Contacts of the helix formed by residues 408 - 431 (chain C) in PDB entry 2X1L
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 ALA 408 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C PHE* 4.5 2.5 - - - +
403C HIS* 2.6 23.7 + - + +
406C VAL* 4.0 16.2 - - + -
407C PRO* 1.3 74.3 - - - +
409C MET* 1.3 65.6 + - - +
410C HIS* 3.2 28.0 - - + -
411C LEU* 3.1 28.2 + - + +
412C ALA 3.4 6.9 + - - -
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Residues in contact with MET 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ALA* 3.9 25.4 - - + +
31C ALA* 4.5 2.9 - - + -
32C ILE* 3.9 13.7 - - + -
329C LEU* 4.0 33.0 - - + +
334C PHE* 3.8 41.6 - - + +
404C PHE* 3.7 32.3 - - + -
407C PRO* 3.8 22.9 - - - -
408C ALA* 1.3 75.3 - - - +
410C HIS* 1.3 61.7 + - - +
412C ALA* 3.2 10.8 + - - +
413C LEU* 3.0 28.3 + - + +
468C VAL* 5.6 0.9 - - + -
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Residues in contact with HIS 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C LEU 3.2 21.6 + - - +
330C ARG* 4.1 13.4 - - - +
332C VAL 4.0 10.3 - - - +
333C PRO* 3.6 27.9 - - + +
334C PHE* 3.1 30.4 + - + +
408C ALA* 3.7 28.3 - - + -
409C MET* 1.3 79.1 - - - +
411C LEU* 1.3 86.1 + - + +
413C LEU* 3.4 4.1 + - - +
414C GLU* 3.0 42.5 + - - +
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Residues in contact with LEU 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C HIS* 3.6 36.9 + - + +
406C VAL* 6.3 0.4 - - + -
408C ALA* 3.1 18.2 + - + +
410C HIS* 1.3 107.2 - - + +
412C ALA* 1.3 59.6 + - - +
414C GLU* 3.6 20.4 + - + +
415C ALA* 3.0 28.1 + - - +
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Residues in contact with ALA 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400C VAL* 4.0 15.3 - - + +
403C HIS* 3.9 17.4 - - + -
404C PHE* 3.7 33.0 - - + -
408C ALA 3.4 3.2 + - - +
409C MET 3.2 11.1 + - - +
411C LEU* 1.3 78.9 - - - +
413C LEU* 1.3 57.3 + - + +
415C ALA* 3.3 3.3 + - - +
416C ILE* 3.1 36.4 + - + +
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Residues in contact with LEU 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C TYR* 3.9 26.9 - - + +
329C LEU* 3.7 42.6 - - + +
330C ARG* 3.8 22.7 - - + +
409C MET 3.0 15.0 + - - +
410C HIS 3.8 3.8 - - - +
412C ALA* 1.3 74.7 - - + +
414C GLU* 1.3 60.9 + - - +
416C ILE* 3.5 4.2 + - + -
417C TRP* 3.0 37.0 + - + +
465C LEU* 3.6 29.2 - - + -
468C VAL* 3.9 21.3 - - + -
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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
----------------------------------------------------------
330C ARG* 3.4 43.5 + - - +
333C PRO* 6.1 0.2 - - - +
410C HIS* 3.0 33.7 + - - +
411C LEU* 3.8 21.2 - - + +
413C LEU* 1.3 75.2 - - - +
415C ALA* 1.3 58.3 + - - +
417C TRP* 3.5 4.4 + - - +
418C SER* 3.0 29.6 + - - -
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Residues in contact with ALA 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C LEU* 3.6 17.1 - - + +
399C ARG* 3.8 34.1 + - + +
400C VAL* 4.9 3.4 - - + -
403C HIS* 4.8 8.3 - - + +
411C LEU 3.0 18.8 + - - +
412C ALA* 3.5 7.4 - - - +
414C GLU* 1.3 75.8 - - - +
416C ILE* 1.3 65.4 + - - +
418C SER* 3.4 8.4 + - - -
419C VAL* 3.4 17.7 + - - +
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Residues in contact with ILE 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C LEU* 3.9 23.8 - - + -
