Contacts of the helix formed by residues 413 - 431 (chain C) in PDB entry 3ER8
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 HIS 413 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C VAL* 4.6 6.3 - - + +
405C LEU* 2.7 43.6 + - + +
406C LEU 3.3 9.7 + - - +
407C SER* 3.6 11.0 - - - +
411C LYS 2.9 5.7 + - - -
412C VAL* 1.3 77.1 - - - +
414C GLU* 1.3 62.7 + - + +
415C ILE* 2.9 58.3 + - + +
416C SER* 3.1 6.3 + - - -
417C ALA 2.9 22.2 + - - -
452C ILE* 2.8 46.1 + - + +
453C PRO 3.5 12.5 + - - -
454C ILE* 5.1 1.9 - - + -
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Residues in contact with GLU 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C PRO* 5.0 14.6 - - + +
407C SER* 5.3 0.8 - - - -
412C VAL 3.5 1.0 + - - -
413C HIS* 1.3 81.2 + - + +
415C ILE* 1.3 64.1 + - + +
417C ALA* 3.1 9.9 + - - +
418C ARG* 2.9 56.1 + - + +
445C SER 3.6 1.2 - - - +
449C ARG* 3.0 44.4 + - - +
450C ASP 5.2 0.3 - - - +
452C ILE* 3.4 32.8 - - + +
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Residues in contact with ILE 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C MET* 3.1 59.2 - - + +
147C VAL* 5.1 0.4 - - + -
286C ILE* 4.3 6.5 - - + +
289C PHE* 3.6 39.0 - - + +
290C SER* 3.9 1.7 - - - +
295C LEU* 4.0 15.3 - - + -
405C LEU* 4.3 2.2 - - + -
413C HIS* 2.9 30.7 - - + +
414C GLU* 1.3 73.1 - - + +
416C SER* 1.3 53.0 + - - +
418C ARG* 3.1 15.8 + - - +
419C GLY* 2.5 32.6 + - - -
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Residues in contact with SER 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C SER* 2.9 24.2 + - - -
404C ILE* 3.6 8.9 - - - -
405C LEU* 2.7 45.3 + - - +
412C VAL* 3.8 10.1 - - - -
413C HIS* 3.1 11.3 + - - -
415C ILE* 1.3 76.4 - - - +
417C ALA* 1.3 61.2 + - - +
419C GLY* 3.7 0.2 - - - -
420C LEU* 2.9 35.5 + - - +
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Residues in contact with ALA 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C PRO* 4.9 16.6 - - + +
333C MET 4.7 5.6 + - - +
335C CYS* 3.7 33.4 - - + -
412C VAL* 3.8 11.2 - - + +
413C HIS 2.9 13.4 + - - +
414C GLU* 3.1 13.0 + - - +
416C SER* 1.3 76.8 - - - +
418C ARG* 1.3 57.3 + - - +
421C CYS* 3.3 25.1 + - - +
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Residues in contact with ARG 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C SER* 5.5 3.4 - - - -
145C MET* 4.7 7.7 - - - +
286C ILE* 3.3 14.4 - - + +
331C MET* 5.8 1.8 - - + -
332C PRO* 4.9 11.9 - - + -
414C GLU* 2.9 41.2 + - - +
415C ILE* 3.5 37.3 - - - +
417C ALA* 1.3 76.5 - - - +
419C GLY* 1.3 59.8 + - - +
420C LEU 3.3 0.2 - - - -
421C CYS* 3.5 6.7 - - - +
422C ALA* 2.8 31.7 + - - +
442C LEU* 3.7 17.5 - - + +
445C SER* 3.1 28.4 + - - -
446C MET* 2.8 49.4 - - - +
449C ARG* 4.1 5.3 - - - +
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Residues in contact with GLY 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C ILE* 3.4 20.6 - - - -
287C LYS* 3.7 11.8 - - - +
290C SER* 4.2 7.2 - - - -
400C PHE* 4.0 7.2 - - - -
415C ILE 2.5 21.1 + - - -
