Contacts of the helix formed by residues 449 - 464 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297A VAL 4.8 0.5 + - - -
298A ASN* 2.9 25.6 + - - -
446A ARG* 3.6 16.7 - - - +
448A LEU* 1.3 75.9 - - - +
450A PRO* 1.3 72.7 - - - +
451A GLU* 3.9 12.4 + - - +
452A ALA* 3.2 29.3 + - - +
453A VAL* 3.2 11.8 + - - +
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Residues in contact with PRO 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A GOL 2.7 29.2 + - - +
437A GLY 4.5 12.6 - - - +
439A PHE* 6.0 3.6 - - + -
446A ARG* 4.3 9.2 - - - +
448A LEU 4.1 3.4 - - - +
449A SER* 1.3 87.0 - - - +
451A GLU* 1.3 56.6 + - - +
453A VAL* 3.5 1.0 + - + -
454A ARG* 3.0 30.4 + - - +
535C HIS* 4.8 3.4 - - + +
536C PHE* 4.7 8.7 - - - +
537C ALA* 3.9 36.3 - - + +
539C LYS* 4.9 3.4 - - - +
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Residues in contact with GLU 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A VAL* 3.9 9.0 - - + +
301A GLY* 4.1 7.8 - - - -
302A THR* 2.7 44.6 + - - +
449A SER* 3.2 11.0 + - - +
450A PRO* 1.3 77.0 - - - +
452A ALA* 1.3 65.2 + - - +
454A ARG* 3.4 24.6 + - - +
455A ASN* 3.1 31.1 + - - +
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Residues in contact with ALA 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A TYR* 4.7 0.7 - - - -
294A ALA* 3.5 29.3 - - - +
297A VAL* 3.6 12.1 - - + +
298A ASN* 3.6 14.8 - - + +
448A LEU* 4.6 5.2 - - + -
449A SER* 3.2 23.9 + - - +
451A GLU* 1.3 79.2 - - - +
453A VAL* 1.3 62.0 + - - +
455A ASN* 3.8 2.4 - - - +
456A THR* 2.8 29.8 + - - -
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Residues in contact with VAL 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A GOL 3.1 31.2 - - - +
434A LEU* 3.2 33.9 - - + +
437A GLY* 4.0 2.7 - - - -
438A GLY* 3.6 26.7 - - - +
448A LEU* 3.7 19.5 - - + -
449A SER 3.2 12.7 + - - +
450A PRO 3.8 4.0 - - - +
452A ALA* 1.3 73.8 - - - +
454A ARG* 1.3 63.1 + - - +
456A THR* 3.4 5.0 + - - -
457A LEU* 3.0 27.0 + - + +
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Residues in contact with ARG 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A GOL 3.5 3.8 + - - +
450A PRO* 3.0 28.0 + - - +
451A GLU* 3.4 27.7 + - - +
453A VAL* 1.3 75.0 - - - +
455A ASN* 1.3 69.7 + - - +
457A LEU* 3.4 2.6 + - - +
458A SER* 2.9 27.1 + - - +
474C PHE 5.6 0.8 + - - +
475C HIS 5.5 0.2 + - - -
522C VAL* 6.1 0.6 - - - +
528C HIS* 3.5 45.4 + - + +
530C TYR* 3.1 25.7 - - - +
531C ASP* 3.0 25.6 + - - -
539C LYS* 3.5 19.8 - - - +
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Residues in contact with ASN 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A TYR* 3.3 28.3 + - + +
297A VAL* 3.6 14.8 - - - +
302A THR* 2.9 35.2 + - - +
451A GLU* 3.1 16.0 + - - +
452A ALA* 3.8 2.5 - - - +
454A ARG* 1.3 89.4 + - - +
456A THR* 1.3 61.7 + - - +
458A SER* 3.3 5.2 + - - -
459A LEU* 3.1 28.4 + - - +
474C PHE* 3.5 26.3 - - + +
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Residues in contact with THR 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A PRO* 3.4 38.4 - - + +
293A TYR* 3.3 22.5 - - + -
294A ALA* 3.5 12.7 - - - +
333A MET* 4.9 1.0 - - + +
434A LEU* 4.5 16.2 - - + -
452A ALA 2.8 20.9 + - - -
453A VAL* 3.7 6.5 - - - -
454A ARG 3.3 0.4 - - - -
455A ASN* 1.3 74.6 - - - +
457A LEU* 1.3 58.4 + - - +
459A LEU* 3.4 3.5 + - - +
460A MET* 2.9 41.0 + - - +
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Residues in contact with LEU 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A GOL 3.4 28.7 - - - +
434A LEU* 3.6 26.9 - - + +
453A VAL* 3.0 17.9 + - + +
456A THR* 1.3 74.7 - - - +
458A SER* 1.3 56.4 + - - +
460A MET* 4.2 8.7 - - - -
461A HIS* 2.8 30.8 + - - +
