Contacts of the helix formed by residues 420 - 436 (chain C) in PDB entry 1FSX
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 420 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416C LYS 5.0 4.0 - - - -
417C VAL* 3.3 20.4 - - - +
418C GLY 3.0 1.2 + - - -
419C GLY* 1.3 84.2 + - - +
421C ALA* 1.3 57.1 + - - +
422C ALA 3.2 3.1 - - - -
423C GLU* 2.8 53.1 + - - +
424C TYR* 2.9 48.1 + - + -
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Residues in contact with ALA 421 (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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414C TRP* 4.3 17.4 - - + +
417C VAL* 3.4 24.3 - - + +
418C GLY 3.5 10.5 + - - +
419C GLY 3.7 0.6 - - - -
420C HIS* 1.3 76.2 - - - +
422C ALA* 1.3 56.6 + - - +
424C TYR* 3.9 2.2 - - - +
425C GLY 3.0 23.4 + - - -
463C ALA* 3.0 23.1 - - + +
467C THR* 4.5 8.3 - - - +
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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
----------------------------------------------------------
420C HIS 3.2 0.8 - - - -
421C ALA* 1.3 76.9 - - - +
423C GLU* 1.3 68.7 + - - +
426C ALA* 3.2 24.9 + - - +
456C LYS* 4.9 1.2 - - - +
459C GLY 4.1 4.0 - - - -
460C ALA* 3.8 28.2 + - + +
463C ALA* 4.0 9.1 - - + +
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Residues in contact with GLU 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C GLY 3.4 9.0 - - - +
420C HIS* 2.8 49.3 + - - +
422C ALA* 1.3 82.9 + - + +
424C TYR* 1.3 68.1 + - + +
426C ALA* 3.7 5.1 + - - +
427C GLU* 3.2 27.2 + - - +
456C LYS* 5.0 17.1 + - - +
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Residues in contact with TYR 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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414C TRP* 6.4 1.8 - - + -
417C VAL* 3.8 31.9 - - + -
420C HIS* 2.9 49.6 + + + +
421C ALA* 4.0 4.0 - - - +
423C GLU* 1.3 85.5 - - + +
425C GLY* 1.3 60.5 + - - +
427C GLU* 3.3 1.7 + - - -
428C ALA* 2.9 29.5 + - - +
505C LEU* 5.2 3.1 - - + +
508C THR* 3.5 19.0 - - + +
509C LEU* 4.4 20.9 - - + -
512C HIS* 3.5 56.1 + + + +
513C LEU* 5.1 9.0 - - + +
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Residues in contact with GLY 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C ALA 3.0 14.6 + - - -
424C TYR* 1.3 77.1 - - - +
426C ALA* 1.3 60.8 + - - +
428C ALA* 3.6 7.6 + - - +
429C LEU* 3.2 27.0 + - - +
459C GLY* 3.7 19.8 - - - -
462C VAL* 5.1 7.8 - - - +
463C ALA* 4.5 6.5 - - - -
466C LEU* 6.2 1.1 - - - -
505C LEU* 5.3 6.1 - - - -
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Residues in contact with ALA 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C ALA 3.2 18.9 + - - +
423C GLU* 4.0 4.5 - - - +
425C GLY* 1.3 75.3 - - - +
427C GLU* 1.3 64.3 + - - +
429C LEU* 3.3 5.1 + - - +
430C GLU* 3.1 21.4 + - - +
455C VAL* 4.1 8.8 - - + +
456C LYS* 3.9 44.0 - - + +
459C GLY* 3.6 11.3 - - - -
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Residues in contact with GLU 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C GLU 3.2 19.6 + - - +
424C TYR* 3.6 6.5 - - - +
425C GLY 3.3 0.2 - - - -
426C ALA* 1.3 75.2 - - - +
428C ALA* 1.3 65.2 + - - +
430C GLU* 3.1 9.5 + - + +
431C ARG* 2.9 67.4 + - + +
508C THR* 3.6 11.3 - - + +
511C SER* 4.1 1.4 + - - -
512C HIS* 2.8 36.6 + - - -
724D PRO* 4.6 9.4 - - + -
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Residues in contact with ALA 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C TYR 2.9 18.3 + - - +
425C GLY* 3.7 7.6 - - - +
426C ALA 3.3 0.2 - - - -
427C GLU* 1.3 76.0 - - - +
429C LEU* 1.3 58.9 + - - +
431C ARG* 3.6 0.8 + - - -
432C MET* 3.1 23.2 + - - +
501C LEU* 4.4 8.0 - - + +
504C SER* 3.3 16.4 - - - +
505C LEU* 3.9 35.2 - - + +
508C THR* 3.5 15.0 + - - +
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Residues in contact with LEU 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C GLY 3.2 8.8 + - - +
426C ALA 3.6 7.2 - - - +
