391C ARG* 3.6 3.5 - - - +
394C LEU* 3.6 16.7 - - + +
423C ALA 4.6 0.2 - - - +
424C ILE* 3.9 20.0 - - - +
427C GLY* 3.3 22.5 - - - +
428C CYS* 3.8 18.6 - - - -
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Residues in contact with ASN 388 (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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384C ASP* 2.7 38.4 + - - -
385C VAL* 3.0 12.9 + - + +
387C ALA* 1.3 75.7 - - - +
389C VAL* 1.3 66.3 + - + +
391C ARG* 4.1 16.3 + - - +
423C ALA 5.5 0.4 + - - -
426C GLU* 3.0 35.1 + - - +
427C GLY* 4.0 17.3 - - - +
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Residues in contact with VAL 389 (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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284C ALA* 3.5 26.7 - - + +
289C CYS* 4.4 16.8 - - + -
290C LYS* 3.9 33.1 + - + +
385C VAL* 3.0 20.0 + - + +
386C LEU* 2.8 13.0 + - - +
388C ASN* 1.3 81.4 - - + +
390C TYR* 1.3 75.3 + - + +
391C ARG* 3.4 8.7 + - - +
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Residues in contact with TYR 390 (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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289C CYS* 3.8 2.3 + - - -
290C LYS* 3.2 50.9 + - + +
293C LEU* 3.2 30.2 - - + +
294C VAL* 5.3 3.1 - - + -
297C LEU* 3.5 40.4 - - + -
386C LEU* 2.9 33.2 + - + +
387C ALA* 2.7 23.9 - - - +
389C VAL* 1.3 76.9 - - + +
391C ARG* 1.3 60.2 + - - +
393C GLU* 3.4 27.6 - - + -
394C LEU* 3.9 25.9 - - + +
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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