Contacts of the helix formed by residues 449 - 464 (chain C) in PDB entry 3UO9
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 449 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298C ASN* 2.8 26.1 + - - -
446C ARG* 5.3 3.6 - - - +
448C LEU* 1.3 77.5 - - - +
450C PRO* 1.4 75.0 - - - +
451C GLU* 3.9 12.4 + - - +
452C ALA* 3.1 21.1 + - - +
453C VAL* 3.1 21.1 + - - +
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Residues in contact with PRO 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A HIS* 5.0 4.9 - - + +
536A PHE* 4.9 9.4 - - - +
537A ALA* 4.5 29.4 - - + +
437C GLY* 4.3 16.2 - - - +
446C ARG* 3.8 26.9 - - - +
448C LEU 4.2 1.6 - - - +
449C SER* 1.4 86.6 - - - +
451C GLU* 1.3 56.4 + - - +
453C VAL* 3.8 4.0 - - + +
454C ARG* 2.9 42.4 + - - +
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Residues in contact with GLU 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C VAL* 4.0 10.9 - - + +
301C GLY* 4.1 7.0 - - - -
302C THR* 2.7 45.1 + - - +
303C GLU* 3.9 7.6 - - - +
449C SER* 4.0 9.5 + - - +
450C PRO* 1.3 76.8 - - - +
452C ALA* 1.3 64.7 + - - +
454C ARG* 3.7 25.6 - - - +
455C ASN* 3.0 32.3 + - - +
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Residues in contact with ALA 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C TYR* 4.7 0.5 - - - -
294C ALA* 3.4 28.7 - - - +
297C VAL* 3.6 11.6 - - + +
298C ASN* 3.7 15.5 - - + +
448C LEU* 4.4 4.9 - - + -
449C SER* 3.1 23.4 + - - +
451C GLU* 1.3 78.2 - - - +
453C VAL* 1.3 60.3 + - - +
455C ASN* 3.8 1.7 - - - +
456C THR* 2.7 33.1 + - - -
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Residues in contact with VAL 453 (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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530A TYR 5.4 2.0 - - - +
532A ASN* 6.3 0.2 - - + -
434C LEU* 3.1 38.8 - - + +
437C GLY* 3.9 13.0 - - - -
438C GLY* 3.6 28.5 - - - +
448C LEU* 3.7 18.8 - - + -
449C SER 3.1 15.1 + - - +
450C PRO* 3.9 4.3 - - + +
452C ALA* 1.3 76.4 - - - +
454C ARG* 1.3 62.4 + - - +
456C THR* 3.3 5.3 + - - -
457C LEU* 3.0 32.9 + - + +
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Residues in contact with ARG 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A PHE 5.5 2.1 + - - +
475A HIS 5.7 0.4 + - - -
522A VAL* 6.1 0.4 - - - +
528A HIS* 3.6 41.9 - - + +
530A TYR* 3.7 24.9 + - - +
531A ASP* 3.0 29.0 + - - +
539A LYS* 4.0 17.9 - - - +
450C PRO* 2.9 34.7 + - - +
451C GLU* 3.7 27.7 - - - +
453C VAL* 1.3 72.8 - - - +
455C ASN* 1.3 61.7 + - - +
457C LEU 3.5 0.2 + - - -
458C SER* 2.8 36.1 + - - +
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Residues in contact with ASN 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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474A PHE* 3.5 31.1 - - + +
293C TYR* 3.3 29.5 + - + +
297C VAL* 3.7 10.9 - - - +
302C THR* 2.9 30.0 + - - +
451C GLU* 3.0 22.7 + - - +
452C ALA* 3.8 2.2 - - - +
454C ARG* 1.3 86.9 + - - +
456C THR* 1.3 62.4 + - - +
458C SER* 3.4 4.1 + - - -
459C LEU* 3.1 29.1 + - - +
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Residues in contact with THR 456 (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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290C PRO* 3.5 39.5 - - + +
293C TYR* 3.4 21.0 - - + -
294C ALA* 3.4 16.2 - - + +
333C MET* 4.7 1.0 - - + +
434C LEU* 4.6 12.8 - - + -
452C ALA 2.7 23.0 + - - -
453C VAL* 3.6 6.5 - - - -
454C ARG 3.3 0.2 - - - -
455C ASN* 1.3 76.3 - - - +
457C LEU* 1.3 56.6 + - + +
459C LEU* 3.4 3.2 + - - +
460C MET* 2.9 38.8 + - - +
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Residues in contact with LEU 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A TYR* 3.5 42.6 - - + +
434C LEU* 3.7 30.1 - - + +
435C ALA* 5.3 0.2 - - - -
453C VAL* 3.0 25.1 + - + +