479A PRO* 3.5 15.3 - - + +
491A VAL* 3.7 35.2 - - + -
493A PRO* 4.4 9.9 - - + -
530C TYR* 3.5 33.4 - - + -
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Residues in contact with SER 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A ARG 2.9 17.1 + - - -
455A ASN* 3.3 9.2 + - - -
457A LEU* 1.3 74.8 - - - +
459A LEU* 1.3 62.2 + - - +
461A HIS* 3.5 12.5 - - - +
462A SER* 3.3 14.7 + - - -
461C HIS* 5.8 1.5 - - - -
473C ALA 4.9 2.9 - - - -
474C PHE* 4.1 27.2 + - - -
528C HIS* 3.5 25.1 + - - -
530C TYR* 3.6 13.2 - - - -
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Residues in contact with LEU 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A TYR* 3.5 42.6 - - + +
306A HIS* 4.5 2.2 - - + -
311A LYS* 3.4 37.5 - - - +
331A ASN* 4.7 4.3 - - + -
332A PRO* 3.8 24.5 - - + -
333A MET* 4.0 18.8 - - + +
455A ASN 3.1 9.6 + - - +
456A THR 3.9 3.1 - - - +
458A SER* 1.3 74.0 - - - +
460A MET* 1.3 62.6 + - - +
461A HIS 3.2 0.2 - - - -
462A SER* 3.3 6.0 + - - +
463A CYS* 2.9 36.6 + - + +
474C PHE* 4.1 13.9 - - + -
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Residues in contact with MET 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A PRO* 3.6 32.3 - - + -
333A MET* 4.6 4.9 - - - +
434A LEU* 4.2 9.6 - - + -
456A THR* 2.9 31.0 + - - +
457A LEU* 3.7 9.0 - - - +
459A LEU* 1.3 77.0 - - - +
461A HIS* 1.3 60.6 + - - +
464A GLY* 3.2 19.8 + - - +
465A MET* 5.6 0.9 - - - +
478A LEU 5.1 0.2 - - - +
479A PRO* 3.9 7.6 - - + +
480A ALA* 3.3 50.1 + - - +
481A LYS* 3.9 10.3 - - + +
489A LEU* 4.0 15.5 - - + +
491A VAL* 4.2 15.7 - - + -
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Residues in contact with HIS 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457A LEU 2.8 17.8 + - - +
458A SER 3.5 7.2 - - - +
460A MET* 1.3 77.4 - - - +
462A SER* 1.3 67.9 + - - +
464A GLY 4.9 0.2 + - - -
469A SER* 4.5 2.9 - - - +
472A PHE* 5.8 2.8 - - - -
473A ALA* 3.7 41.9 + - + +
477A GLY* 5.1 5.8 - - - -
478A LEU 4.8 3.8 - - - +
479A PRO* 3.9 12.1 - - + +
529A ASN* 4.6 14.9 - - + -
530A TYR* 5.0 5.2 - + - -
458C SER 5.8 0.6 + - - -
461C HIS* 3.3 38.6 + + - -
462C SER* 5.8 2.0 - - - -
530C TYR* 2.8 30.6 + + + +
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Residues in contact with SER 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A LYS 5.0 1.0 + - - -
313A PRO* 3.9 36.4 - - - +
458A SER 3.3 14.3 + - - -
459A LEU* 3.3 10.2 + - - +
461A HIS* 1.3 90.1 - - - +
463A CYS* 1.3 65.0 + - - +
464A GLY 3.7 0.9 - - - -
469A SER* 3.2 19.7 - - - -
470A GLY* 5.6 0.2 - - - -
473A ALA* 5.3 2.2 - - - -
461C HIS* 5.7 2.2 - - - -
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Residues in contact with CYS 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A GLU 5.5 0.2 - - - -
313A PRO* 4.5 11.0 - - + -
314A SER* 5.4 1.1 - - - -
331A ASN* 3.0 44.0 - - + +
333A MET* 3.3 19.1 - - + +
334A VAL* 4.4 9.6 - - - -
459A LEU* 2.9 14.9 + - + +
462A SER* 1.3 86.5 - - - +
464A GLY* 1.3 58.4 + - - +
465A MET 3.7 0.3 + - - -
466A TYR* 4.7 4.9 + - - -
469A SER* 3.4 9.6 + - - -
481A LYS* 4.8 1.4 + - - -
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Residues in contact with GLY 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A MET* 4.8 0.4 - - - -
460A MET* 3.2 14.0 + - - -
462A SER 3.7 0.8 - - - -
463A CYS* 1.3 79.7 - - - +
465A MET* 1.3 63.6 + - - +
466A TYR 3.7 1.6 - - - -
469A SER* 3.4 2.0 + - - -
480A ALA 3.2 17.5 - - - -
481A LYS* 3.3 22.3 + - - -
482A SER 3.2 24.1 + - - -
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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
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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