416C SER 3.2 2.4 + - - -
418C ARG* 1.3 72.5 - - - +
420C LEU* 1.3 62.2 + - - +
422C ALA* 3.1 6.4 + - - +
423C HIS* 3.0 18.5 + - - +
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Residues in contact with LEU 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C CYS* 3.7 19.5 - - + -
344C VAL* 3.1 34.3 - - + -
346C VAL* 3.8 11.0 - - + -
359C VAL* 3.6 35.0 - - + +
400C PHE* 3.7 27.6 - - + -
404C ILE* 3.9 13.9 - - + -
412C VAL* 4.4 4.0 - - + -
416C SER 2.9 25.1 + - - +
417C ALA* 3.9 3.8 - - - +
419C GLY* 1.3 71.7 - - - +
421C CYS* 1.3 64.5 + - - +
423C HIS* 3.0 22.0 - - - +
424C ILE* 3.1 13.0 + - - +
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Residues in contact with CYS 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C MET* 3.5 33.4 - - - -
332C PRO* 6.0 0.4 - - + -
333C MET* 3.6 29.4 - - + +
346C VAL* 5.3 1.8 - - + +
417C ALA 3.3 17.4 + - - +
418C ARG* 3.5 7.0 - - - +
420C LEU* 1.3 78.6 - - - +
422C ALA* 1.3 62.9 + - - +
424C ILE* 3.2 23.8 + - - +
425C LEU* 3.2 20.3 + - - +
438C CYS* 5.9 0.7 - - - -
442C LEU* 3.8 12.3 - - + -
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Residues in contact with ALA 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C LEU* 3.1 63.2 - - + +
286C ILE* 3.6 14.1 - - + -
287C LYS* 3.9 4.3 - - + +
418C ARG 2.8 18.5 + - - +
419C GLY 3.2 9.9 - - - +
421C CYS* 1.3 72.5 - - - +
423C HIS* 1.3 65.8 + - - +
425C LEU 3.1 2.9 + - - -
426C LEU* 3.2 3.0 + - - +
442C LEU* 3.8 5.1 - - + +
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Residues in contact with HIS 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C LYS* 3.0 42.5 + - + +
359C VAL* 5.7 2.0 - - + -
385C THR* 3.4 10.3 - - - -
387C SER* 4.0 3.3 - - - -
389C TYR* 3.0 39.4 + + - -
398C THR* 3.1 34.6 + - + -
399C TYR 3.8 15.4 + - - -
400C PHE* 4.6 7.2 - + + -
419C GLY 3.0 10.1 + - - +
420C LEU* 3.0 17.9 + - - +
422C ALA* 1.3 74.5 - - - +
424C ILE* 1.3 56.0 + - + +
426C LEU* 2.6 43.1 + - - +
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Residues in contact with ILE 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C MET* 4.9 0.9 - - - -
346C VAL* 3.7 20.0 - - + -
348C THR* 3.4 27.8 - - + -
352C PHE* 4.3 14.8 - - + -
354C PHE* 4.3 12.6 - - + -
357C CYS* 3.9 22.9 - - - -
359C VAL* 5.2 2.9 - - + -
389C TYR* 4.5 9.0 - - - -
396C MET* 4.1 22.9 - - + -
420C LEU 3.1 12.7 + - - +
421C CYS* 3.2 10.5 + - - +
423C HIS* 1.3 80.1 - - + +
425C LEU* 1.3 61.3 + - + +
427C TYR* 3.2 19.8 + - - +
428C GLN* 3.6 6.8 + - - +
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Residues in contact with LEU 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C LEU* 3.2 37.4 - - + +
352C PHE* 4.0 14.1 - - + -
421C CYS* 3.2 13.2 + - - +
422C ALA 3.1 2.8 + - - +
423C HIS 3.0 0.8 - - - -
424C ILE* 1.3 77.6 - - + +
426C LEU* 1.3 63.9 + - - +
427C TYR 3.2 0.2 - - - -
428C GLN* 3.3 8.1 + - + +
429C MET* 3.3 21.4 + - + +
435C TYR* 3.8 28.3 - - + +
438C CYS* 3.6 36.8 - - + -
439C LEU* 4.0 12.8 - - + +
442C LEU* 4.0 19.7 - - + -
