Contacts of the helix formed by residues 433 - 453 (chain Q) in PDB entry 4UJ3
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 ASP 433 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431Q GLN 3.8 6.0 + - - +
432Q GLN* 1.3 75.1 - - - +
434Q VAL* 1.3 67.5 + - - +
435Q ASP* 3.1 8.1 - - + +
436Q GLN* 3.0 32.7 + - + +
437Q MET* 3.1 9.5 + - - +
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Residues in contact with VAL 434 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302Q TYR* 4.1 6.5 - - + +
305Q PHE* 3.9 15.7 - - + -
306Q ARG* 3.1 54.7 - - - +
309Q LYS* 4.3 26.7 - - + -
432Q GLN 3.8 1.3 + - - +
433Q ASP* 1.3 73.2 - - - +
435Q ASP* 1.3 57.4 + - - +
437Q MET* 3.3 9.8 + - + +
438Q PHE* 2.9 26.3 + - - +
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Residues in contact with ASP 435 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302Q TYR* 2.7 37.0 + - - -
433Q ASP* 3.1 5.8 - - + +
434Q VAL* 1.3 78.8 - - - +
436Q GLN* 1.3 63.3 + - + +
438Q PHE* 3.3 6.8 + - - +
439Q TRP* 3.0 38.0 + - + -
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Residues in contact with GLN 436 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P GLU* 4.6 4.4 + - - +
431Q GLN 4.3 2.4 - - - +
432Q GLN* 2.9 30.5 - - - +
433Q ASP* 3.0 35.9 + - + +
435Q ASP* 1.3 79.7 - - + +
437Q MET* 1.3 57.1 + - - +
439Q TRP* 3.2 7.1 + - - +
440Q GLU* 2.8 30.0 + - - +
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Residues in contact with MET 437 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305Q PHE* 3.8 11.9 - - + -
309Q LYS* 4.2 30.1 - - + +
420Q TYR* 3.6 19.5 - - + +
424Q ILE* 3.2 49.6 - - + -
429Q VAL* 3.8 22.0 - - + +
432Q GLN* 3.8 24.5 - - + +
433Q ASP 3.1 10.7 + - - +
434Q VAL* 3.3 12.1 + - - +
436Q GLN* 1.3 76.4 - - - +
438Q PHE* 1.3 62.1 + - - +
440Q GLU* 3.3 3.2 + - - +
441Q VAL* 3.1 27.0 + - - +
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Residues in contact with PHE 438 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297Q ALA* 3.7 25.4 - - + -
298Q ASP 4.5 2.2 - - - -
301Q LEU* 3.8 8.7 - - + -
302Q TYR* 3.6 51.4 - + + -
305Q PHE* 3.5 33.1 - + + -
434Q VAL 2.9 13.5 + - - +
435Q ASP* 3.4 7.4 - - - +
437Q MET* 1.3 77.4 - - - +
439Q TRP* 1.3 75.9 + + - +
441Q VAL* 3.1 9.0 + - + +
442Q MET* 2.9 69.9 + - + +
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Residues in contact with TRP 439 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295Q LYS* 3.7 58.2 - - + +
296Q GLU* 3.6 24.7 - - - -
297Q ALA* 3.3 31.4 - - - +
298Q ASP 5.4 0.2 - - - -
435Q ASP* 3.0 33.4 + - + +
436Q GLN* 3.9 6.3 - - - +
438Q PHE* 1.3 85.4 - + - +
440Q GLU* 1.3 60.8 + - - +
442Q MET* 3.6 29.2 - - + +
443Q GLN* 3.0 36.6 + - - +
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Residues in contact with GLU 440 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420Q TYR* 3.6 34.9 - - + +
432Q GLN* 4.1 14.1 + - - +
436Q GLN 2.8 17.4 + - - +
437Q MET 3.6 5.4 - - - +
438Q PHE 3.2 0.2 - - - -
439Q TRP* 1.3 75.3 - - - +
441Q VAL* 1.3 58.7 + - - +
443Q GLN* 3.3 14.1 + - - +
444Q LEU* 2.8 52.1 + - + +
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Residues in contact with VAL 441 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305Q PHE* 3.7 24.2 - - + -
320Q PHE* 3.8 25.8 - - + -
324Q ILE* 4.5 1.3 - - + -
417Q PHE* 4.2 19.1 - - + -
420Q TYR* 4.0 18.4 - - + -
421Q ILE* 5.1 3.6 - - + -
424Q ILE* 5.0 0.9 - - + -
437Q MET 3.1 15.7 - - - +
438Q PHE* 3.1 8.7 + - + +
440Q GLU* 1.3 75.8 - - - +
442Q MET* 1.3 60.8 + - - +
444Q LEU* 3.2 8.7 + - - +
445Q ARG* 2.9 35.6 + - + +
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Residues in contact with MET 442 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298Q ASP* 4.9 8.3 - - + +
301Q LEU* 3.7 28.7 - - + -
438Q PHE* 2.9 58.8 + - + +
439Q TRP* 3.6 31.2 - - + +
440Q GLU 3.2 0.2 - - - -
441Q VAL* 1.3 76.7 - - - +
443Q GLN* 1.3 54.0 + - - +
445Q ARG* 3.1 20.2 + - - +
446Q LYS* 2.7 34.5 + - - +
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Residues in contact with GLN 443 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295Q LYS* 5.9 3.2 - - - +
439Q TRP* 3.0 28.9 + - - +
