Contacts of the helix formed by residues 386 - 401 (chain C) in PDB entry 6N0M
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 386 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C MET* 3.8 7.2 - - + -
374C THR* 3.1 7.8 + - - +
376C ASN* 4.7 1.4 + - - -
377C THR 3.3 31.9 - - - +
378C ILE* 4.0 16.2 - - + -
384C VAL 3.5 4.5 + - - +
385C ASP* 1.3 73.2 + - - +
387C SER* 1.3 54.5 + - - +
388C VAL 2.8 4.3 + - - -
389C LEU* 2.7 28.7 + - - -
390C ARG* 2.8 22.6 + - - -
900C K94 2.7 44.8 + - + +
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Residues in contact with SER 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C GLN* 4.4 6.8 + - - -
371C TYR* 5.1 2.4 - - - -
385C ASP* 2.4 27.6 + - - -
386C THR* 1.3 77.2 + - - +
388C VAL* 1.3 59.6 + - - +
390C ARG* 3.6 23.8 - - - +
391C ARG* 3.3 40.5 + - - +
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Residues in contact with VAL 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C MET* 3.8 32.8 - - + +
268C LEU* 4.6 11.2 - - + +
269C GLN* 4.1 32.1 - - + +
385C ASP 5.0 1.1 + - - +
386C THR 2.8 6.2 + - - +
387C SER* 1.3 72.6 - - - +
389C LEU* 1.3 62.0 + - - +
390C ARG 3.1 1.8 - - - -
391C ARG* 3.5 22.7 + - - +
392C ALA* 2.8 30.7 + - - +
408C TYR* 4.9 0.9 + - - -
412C GLU* 4.7 12.1 - - - +
416C LEU* 3.7 21.0 - - + +
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Residues in contact with LEU 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C LEU* 3.7 19.3 - - + -
265C MET* 4.1 14.8 - - + -
378C ILE* 3.7 28.9 - - + -
386C THR 2.7 14.5 + - - +
388C VAL* 1.3 76.4 - - - +
390C ARG* 1.3 57.3 + - - +
392C ALA* 3.8 1.5 - - - +
393C ILE* 3.4 20.3 + - - +
416C LEU* 3.7 42.0 - - + +
417C LEU* 3.8 8.1 - - + -
444C TRP* 3.9 25.1 - - + -
447C PHE* 4.9 0.2 - - + -
900C K94 3.9 16.2 - - + -
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Residues in contact with ARG 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C ALA 4.5 1.6 + - - -
371C TYR* 2.5 38.0 + - + -
372C SER* 4.7 2.6 + - - +
373C LEU 3.5 20.5 + - - -
374C THR* 3.8 16.1 - - - +
386C THR* 2.8 26.9 + - - +
387C SER* 3.6 27.0 - - - +
388C VAL 3.1 0.6 - - - -
389C LEU* 1.3 74.7 - - - +
391C ARG* 1.3 54.6 + - - +
392C ALA 3.1 0.9 - - - -
393C ILE* 2.9 7.6 + - - +
394C TRP* 2.8 35.1 + - - +
454C HIS* 4.0 11.2 - - - -
458C LEU* 4.1 17.3 - - + +
900C K94 3.5 39.9 + - + -
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Residues in contact with ARG 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C TYR* 3.4 40.6 + - - +
387C SER* 3.3 39.8 + - - +
388C VAL* 3.6 21.2 - - - +
390C ARG* 1.3 77.2 - - - +
392C ALA* 1.3 57.0 + - - +
394C TRP* 4.4 2.7 - - - -
395C ASN* 2.9 51.5 + - - +
408C TYR* 3.7 24.3 - - + -
412C GLU* 5.3 2.6 + - - -
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Residues in contact with ALA 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C VAL 2.8 20.9 + - - +
389C LEU 3.8 2.2 - - - +
391C ARG* 1.3 72.4 - - - +
393C ILE* 1.3 59.2 + - - +
396C TYR* 2.9 30.7 + - - +
408C TYR* 3.4 20.2 + - - +
413C VAL* 3.8 9.8 - - - +
416C LEU* 3.9 15.3 - - + -
417C LEU* 3.3 27.8 - - + +
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Residues in contact with ILE 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C LEU 3.4 12.5 + - - +
390C ARG* 2.9 9.4 + - - +
392C ALA* 1.3 73.4 - - - +
394C TRP* 1.3 66.3 + - - +
396C TYR* 3.1 13.2 + - - +
397C ILE* 3.1 31.9 + - + +
417C LEU* 3.8 21.1 - - + -
421C LEU* 4.1 5.6 - - + -
425C ILE* 4.0 14.1 - - + -
444C TRP* 3.9 17.5 - - + -
455C VAL* 4.0 15.5 - - + -
458C LEU* 4.2 20.6 - - + -
459C LEU 4.9 0.4 - - - +
900C K94 3.5 28.0 - - - -
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Residues in contact with TRP 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C PHE* 4.5 13.9 - + + -
370C ALA* 5.0 0.2 - - + -
371C TYR* 4.6 42.7 - + + -
390C ARG 2.8 18.2 + - - +
391C ARG* 3.9 7.6 - - - +
