Contacts of the helix formed by residues 441 - 457 (chain B) in PDB entry 5UFL
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 THR 441 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438B LYS 5.8 1.6 - - - +
439B ILE 3.4 9.8 + - - +
440B LEU* 1.3 81.1 - - - +
442B THR* 1.3 64.3 + - - +
443B VAL* 3.4 10.6 + - - +
444B LYS* 3.3 24.4 + - - +
445B CYS* 3.6 21.0 + - - -
493B VAL* 5.1 3.6 - - - -
496B MET* 4.1 2.0 - - - -
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Residues in contact with THR 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B THR* 1.3 73.2 - - - +
443B VAL* 1.3 60.7 + - + +
445B CYS* 3.5 4.0 + - - +
446B THR* 3.1 28.1 + - + +
493B VAL* 3.7 11.0 - - - +
494B PRO 4.2 2.6 + - - -
495B GLY 4.0 3.4 - - - +
496B MET* 3.3 47.5 + - + +
499B SER* 3.5 34.3 - - - +
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Residues in contact with VAL 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B THR* 3.2 10.0 - - - +
442B THR* 1.3 79.2 - - + +
444B LYS* 1.3 55.2 + - - +
446B THR* 2.8 9.1 + - - +
447B THR* 2.7 51.5 + - - +
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Residues in contact with LYS 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B LEU* 3.6 38.0 + - + +
395B ASP* 5.3 0.2 - - - +
397B LEU* 4.3 17.8 + - + +
398B GLN* 3.5 26.5 + - - +
439B ILE 5.9 0.4 - - - +
440B LEU* 3.9 23.6 - - + -
441B THR* 3.3 20.4 + - - +
442B THR 3.5 0.2 - - - -
443B VAL* 1.3 79.0 - - - +
445B CYS* 1.3 56.7 + - - +
447B THR* 4.0 6.4 - - - -
448B LEU* 3.1 27.2 + - - +
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Residues in contact with CYS 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B LEU* 6.5 0.2 - - - -
440B LEU* 3.8 30.5 - - - -
441B THR 3.6 13.4 + - - -
442B THR* 3.5 10.4 + - + +
443B VAL 3.2 0.8 - - - -
444B LYS* 1.3 76.0 - - - +
446B THR* 1.3 59.0 + - + +
448B LEU* 3.3 8.2 + - - +
449B ILE* 3.0 32.5 + - - +
482B THR* 4.0 10.7 - - + +
485B LEU* 5.2 4.7 - - - -
486B ILE* 3.8 34.1 - - + -
489B LEU* 5.5 0.2 - - - -
496B MET* 4.3 7.6 - - + -
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Residues in contact with THR 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B THR* 3.1 15.4 + - + +
443B VAL* 2.8 26.0 + - - +
445B CYS* 1.3 73.7 - - + +
447B THR* 1.3 60.2 + - - +
449B ILE* 3.3 10.1 + - - +
450B GLU* 3.0 34.9 + - - +
486B ILE* 5.8 0.7 - - + -
499B SER* 3.1 28.5 - - - +
503B ILE* 4.0 16.4 - - + -
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Residues in contact with THR 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B VAL* 2.7 40.5 + - - +
444B LYS* 4.0 6.7 - - - -
446B THR* 1.3 73.4 + - - +
448B LEU* 1.3 58.1 + - - +
450B GLU* 3.6 8.3 + - + +
451B GLN* 3.1 43.5 + - + +
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Residues in contact with LEU 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B LEU* 3.9 31.6 - - + +
398B GLN* 4.8 0.4 - - - +
399B PHE* 5.5 0.4 - - + -
416B ILE* 4.0 20.2 - - + -
420B ILE* 4.0 18.2 - - + -
444B LYS 3.1 19.4 + - - +
445B CYS* 3.5 6.1 - - - +
446B THR 3.3 0.2 - - - -
447B THR* 1.3 74.8 - - - +
449B ILE* 1.3 64.2 + - - +
451B GLN* 3.2 13.8 + - + +
