Contacts of the helix formed by residues 448 - 463 (chain C) in PDB entry 5I94
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 SER 448 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297C ASN* 3.0 24.4 + - - -
445C ARG* 3.4 17.0 - - - +
447C LEU* 1.3 77.4 - - - +
449C PRO* 1.3 73.6 - - - +
450C GLU* 3.4 14.6 + - - +
451C ALA* 2.9 25.2 + - - +
452C VAL* 3.1 18.5 + - - +
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Residues in contact with PRO 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C GLY* 4.2 14.4 - - - +
438C PHE* 6.2 2.2 - - + -
445C ARG* 3.7 13.7 - - + +
447C LEU 4.2 1.3 - - - +
448C SER* 1.3 86.9 - - - +
450C GLU* 1.3 62.3 + - - +
452C VAL* 3.1 4.3 + - + +
453C ARG* 2.9 34.0 + - - +
534D HIS* 4.4 18.2 - - + +
535D PHE* 5.0 2.7 - - - -
536D ALA* 3.9 33.9 - - + +
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Residues in contact with GLU 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C VAL* 3.9 9.2 - - + +
300C GLY* 3.7 16.6 - - - -
301C THR* 3.0 40.7 + - - +
448C SER* 3.5 9.0 + - - +
449C PRO* 1.3 80.1 - - - +
451C ALA* 1.3 62.0 + - - +
453C ARG* 3.7 25.1 - - - +
454C ASN* 3.0 28.1 + - - +
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Residues in contact with ALA 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C TYR* 5.0 0.2 - - - -
293C ALA* 3.5 26.5 - - - +
296C VAL* 3.6 12.9 - - - +
297C ASN* 3.7 17.9 - - + +
447C LEU* 4.2 7.4 - - + -
448C SER* 2.9 23.5 + - - +
450C GLU* 1.3 75.8 - - - +
452C VAL* 1.3 55.7 + - - +
454C ASN* 3.6 1.9 - - - +
455C THR* 2.6 34.7 + - - -
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Residues in contact with VAL 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433C LEU* 3.2 44.6 - - + +
436C GLY* 3.9 8.1 - - - -
437C GLY* 3.6 31.2 - - - +
447C LEU* 3.6 19.5 - - + -
448C SER 3.2 14.1 - - - +
449C PRO* 3.1 6.7 + - + +
451C ALA* 1.3 73.1 - - - +
453C ARG* 1.3 66.9 - - - +
455C THR* 3.3 5.2 + - - -
456C LEU* 3.1 29.7 + - + +
529D TYR 5.6 0.9 - - - +
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Residues in contact with ARG 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449C PRO* 2.9 23.4 + - - +
450C GLU* 3.7 32.8 - - - +
452C VAL* 1.3 73.5 - - - +
454C ASN* 1.3 75.2 + - - +
455C THR 3.1 0.3 + - - -
456C LEU* 3.2 4.9 + - - +
457C SER* 2.9 25.8 + - - +
473D PHE 5.4 2.9 + - - +
474D HIS 5.7 0.6 + - - -
527D HIS* 3.6 42.6 - - + +
529D TYR* 3.7 21.9 + - - +
530D ASP* 3.0 27.8 + - - +
538D LYS* 3.4 19.6 - - - +
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Residues in contact with ASN 454 (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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292C TYR* 3.3 20.1 + - + +
296C VAL* 4.4 6.0 - - + +
301C THR* 3.4 30.6 + - - +
305C HIS* 4.1 0.3 + - - -
450C GLU* 3.0 26.1 + - - +
451C ALA* 3.6 7.4 - - - +
453C ARG* 1.3 91.1 - - - +
455C THR* 1.3 61.9 + - - +
457C SER* 3.3 6.7 + - - -
458C LEU* 3.3 26.9 + - - +
473D PHE* 3.0 34.5 + - - -
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Residues in contact with THR 455 (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 PRO* 3.4 43.3 - - + +
292C TYR* 3.6 17.5 - - + -
293C ALA* 3.5 17.3 - - + +
332C MET* 4.4 1.1 - - + +
433C LEU* 4.9 11.0 - - + -
451C ALA 2.6 21.9 + - - -
452C VAL* 3.7 6.5 - - - -
453C ARG 3.1 1.8 - - - -
454C ASN* 1.3 76.7 - - - +
456C LEU* 1.3 58.1 + - - +
458C LEU* 3.2 4.8 + - - +
459C MET* 2.9 38.6 + - - +
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Residues in contact with LEU 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433C LEU* 3.6 32.8 - - + +
452C VAL* 3.1 22.0 + - + +
453C ARG 3.7 2.7 - - - +
455C THR* 1.3 72.3 - - - +
457C SER* 1.3 65.4 + - - +
459C MET* 4.3 8.7 - - - -
460C HIS* 3.1 22.7 + - - +
478C PRO* 3.8 13.3 - - + +
490C VAL* 3.7 42.0 - - + -