427C GLU 3.1 0.4 - - - -
428C ALA* 1.3 77.4 - - - +
430C GLU* 1.3 65.2 + - - +
432C MET* 3.1 25.4 + - + +
433C PHE* 3.0 45.8 + - + -
443C PHE* 5.2 1.8 - - + -
455C VAL* 4.1 12.3 - - + +
458C HIS* 3.9 18.6 - - + -
459C GLY* 3.6 34.5 - - - +
462C VAL* 4.3 6.3 - - + -
501C LEU* 4.2 14.8 - - + -
542C CMO 4.1 16.6 - - - +
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Residues in contact with GLU 430 (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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426C ALA 3.1 14.7 + - - +
427C GLU* 3.1 12.0 + - - +
429C LEU* 1.3 73.9 - - - +
431C ARG* 1.3 57.9 + - - +
433C PHE* 3.1 11.7 + - + +
434C LEU* 3.0 49.3 + - + +
448C LEU 6.1 1.1 - - - +
450C HIS* 2.9 46.6 + - + +
451C GLY* 4.7 3.1 + - - -
455C VAL* 4.7 7.4 - - + +
724D PRO* 4.3 16.6 - - + +
725D VAL* 5.9 0.5 - - - +
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Residues in contact with ARG 431 (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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427C GLU* 2.9 43.2 + - - +
428C ALA 3.8 4.5 - - - +
430C GLU* 1.3 76.7 - - - +
432C MET* 1.3 57.7 + - - +
434C LEU* 4.6 2.2 - - - +
435C SER* 2.9 36.0 + - - -
504C SER* 4.2 13.8 + - - -
507C VAL* 3.8 15.4 - - - +
508C THR* 3.4 20.6 + - - +
511C SER* 4.2 12.6 + - - -
715D ALA* 6.3 0.2 - - - +
719D GLY 5.2 0.4 + - - -
722D PHE* 2.9 23.0 + - - -
723D THR* 3.5 18.0 + - - +
724D PRO* 3.6 33.9 - - + +
727D GLN* 2.9 34.4 + - - +
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Residues in contact with MET 432 (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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428C ALA 3.1 17.1 + - - +
429C LEU* 3.1 23.5 + - + +
431C ARG* 1.3 75.3 - - - +
433C PHE* 1.3 91.5 - - + +
436C PHE* 2.8 40.1 + - + +
439C THR* 3.9 25.6 - - + +
443C PHE* 5.0 1.3 - - + -
497C ASN 4.7 1.8 - - - +
500C LEU 4.1 9.2 - - - +
501C LEU* 3.8 30.5 - - + -
504C SER* 3.4 18.4 - - - +
543C HEM 4.6 13.5 - - + -
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Residues in contact with PHE 433 (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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429C LEU* 3.0 37.6 + - + +
430C GLU* 3.6 8.3 - - + +
432C MET* 1.3 98.6 - - + +
434C LEU* 1.3 61.9 - - + +
437C PRO* 3.4 23.9 - - - +
439C THR* 3.5 18.8 - - - -
440C LYS* 3.5 35.4 - - + -
443C PHE* 3.7 42.2 - + - -
446C PHE* 5.5 1.8 - + - -
448C LEU* 3.8 31.9 - - + +
455C VAL* 4.2 14.6 - - + -
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Residues in contact with LEU 434 (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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430C GLU* 3.0 30.6 + - + +
431C ARG 4.2 2.7 - - - +
433C PHE* 1.3 78.2 - - + +
435C SER* 1.3 64.1 + - - +
437C PRO* 3.7 11.7 - - - +
440C LYS* 5.3 7.0 - - - +
724D PRO* 3.7 33.0 - - + +
725D VAL* 3.8 26.9 - - + -
728D ALA* 3.8 20.7 - - + +
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Residues in contact with SER 435 (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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431C ARG 2.9 20.1 + - - -
434C LEU* 1.3 77.1 - - - +
436C PHE* 1.3 82.7 + - - +
437C PRO* 3.4 6.7 - - - +
724D PRO 4.6 1.6 + - - -
727D GLN* 3.5 18.4 + - - -
728D ALA* 3.5 23.4 + - - +
731D GLN* 3.7 23.0 - - - +
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Residues in contact with PHE 436 (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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432C MET* 2.8 22.8 + - + +
433C PHE 3.7 0.6 - - - +
435C SER* 1.3 97.2 - - - +
437C PRO* 1.3 56.6 - - - +
438C THR* 3.0 9.7 + - - +
439C THR* 2.7 32.8 + - + -
500C LEU* 3.9 60.3 - - + -
503C HIS* 4.0 20.9 - + - -
504C SER* 4.1 5.2 - - - -
708D ASN* 5.3 2.9 - - - -
727D GLN* 5.3 0.7 - - - -
731D GLN* 3.5 31.2 - - + -
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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