Contacts of the helix formed by residues 433 - 453 (chain T) 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 T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431T GLN 4.1 8.5 - - - +
432T GLN* 1.3 75.9 - - - +
434T VAL* 1.3 66.9 + - - +
435T ASP* 3.2 5.6 - - + +
436T GLN* 3.0 33.0 + - + +
437T MET* 3.2 8.5 + - - +
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Residues in contact with VAL 434 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302T TYR* 4.4 6.5 - - + +
305T PHE* 3.8 22.0 - - + -
306T ARG* 3.4 44.2 - - + +
309T LYS* 4.2 28.5 - - + -
432T GLN 3.9 0.8 + - - +
433T ASP* 1.3 73.1 - - - +
435T ASP* 1.3 56.8 + - - +
437T MET* 3.2 12.3 + - + +
438T PHE* 2.9 27.9 + - - +
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Residues in contact with ASP 435 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302T TYR* 3.1 34.9 + - - -
433T ASP* 3.1 4.7 + - + +
434T VAL* 1.3 77.7 - - - +
436T GLN* 1.3 65.7 + - + +
438T PHE* 3.3 5.7 + - - +
439T TRP* 3.2 36.2 + - + +
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Residues in contact with GLN 436 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431T GLN 4.4 1.9 - - - +
432T GLN* 3.6 25.7 + - + +
433T ASP* 3.0 37.8 + - + +
435T ASP* 1.3 78.8 - - + +
437T MET* 1.3 57.2 + - - +
439T TRP* 3.3 7.8 + - - +
440T GLU* 2.9 27.2 + - - +
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Residues in contact with MET 437 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305T PHE* 4.0 11.4 - - + -
309T LYS* 4.6 17.5 - - + +
420T TYR* 3.5 22.2 - - + +
424T ILE* 3.2 46.0 - - + -
429T VAL* 4.0 15.3 - - + +
432T GLN* 3.7 28.3 - - + +
433T ASP 3.2 9.1 + - - +
434T VAL* 3.2 21.5 + - - +
436T GLN* 1.3 72.6 - - - +
438T PHE* 1.3 65.2 + - - +
440T GLU* 3.1 4.8 - - - +
441T VAL* 3.0 25.8 + - - +
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Residues in contact with PHE 438 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297T ALA* 3.8 25.4 - - + -
298T ASP 4.4 5.2 - - - -
301T LEU* 3.7 29.4 - - + -
302T TYR* 3.8 20.2 - + + -
305T PHE* 3.8 35.8 - + + -
434T VAL 2.9 13.3 + - - +
435T ASP* 3.5 9.0 - - - +
437T MET* 1.3 77.3 - - - +
439T TRP* 1.3 76.2 + + - +
441T VAL* 2.9 12.6 + - + +
442T MET* 2.9 71.3 + - + +
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Residues in contact with TRP 439 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295T LYS* 3.5 63.9 - - + +
296T GLU* 3.6 18.4 - - - -
297T ALA* 3.4 29.1 - - + +
435T ASP* 3.2 29.7 + - + +
436T GLN* 3.3 6.5 + - - +
438T PHE* 1.3 88.3 - + - +
440T GLU* 1.3 60.9 + - - +
442T MET* 3.7 30.2 - - + +
443T GLN* 3.0 27.0 + - - +
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Residues in contact with GLU 440 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420T TYR* 3.3 40.5 + - + -
432T GLN* 3.0 24.3 + - - +
436T GLN 2.9 12.6 + - - +
437T MET* 3.1 15.9 - - - +
439T TRP* 1.3 77.5 - - - +
441T VAL* 1.3 55.0 + - - +
443T GLN* 3.2 7.6 + - - +
444T LEU* 2.8 42.7 + - + +
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Residues in contact with VAL 441 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305T PHE* 3.7 25.8 - - + -
320T PHE* 3.8 28.5 - - + -
417T PHE* 4.2 16.6 - - + -
420T TYR* 4.3 15.3 - - + -
421T ILE* 5.1 3.4 - - + -
424T ILE* 5.0 2.0 - - + -
437T MET 3.1 15.0 - - - +
438T PHE* 2.9 10.7 + - + +
440T GLU* 1.3 77.7 - - - +
442T MET* 1.3 57.6 + - + +
444T LEU* 3.2 9.0 + - - +
445T ARG* 2.8 44.8 + - + +
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Residues in contact with MET 442 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296T GLU 6.0 0.2 - - - +
298T ASP* 4.8 8.1 - - + +
301T LEU* 3.6 29.6 - - + -
438T PHE* 2.9 58.3 + - + +
439T TRP* 3.7 31.0 - - + +
440T GLU 3.2 0.2 - - - -
441T VAL* 1.3 77.0 - - - +
443T GLN* 1.3 55.7 + - - +
445T ARG* 3.3 19.6 + - - +
446T LYS* 2.8 34.2 + - - +
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Residues in contact with GLN 443 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439T TRP 3.0 14.0 + - - +
440T GLU* 3.2 11.4 + - - +
442T MET* 1.3 74.7 - - - +