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Residues in contact with LEU 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C PHE* 3.5 32.4 - - + -
283C LEU* 3.3 29.8 - - + +
284C ASN* 3.5 35.2 - - + +
287C LYS* 4.3 9.4 - - + +
384C VAL 4.3 13.7 - - - +
385C THR* 4.5 7.6 - - + -
389C TYR* 4.1 6.5 - - - +
422C ALA 3.2 9.4 + - - +
423C HIS* 2.6 36.6 + - - +
425C LEU* 1.3 69.8 - - - +
427C TYR* 1.3 63.7 + - - +
429C MET 3.3 2.8 + - - -
430C LEU* 3.0 27.6 + - - +
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Residues in contact with TYR 427 (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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354C PHE* 5.0 1.1 - + - -
379C CYS* 4.4 18.5 - - - -
381C PHE* 4.0 11.2 - + - -
389C TYR* 3.5 38.5 + + + -
391C ILE* 3.3 27.8 - - + +
396C MET* 3.1 31.6 - - + -
423C HIS 3.5 1.0 + - - -
424C ILE 3.2 9.5 + - - +
426C LEU* 1.3 76.7 - - - +
428C GLN* 1.3 83.1 + - - +
430C LEU* 2.8 19.4 + - - +
431C THR* 2.8 49.2 + - + +
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Residues in contact with GLN 428 (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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352C PHE* 3.3 31.3 - - + -
354C PHE* 3.7 21.2 - - - -
424C ILE* 3.9 11.6 + - - +
425C LEU* 3.5 15.7 - - + +
426C LEU 3.3 0.4 - - - -
427C TYR* 1.3 92.1 - - - +
429C MET* 1.3 51.6 + - - +
431C THR* 2.8 10.8 + - - -
432C SER 2.7 32.2 + - - -
433C GLY* 3.1 15.4 + - - +
434C GLU* 3.1 40.0 + - - +
435C TYR* 3.8 9.9 - - + -
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Residues in contact with MET 429 (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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264C VAL 3.8 7.6 - - - +
266C PRO* 4.0 17.1 - - + +
277C ASP* 5.3 1.1 - - - +
279C THR* 4.0 10.1 - - + +
280C PHE* 3.2 49.4 - - + -
283C LEU* 3.1 46.7 - - + -
425C LEU* 3.3 2.6 + - + +
426C LEU 3.3 10.0 + - - +
427C TYR 3.2 0.4 - - - -
428C GLN* 1.3 77.3 - - - +
430C LEU* 1.3 59.7 - - - +
432C SER* 4.0 9.9 + - - +
433C GLY 5.2 0.2 - - - +
435C TYR* 3.9 39.9 - - + -
439C LEU* 5.7 1.8 - - + -
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Residues in contact with LEU 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C VAL* 3.0 51.2 - - + +
265C VAL* 4.0 7.0 - - + -
266C PRO* 3.4 19.3 - - + -
280C PHE* 4.0 14.1 - - + -
381C PHE* 3.3 33.8 - - + -
384C VAL* 4.3 8.3 - - + -
385C THR* 3.6 31.2 - - + -
426C LEU 3.0 21.1 - - - +
427C TYR* 2.8 8.4 + - - +
429C MET* 1.3 76.9 - - - +
431C THR* 1.3 64.1 + - - +
432C SER* 3.5 2.7 + - - -
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Residues in contact with THR 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C VAL* 6.0 0.4 - - + -
379C CYS* 4.9 7.0 - - - -
381C PHE* 4.3 9.4 - - + -
427C TYR* 2.8 54.8 + - + +
428C GLN* 2.8 7.8 + - - -
430C LEU* 1.3 81.0 - - - +
432C SER* 1.3 73.1 + - - +
433C GLY* 3.5 2.3 + - - -
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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