400C VAL* 4.1 17.5 - - + -
404C PHE* 6.3 0.4 - - + -
412C ALA* 3.1 22.2 + - + +
413C LEU* 3.9 5.8 - - + +
415C ALA* 1.3 76.4 - - - +
417C TRP* 1.3 72.7 + - + +
419C VAL* 3.1 6.8 + - - +
420C LEU* 2.9 29.1 + - + +
461C ALA* 4.0 28.3 - - + -
464C LEU* 4.2 22.2 - - + +
465C LEU* 3.8 24.9 - - + -
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Residues in contact with TRP 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C TYR* 3.6 35.0 - + - +
330C ARG* 5.9 2.7 - - - +
352C ASP* 2.8 46.6 + - + +
353C LEU* 3.8 22.0 - - + -
356C GLU* 3.6 26.1 - - + +
357C LEU* 4.0 12.6 - - + -
413C LEU* 3.0 29.3 + - + +
414C GLU* 4.0 5.6 - - - +
416C ILE* 1.3 77.1 - - + +
418C SER* 1.3 58.8 + - - +
419C VAL 3.3 0.2 - - - -
420C LEU* 3.7 15.4 - - + +
421C GLY* 2.9 24.9 + - - -
465C LEU* 3.6 42.4 - - + -
469C MET* 4.3 1.3 - - + -
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Residues in contact with SER 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C ARG* 5.7 3.8 - - - -
414C GLU 3.0 18.2 + - - -
415C ALA* 3.5 9.4 - - - -
416C ILE 3.3 0.2 - - - -
417C TRP* 1.3 76.9 - - - +
419C VAL* 1.3 58.2 + - - +
421C GLY* 3.5 2.0 + - - -
422C ALA* 3.1 25.3 + - - +
425C ARG* 4.7 4.2 + - - -
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Residues in contact with VAL 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C LEU* 4.1 5.7 - - + +
392C ALA* 3.6 32.8 - - + +
393C ALA* 4.1 21.5 - - + +
396C LEU* 3.8 17.9 - - + -
399C ARG* 5.0 4.7 - - - +
415C ALA 3.4 13.9 + - - +
416C ILE 3.1 8.4 + - - +
418C SER* 1.3 76.5 - - - +
420C LEU* 1.3 61.0 + - + +
422C ALA* 3.2 8.0 + - - +
423C ALA* 2.8 26.7 + - - +
457C VAL* 3.9 21.3 - - + -
461C ALA* 6.4 0.9 - - + -
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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
----------------------------------------------------------
356C GLU* 4.0 10.3 - - + +
357C LEU* 4.0 28.5 - - + -
360C LEU* 3.9 21.8 - - + +
416C ILE* 2.9 22.1 + - + +
417C TRP* 3.7 46.0 - - + +
418C SER 3.4 0.2 - - - -
419C VAL* 1.3 76.1 - - + +
421C GLY* 1.3 57.1 + - - +
423C ALA* 3.4 6.3 + - - +
424C ASN* 3.0 36.4 + - - -
457C VAL* 4.6 9.9 - - + +
458C VAL* 5.1 2.5 - - - -
461C ALA* 3.9 21.5 - - + -
465C LEU* 5.1 0.2 - - + -
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Residues in contact with GLY 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C GLU* 3.2 19.2 + - - -
417C TRP 2.9 17.0 + - - -
418C SER* 3.5 2.9 + - - -
419C VAL 3.2 0.2 - - - -
420C LEU* 1.3 75.1 - - - +
422C ALA* 1.3 58.2 + - - +
424C ASN* 3.3 3.6 + - - +
425C ARG* 3.1 44.6 + - - +
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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
----------------------------------------------------------
389C LEU* 3.8 15.6 - - + +
392C ALA* 5.9 4.0 - - + -
418C SER 3.1 14.9 + - - +
419C VAL* 3.2 11.2 + - - +
421C GLY* 1.3 75.2 - - - +
423C ALA* 1.3 57.8 + - - +
425C ARG* 3.4 24.6 + - - +
426C TYR* 2.8 30.1 + - - +
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Residues in contact with ALA 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C LEU* 3.8 19.8 - - + +
389C LEU* 3.6 17.9 - - + +
419C VAL 2.8 15.7 + - - +
420C LEU 3.6 6.7 - - - +
422C ALA* 1.3 77.4 - - - +
424C ASN* 1.3 52.2 + - - +
426C TYR* 3.4 4.9 + - + +