456C THR* 1.3 76.0 - - + +
458C SER* 1.3 55.8 + - - +
460C MET* 3.2 9.5 + - - +
461C HIS* 2.9 30.5 + - - +
479C PRO* 3.6 14.2 - - + +
491C VAL* 3.7 39.3 - - + -
493C PRO* 4.6 8.5 - - + -
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Residues in contact with SER 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A HIS* 5.8 0.7 + - - -
473A ALA 4.9 2.7 - - - -
474A PHE* 4.2 26.7 + - - -
528A HIS* 3.4 25.1 + - - -
530A TYR* 3.5 13.2 - - - -
454C ARG 2.8 23.1 + - - -
455C ASN* 3.4 6.6 + - - -
457C LEU* 1.3 75.1 - - - +
459C LEU* 1.3 62.6 - - - +
461C HIS* 3.4 4.2 + - - +
462C SER* 3.3 22.5 + - - -
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Residues in contact with LEU 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A PHE* 4.0 15.5 - - + -
293C TYR* 3.5 30.1 - - + +
306C HIS* 4.3 3.4 - - + -
311C LYS* 3.4 37.5 - - - +
312C GLU 5.8 0.2 - - - -
331C ASN* 4.7 9.0 - - + -
332C PRO* 3.4 27.4 - - + -
333C MET* 4.0 20.3 - - + +
455C ASN 3.1 10.6 + - - +
456C THR 3.8 3.4 - - - +
458C SER* 1.3 73.6 - - - +
460C MET* 1.3 59.8 + - - +
462C SER* 3.5 7.7 + - - +
463C CYS* 2.9 34.3 + - + +
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Residues in contact with MET 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C PRO* 3.6 32.5 - - + -
333C MET* 4.6 7.0 - - - -
434C LEU* 4.4 7.6 - - + -
456C THR* 2.9 31.1 + - - +
457C LEU* 3.2 14.8 + - - +
459C LEU* 1.3 72.3 - - - +
461C HIS* 1.3 66.8 + - - +
464C GLY* 3.0 26.3 + - - +
465C MET* 5.7 0.5 - - - +
478C LEU 5.2 0.2 - - - +
479C PRO* 3.9 7.2 - - + +
480C ALA* 3.5 45.7 + - - +
481C LYS* 3.8 10.5 - - + +
489C LEU* 4.0 11.0 - - + +
491C VAL* 4.3 13.9 - - + -
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Residues in contact with HIS 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A SER 5.8 1.3 - - - -
461A HIS* 3.3 36.9 + + + +
462A SER* 5.7 2.7 - - - -
530A TYR* 2.9 35.2 - + + +
457C LEU 2.9 10.7 + - - +
458C SER 3.4 10.7 + - - +
460C MET* 1.3 79.6 - - - +
462C SER* 1.3 66.3 + - - +
464C GLY 4.5 0.9 + - - -
469C SER* 4.3 4.3 - - - +
472C PHE* 5.8 2.9 - - - -
473C ALA* 3.9 40.7 + - + +
477C GLY* 5.0 11.4 - - - -
478C LEU 4.8 3.8 - - - +
479C PRO* 4.0 10.2 - - + +
529C ASN* 3.7 19.6 + - - +
530C TYR* 5.0 2.8 - + - -
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Residues in contact with SER 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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461A HIS* 5.8 1.8 - - - -
311C LYS 5.2 0.7 + - - -
313C PRO* 4.0 37.7 - - - +
458C SER 3.3 13.3 + - - -
459C LEU* 3.5 11.8 + - - +
461C HIS* 1.3 87.0 + - - +
463C CYS* 1.3 60.6 + - - +
464C GLY 3.9 0.7 - - - -
469C SER* 3.4 17.6 - - - -
470C GLY* 4.9 1.0 + - - -
473C ALA* 5.5 2.5 - - - -
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Residues in contact with CYS 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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313C PRO* 4.8 8.5 - - + -
331C ASN* 3.2 40.8 - - + +
333C MET* 3.4 21.1 - - + +
334C VAL* 4.3 11.4 - - - -
459C LEU* 2.9 17.1 + - + +
462C SER* 1.3 81.9 - - - +
464C GLY* 1.3 62.7 + - - +
466C TYR* 4.6 5.7 + - - -
469C SER* 3.3 9.9 - - - -
481C LYS* 4.7 1.7 - - - -
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Residues in contact with GLY 464 (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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460C MET* 3.0 13.6 + - - -
461C HIS 4.5 0.4 + - - -
462C SER 3.9 0.6 - - - -
463C CYS* 1.3 78.0 - - - +
465C MET* 1.3 64.3 + - - +
466C TYR 3.5 1.5 + - - -
469C SER* 3.3 1.8 + - - -
480C ALA 3.1 23.1 - - - -
481C LYS* 3.0 35.7 + - - +
482C SER* 3.5 7.6 + - - -
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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