444T LEU* 1.3 68.4 + - + +
446T LYS* 3.0 35.5 + - - +
447T GLU* 3.1 54.7 + - + +
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Residues in contact with LEU 444 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413T SER 4.7 2.2 - - - +
416T ASN* 3.6 40.8 - - + +
417T PHE* 3.6 26.7 - - + +
420T TYR* 4.3 15.5 - - + -
440T GLU* 2.8 53.0 + - + +
441T VAL* 3.4 9.6 - - - +
443T GLN* 1.3 79.0 - - + +
445T ARG* 1.3 61.8 + - - +
447T GLU* 3.4 17.2 + - + +
448T MET* 3.4 19.9 + - - +
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Residues in contact with ARG 445 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301T LEU* 3.9 34.2 - - - +
320T PHE* 6.1 0.4 - - - -
323T LYS* 4.0 10.4 - - - +
324T ILE* 3.9 25.5 - - + +
327T GLU* 3.2 28.3 + - - +
328T ASP* 2.7 36.7 + - - +
417T PHE* 4.9 1.1 - - + -
441T VAL* 2.8 35.4 + - + +
442T MET* 3.6 17.8 - - - +
444T LEU* 1.3 70.1 - - - +
446T LYS* 1.3 60.7 + - - +
448T MET* 3.3 16.1 + - + +
449T SER* 2.9 35.9 + - - +
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Residues in contact with LYS 446 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442T MET 2.8 20.8 + - - +
443T GLN* 3.0 35.8 + - - +
445T ARG* 1.3 73.0 - - - +
447T GLU* 1.3 63.2 + - - +
449T SER* 3.3 8.0 + - - -
450T LEU* 2.9 58.4 + - + +
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Residues in contact with GLU 447 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409T TYR* 2.3 37.6 + - - -
413T SER* 4.3 17.0 + - - +
443T GLN* 3.1 40.6 + - + +
444T LEU* 3.4 14.1 - - + +
445T ARG 3.1 0.2 - - - -
446T LYS* 1.3 76.2 + - - +
448T MET* 1.3 59.2 + - - +
450T LEU* 3.1 15.3 + - - +
451T ALA* 2.9 30.3 + - - +
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Residues in contact with MET 448 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324T ILE* 4.0 13.0 - - + -
328T ASP* 3.6 40.4 - - + +
329T ILE* 4.0 14.8 - - - -
332T CYS* 3.3 13.7 - - - -
413T SER* 3.8 24.2 - - - +
414T VAL* 4.0 20.4 - - + +
417T PHE* 4.0 28.5 - - + -
444T LEU 3.4 5.3 + - - +
445T ARG* 3.3 20.5 + - + +
447T GLU* 1.3 79.0 - - - +
449T SER* 1.3 54.0 + - - +
451T ALA* 4.6 0.2 - - - -
452T LYS* 2.7 37.7 + - - +
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Residues in contact with SER 449 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328T ASP* 3.7 14.7 + - - -
445T ARG* 2.9 22.0 + - - +
446T LYS* 3.4 10.7 - - - -
448T MET* 1.3 79.3 - - - +
450T LEU* 1.3 60.2 + - - +
452T LYS* 3.5 18.1 + - - +
453T LEU* 3.2 32.7 - - - +
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Residues in contact with LEU 450 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409T TYR* 5.2 4.3 - - + +
446T LYS* 2.9 44.0 + - + +
447T GLU* 3.1 14.5 + - - +
449T SER* 1.3 78.1 - - - +
451T ALA* 1.3 66.0 + - - +
453T LEU* 3.1 12.3 + - + +
455T TYR* 2.9 55.2 + - + +
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Residues in contact with ALA 451 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332T CYS* 4.3 4.3 - - - -
406T PHE* 3.9 9.4 - - - -
409T TYR* 3.7 22.0 - - + -
410T ARG* 3.9 32.9 + - + -
413T SER* 4.3 4.5 - - - +
447T GLU 2.9 16.1 + - - +
448T MET* 3.9 2.5 - - - +
450T LEU* 1.3 75.8 - - - +
452T LYS* 1.3 56.8 + - - +
454T GLY* 2.8 23.6 + - - -
455T TYR 3.3 10.2 + - - -
456T PHE* 5.1 0.9 - - - -
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Residues in contact with LYS 452 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327T GLU* 2.9 30.7 + - - +
328T ASP* 4.3 3.7 + - - +
331T PRO* 3.6 29.6 - - + -
332T CYS* 3.9 11.8 - - - +
406T PHE* 5.5 0.5 - - - -
410T ARG* 3.9 18.3 + - - +
448T MET 2.7 23.3 + - - +
449T SER* 3.5 23.3 + - - +
451T ALA* 1.3 73.0 - - - +
453T LEU* 1.3 76.5 + - + +
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Residues in contact with LEU 453 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449T SER 3.2 18.8 - - - +
450T LEU* 3.1 10.3 + - + +
451T ALA 3.1 0.8 - - - -
452T LYS* 1.3 104.0 - - + +
454T GLY* 1.3 58.9 + - - +
455T TYR* 3.5 25.8 + - + -
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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