440Q GLU* 3.3 14.7 + - - +
442Q MET* 1.3 74.3 - - - +
444Q LEU* 1.3 66.4 + - + +
446Q LYS* 2.9 40.5 + - - +
447Q GLU* 3.0 19.7 + - + +
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Residues in contact with LEU 444 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413Q SER* 4.6 3.6 - - - +
416Q ASN* 3.7 33.4 - - + +
417Q PHE* 3.9 29.2 - - + +
420Q TYR* 4.8 11.2 - - + -
440Q GLU* 2.8 53.1 + - + +
441Q VAL* 3.2 12.8 + - - +
443Q GLN* 1.3 78.3 - - + +
445Q ARG* 1.3 60.6 + - - +
447Q GLU* 3.5 10.7 + - + +
448Q MET* 3.3 27.1 + - - +
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Residues in contact with ARG 445 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301Q LEU* 4.1 27.1 - - - +
323Q LYS* 4.1 15.9 - - - +
324Q ILE* 3.8 29.1 - - + +
327Q GLU* 2.6 35.6 + - - +
328Q ASP* 2.5 32.6 + - - +
417Q PHE* 5.1 1.3 - - + -
441Q VAL* 2.9 27.1 + - + +
442Q MET* 3.5 19.6 - - - +
444Q LEU* 1.3 73.9 - - - +
446Q LYS* 1.3 56.3 + - - +
448Q MET* 3.3 15.4 + - + +
449Q SER* 2.8 41.4 + - - +
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Residues in contact with LYS 446 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442Q MET 2.7 17.1 + - - +
443Q GLN* 2.9 33.7 + - - +
445Q ARG* 1.3 73.2 - - - +
447Q GLU* 1.3 70.7 + - + +
449Q SER* 3.2 8.4 + - - -
450Q LEU* 2.9 46.7 + - + +
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Residues in contact with GLU 447 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409Q TYR* 2.1 38.2 + - - +
413Q SER* 4.1 15.1 + - - +
443Q GLN* 3.0 16.2 + - + +
444Q LEU* 3.7 14.4 - - + +
446Q LYS* 1.3 83.6 + - + +
448Q MET* 1.3 65.7 + - - +
450Q LEU* 3.1 21.5 + - - +
451Q ALA* 3.0 23.7 + - - +
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Residues in contact with MET 448 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324Q ILE* 3.8 15.5 - - + -
328Q ASP* 3.5 34.3 - - + +
329Q ILE* 3.9 22.4 - - - -
332Q CYS* 3.3 18.0 - - - -
413Q SER* 3.7 26.5 - - - +
414Q VAL* 4.0 18.6 - - - +
417Q PHE* 4.2 15.7 - - + -
444Q LEU 3.3 9.4 + - - +
445Q ARG* 3.3 19.9 + - + +
447Q GLU* 1.3 78.6 - - - +
449Q SER* 1.3 56.1 + - - +
451Q ALA* 4.5 0.2 - - - -
452Q LYS* 2.9 32.4 + - - +
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Residues in contact with SER 449 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328Q ASP* 3.7 15.8 + - - -
445Q ARG* 2.8 22.1 + - - +
446Q LYS* 3.4 9.0 - - - -
448Q MET* 1.3 78.0 - - - +
450Q LEU* 1.3 61.0 + - - +
452Q LYS* 3.5 17.4 + - - +
453Q LEU* 3.4 30.8 - - - +
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Residues in contact with LEU 450 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409Q TYR* 4.8 3.4 - - + +
446Q LYS* 2.9 31.4 + - + +
447Q GLU* 3.1 29.6 + - - +
449Q SER* 1.3 76.4 - - - +
451Q ALA* 1.3 58.9 + - - +
453Q LEU* 3.3 4.8 + - - +
454Q GLY 3.2 4.9 + - - -
455Q TYR* 2.8 64.8 + - + +
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Residues in contact with ALA 451 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332Q CYS* 4.1 4.5 - - - -
406Q PHE* 3.7 5.6 - - - -
409Q TYR* 3.8 19.7 - - + -
410Q ARG* 3.6 41.6 + - + -
413Q SER* 4.1 3.8 - - - +
447Q GLU 3.0 14.9 + - - +
448Q MET 3.8 3.1 - - - +
450Q LEU* 1.3 72.7 - - - +
452Q LYS* 1.3 66.7 + - - +
454Q GLY* 2.9 14.5 + - - +
455Q TYR 3.7 9.3 + - - +
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Residues in contact with LYS 452 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327Q GLU* 2.8 31.6 + - - +
328Q ASP* 4.0 10.0 + - - +
331Q PRO* 3.6 26.7 - - + -
332Q CYS* 3.9 9.9 - - - -
406Q PHE* 5.5 0.5 - - - -
410Q ARG* 3.8 20.4 + - - +
448Q MET 2.9 16.8 + - - +
449Q SER* 3.5 20.0 + - - +
451Q ALA* 1.3 76.1 - - - +
453Q LEU* 1.3 79.7 + - + +
454Q GLY 3.6 0.2 + - - -
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Residues in contact with LEU 453 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449Q SER 3.4 14.1 - - - +
450Q LEU* 3.3 7.3 + - - +
451Q ALA 3.1 0.4 - - - -
452Q LYS* 1.3 111.1 - - + +
454Q GLY* 1.3 59.3 + - - +
455Q TYR* 3.6 25.5 + - + -
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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