393C ILE* 1.3 76.7 - - - +
395C ASN* 1.3 76.6 + - - +
397C ILE* 3.3 2.6 + - - +
398C HIS* 3.3 43.2 + + - -
405C TYR* 4.0 5.6 + + - -
458C LEU* 3.7 28.2 - - + +
461C GLU* 3.6 17.3 - - + -
462C ALA* 3.4 44.8 - - + +
465C GLN* 3.4 28.1 + - - -
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Residues in contact with ASN 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C TYR* 5.4 2.0 + - - -
391C ARG* 2.9 42.1 + - - +
392C ALA 4.3 0.2 - - - +
394C TRP* 1.3 84.0 - - - +
396C TYR* 1.3 60.6 + - - +
398C HIS* 3.5 5.4 + - - +
399C CYS* 3.0 28.1 + - - +
405C TYR* 3.2 32.7 - - - +
408C TYR* 3.6 38.8 - - + +
410C TYR* 3.6 11.7 + - + +
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Residues in contact with TYR 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C GLU* 4.1 25.6 + - + -
293C GLU* 4.3 1.8 + - - +
295C LEU* 3.5 26.7 - - - +
392C ALA 2.9 20.4 + - - +
393C ILE 3.1 4.4 + - - +
395C ASN* 1.3 74.6 - - - +
397C ILE* 1.3 59.1 - - - +
399C CYS* 3.4 6.1 - - - +
400C VAL* 3.1 46.0 + - + +
413C VAL* 3.8 20.6 - - + +
417C LEU* 3.5 18.4 - - + -
422C LYS* 3.8 40.6 + - + -
425C ILE* 4.0 26.2 - - + -
426C LYS* 4.1 10.2 + - + +
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Residues in contact with ILE 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C ILE* 3.1 32.9 + - + +
394C TRP 3.3 5.1 + - - +
396C TYR* 1.3 75.6 - - + +
398C HIS* 1.3 61.8 + - + +
400C VAL* 3.1 10.4 + - + +
401C PHE* 3.1 33.0 + - + -
425C ILE* 3.4 30.7 - - + -
426C LYS* 6.0 0.2 - - - -
429C ALA* 4.6 8.5 - - + -
459C LEU* 3.4 37.9 - - + +
462C ALA* 3.7 9.0 - - + -
463C ARG* 3.7 35.4 - - + +
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Residues in contact with HIS 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C TRP* 3.3 24.4 + - - +
395C ASN 3.9 4.3 - - - +
397C ILE* 1.3 78.9 - - + +
399C CYS* 1.3 60.1 + - - +
401C PHE* 3.0 6.5 + - - +
402C GLY 2.8 11.8 + - - -
403C ILE* 2.8 47.1 + - + +
405C TYR* 3.0 30.1 + + + -
462C ALA* 3.1 39.5 + - + -
465C GLN* 3.2 26.4 + - + -
466C ALA* 3.9 19.5 + - + -
469C LEU* 5.3 2.7 - - + -
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Residues in contact with CYS 399 (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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287C PHE* 3.5 28.9 - - + -
290C GLU* 3.7 21.3 - - - -
291C LYS* 3.7 45.5 - - - +
395C ASN 3.0 15.3 + - - +
396C TYR* 3.4 14.1 - - + +
398C HIS* 1.3 74.7 - - - +
400C VAL* 1.3 59.2 + - - +
402C GLY* 2.9 19.1 + - - -
403C ILE 3.9 1.2 + - - -
410C TYR* 3.9 7.6 - - + -
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Residues in contact with VAL 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C GLU 5.7 1.3 - - - +
291C LYS* 5.3 3.8 - - - +
323C TYR* 2.7 38.0 + - + +
334C PRO* 3.1 11.3 - - - +
396C TYR* 3.1 48.3 + - + +
397C ILE* 3.2 13.7 - - + +
398C HIS 3.1 0.4 - - - -
399C CYS* 1.3 77.4 - - - +
401C PHE* 1.3 65.0 + - + +
426C LYS* 3.9 16.6 - - + -
429C ALA* 5.5 1.1 - - + -
430C CYS* 3.6 28.5 - - - -
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Residues in contact with PHE 401 (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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166C LEU 4.9 1.3 - - - -
167C ALA 4.7 7.0 - - - -
168C HIS 5.5 0.9 - - - -
170C PRO* 3.5 36.3 - - + -
171C TRP* 4.1 9.6 - + + -
323C TYR* 4.8 5.8 - + - -
334C PRO* 3.9 7.6 - - - -
397C ILE* 3.1 20.1 + - + +
398C HIS 3.0 10.9 + - - +
400C VAL* 1.3 92.4 - - + +
402C GLY* 1.3 49.4 + - - +
403C ILE* 3.7 0.9 - - - +
429C ALA* 3.8 27.6 - - + -
430C CYS* 4.1 14.4 - - - -
463C ARG* 3.9 30.3 - - + -
466C ALA* 4.0 26.2 - - + -
470C TYR* 2.5 35.0 + - + -
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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
------------------------------------------------------------
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