427C PHE* 2.8 34.0 + - - +
454C THR* 5.2 4.9 - - + +
457C VAL* 3.8 25.1 - - + -
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Residues in contact with ASN 424 (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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355C ASN 5.1 1.5 - - - +
356C GLU* 2.9 46.8 + - - +
360C LEU* 3.4 29.3 + - - +
363C ARG* 4.4 13.0 + - - -
420C LEU 3.0 23.6 + - - +
421C GLY 3.3 5.6 + - - +
423C ALA* 1.3 73.9 - - - +
425C ARG* 1.3 60.7 + - + +
427C PHE* 3.4 4.5 + - - +
428C SER* 3.0 31.7 + - - -
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Residues in contact with ARG 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C SER 4.7 3.2 + - - -
421C GLY* 3.1 31.5 + - - +
422C ALA* 3.5 31.0 - - - +
424C ASN* 1.3 73.0 - - + +
426C TYR* 1.3 60.2 + - - +
428C SER* 3.4 6.4 + - - -
429C ALA* 2.9 32.1 + - - +
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Residues in contact with TYR 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C GLU* 4.0 21.1 - - + -
386C ASP* 2.6 34.4 + - - -
389C LEU* 3.6 29.4 - - + -
422C ALA 2.8 18.0 + - - +
423C ALA 3.4 5.2 - - - +
425C ARG* 1.3 76.6 - - - +
427C PHE* 1.3 59.6 + - - +
429C ALA* 3.4 3.8 + - - -
430C GLN* 3.0 59.0 + - + +
450C VAL* 3.4 33.5 - - + +
453C THR* 3.6 12.8 - - + -
454C THR* 3.8 22.9 - - - -
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Residues in contact with PHE 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C LEU* 4.5 8.1 - - + -
363C ARG* 4.1 40.6 - - + -
364C SER* 4.4 10.1 - - - -
367C MET* 3.9 23.6 - - + -
423C ALA 2.8 21.0 + - - +
424C ASN* 3.6 9.6 - - - +
425C ARG 3.3 0.2 - - - -
426C TYR* 1.3 76.8 - - - +
428C SER* 1.3 62.0 + - - +
430C GLN* 5.0 1.1 - - - -
431C GLU 3.4 1.2 + - - -
432C PRO* 3.1 57.0 - - + +
433C TRP* 3.7 15.3 - + - -
450C VAL* 4.9 2.9 - - + -
451C LEU* 4.9 4.0 - - + -
454C THR* 3.6 34.3 - - + +
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Residues in contact with SER 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C ARG* 5.8 1.6 + - - -
424C ASN 3.0 18.1 + - - -
425C ARG* 3.7 6.9 - - - -
426C TYR 3.3 0.2 - - - -
427C PHE* 1.3 76.9 - - - +
429C ALA* 1.3 63.3 + - - +
431C GLU* 3.3 23.4 + - - +
433C TRP* 3.8 14.4 - - - -
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Residues in contact with ALA 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C ARG 2.9 18.2 + - - +
426C TYR* 3.4 5.4 + - - +
428C SER* 1.3 76.6 - - - +
430C GLN* 1.3 65.4 + - + +
431C GLU* 3.5 8.9 + - - +
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Residues in contact with GLN 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C GLU* 3.8 29.5 + - - +
426C TYR* 3.0 37.1 + - + +
427C PHE 4.4 1.6 - - - +
429C ALA* 1.3 80.1 - - + +
431C GLU* 1.3 70.8 + - - +
432C PRO 3.4 0.5 - - - -
435C LEU* 3.4 19.2 - - - +
446C ARG* 2.9 35.1 + - - +
450C VAL* 3.4 30.9 - - + +
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Residues in contact with GLU 431 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C PHE 3.4 0.2 + - - -
428C SER 3.3 19.7 + - - +
429C ALA 3.3 7.2 - - - +
430C GLN* 1.3 79.9 - - - +
432C PRO* 1.4 68.0 - - - +
433C TRP* 3.2 22.1 - - + -
434C VAL* 3.0 41.3 + - + +
435C LEU* 3.3 9.0 + - - +
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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