492C PRO* 4.6 8.1 - - + -
529D TYR* 3.5 41.8 - - + +
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Residues in contact with SER 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453C ARG* 2.9 17.8 + - - +
454C ASN* 3.4 11.5 + - - -
455C THR 3.2 0.4 - - - -
456C LEU* 1.3 75.8 - - - +
458C LEU* 1.3 60.7 + - - +
460C HIS* 3.2 21.1 - - - +
461C SER* 3.5 9.1 + - - -
472D ALA 5.0 2.7 - - - -
473D PHE* 4.2 25.7 + - - -
527D HIS* 3.2 29.1 + - - -
529D TYR* 3.7 10.8 - - - -
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Residues in contact with LEU 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C TYR* 3.5 42.6 - - + +
305C HIS* 4.7 1.8 - - + -
310C LYS* 3.8 31.9 - - - +
311C GLU 4.7 0.4 - - - +
330C ASN* 4.8 0.4 - - + -
331C PRO* 3.6 23.8 - - + -
332C MET* 3.9 16.2 - - + +
454C ASN 3.3 6.9 + - - +
455C THR 3.2 6.0 + - - +
457C SER* 1.3 74.7 - - - +
459C MET* 1.3 62.7 + - - +
460C HIS 3.2 1.3 - - - -
461C SER* 4.0 4.5 - - - +
462C CYS* 2.9 42.9 + - - +
473D PHE* 3.8 19.1 - - + -
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Residues in contact with MET 459 (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 PRO* 3.7 29.4 - - + -
332C MET* 4.2 7.0 - - + -
433C LEU* 4.4 6.1 - - - -
455C THR* 2.9 29.5 + - - +
456C LEU* 4.1 17.0 - - - +
458C LEU* 1.3 74.2 - - - +
460C HIS* 1.3 67.7 + - - +
463C GLY* 3.4 15.0 + - - -
464C MET* 5.5 1.7 - - - +
471C PHE* 5.8 0.9 - - - -
477C LEU 4.8 0.7 - - - +
478C PRO* 4.0 7.2 - - + +
479C ALA* 3.3 57.2 + - - +
480C LYS* 3.7 11.4 - - + +
488C LEU* 3.7 18.4 - - + +
490C VAL* 4.5 8.1 - - + -
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Residues in contact with HIS 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456C LEU 3.1 9.9 + - - +
457C SER 3.2 14.4 - - - +
459C MET* 1.3 80.2 - - - +
461C SER* 1.3 69.3 + - - +
463C GLY 4.8 0.9 + - - -
468C SER* 4.3 4.0 - - - +
471C PHE* 5.3 3.5 - - - -
472C ALA* 3.8 44.1 + - + +
476C GLY* 4.7 14.2 - - - -
477C LEU 4.7 5.9 + - - +
478C PRO* 4.0 8.9 - - - +
527C HIS* 6.5 0.2 - + - -
528C ASN* 4.6 10.8 - - - -
529C TYR* 5.1 5.6 - + - -
460D HIS* 3.3 40.0 - + - -
461D SER* 5.9 1.1 - - - -
529D TYR* 2.7 31.1 + + + +
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Residues in contact with SER 461 (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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310C LYS 5.6 0.5 + - - -
312C PRO* 3.6 33.9 - - - +
457C SER 3.5 10.7 + - - -
458C LEU* 3.3 6.1 + - - +
459C MET 3.3 0.2 - - - -
460C HIS* 1.3 90.4 - - - +
462C CYS* 1.3 73.0 + - - +
463C GLY 3.7 0.7 - - - -
468C SER* 3.1 20.6 - - - -
469C GLY* 5.7 0.3 - - - -
472C ALA* 5.3 3.6 - - - -
461D SER* 6.4 1.6 - - - -
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Residues in contact with CYS 462 (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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311C GLU 3.9 2.5 - - - -
312C PRO* 3.7 19.1 - - + -
330C ASN* 3.3 32.3 - - - +
332C MET* 3.2 32.1 - - + +
333C VAL* 5.3 3.6 - - + +
458C LEU* 2.9 19.3 + - - +
461C SER* 1.3 94.7 - - - +
463C GLY* 1.3 60.4 + - - +
464C MET 3.7 0.2 + - - -
465C TYR* 4.4 4.0 + - - -
468C SER* 3.3 11.2 + - - -
480C LYS* 4.8 0.5 + - - -
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Residues in contact with GLY 463 (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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332C MET* 4.9 0.2 - - - -
459C MET* 3.4 13.5 + - - -
460C HIS 4.8 0.4 + - - -
461C SER 3.7 0.2 - - - -
462C CYS* 1.3 80.7 - - - +
464C MET* 1.3 64.5 + - - +
465C TYR 3.5 1.1 + - - -
468C SER* 3.2 2.8 + - - -
479C ALA 3.4 18.8 - - - -
480C LYS* 3.1 35.9 + - - +
481C SER* 3.4 9.2 + - - -
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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