452B GLN* 3.0 43.5 + - + +
478B VAL* 4.5 3.1 - - + -
482B THR* 3.5 29.4 - - + +
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Residues in contact with ILE 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B CYS 3.0 22.0 + - - +
446B THR* 3.3 10.7 + - - +
448B LEU* 1.3 74.7 - - + +
450B GLU* 1.3 65.2 + - + +
452B GLN* 3.3 4.7 + - - +
453B PHE* 3.1 50.6 + - + -
479B ILE* 3.6 37.6 - - + +
482B THR* 3.6 27.1 - - + -
483B LEU* 4.4 9.6 - - + -
486B ILE* 4.8 1.6 - - + -
503B ILE* 4.4 25.4 - - + -
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Residues in contact with GLU 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B THR* 3.0 21.5 + - - +
447B THR* 3.8 7.6 - - - +
449B ILE* 1.3 78.7 - - + +
451B GLN* 1.3 57.5 + - + +
453B PHE* 3.4 6.5 + - - +
454B THR* 3.0 38.2 + - - +
506B ASP* 4.6 1.9 - - - +
508B ARG* 3.0 40.6 + - - -
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Residues in contact with GLN 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B LEU 4.8 0.2 - - - +
398B GLN* 3.9 10.6 - - - +
399B PHE* 3.1 54.9 + - + +
447B THR* 3.1 34.9 + - + +
448B LEU* 3.2 14.8 + - + +
450B GLU* 1.3 76.1 - - + +
452B GLN* 1.3 57.6 + - - +
454B THR* 4.6 1.8 - - - -
455B TYR* 2.8 59.0 + - + +
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Residues in contact with GLN 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B PHE* 3.6 12.5 - - - -
413B CYS* 3.4 23.4 - - - -
416B ILE* 3.4 30.9 - - - +
448B LEU* 3.0 23.9 + - + +
449B ILE* 3.7 2.0 - - - +
451B GLN* 1.3 73.2 - - - +
453B PHE* 1.3 60.6 + - - +
456B GLY* 2.9 30.7 + - - +
458B ILE* 4.2 1.6 - - - +
475B ALA* 3.4 20.2 - - - +
478B VAL* 3.6 35.0 - - + +
479B ILE* 3.5 26.2 - - + -
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Residues in contact with PHE 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B ILE* 3.1 44.4 + - + -
450B GLU* 3.4 4.5 + - - +
452B GLN* 1.3 77.2 - - - +
454B THR* 1.3 64.3 + - - +
457B LYS* 3.4 11.3 + - - -
458B ILE* 3.7 21.7 + - + -
459B ASP* 4.3 10.5 - - - +
479B ILE* 3.5 29.8 - - + -
503B ILE* 5.4 4.0 - - + -
506B ASP* 4.1 15.3 - - - -
508B ARG* 3.2 79.4 - - + +
509B LEU* 3.8 10.1 - - + -
512B PRO* 4.4 5.4 - - + -
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Residues in contact with THR 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450B GLU* 3.0 20.7 + - - +
451B GLN* 4.0 4.3 - - - -
453B PHE* 1.3 80.5 - - - +
455B TYR* 1.3 82.8 + - + +
457B LYS* 3.4 16.3 + - - +
508B ARG* 4.4 8.7 + - - +
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Residues in contact with TYR 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B PHE* 4.0 41.5 - + + -
402B GLN* 4.3 26.3 + - - -
409B THR* 4.6 9.9 - - + +
451B GLN* 2.8 55.3 + - + +
454B THR* 1.3 88.1 - - + +
456B GLY* 1.3 63.0 + - - +
457B LYS* 3.5 15.1 + - - +
471B LEU* 4.5 7.6 - - - +
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Residues in contact with GLY 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B PHE* 6.1 0.2 - - - -
452B GLN* 2.9 20.3 + - - +
455B TYR* 1.3 76.3 - - - +
457B LYS* 1.3 71.6 - - - +
458B ILE* 3.4 3.5 + - - -
471B LEU* 3.9 24.8 - - - +
472B CYS* 4.2 12.0 - - - -
475B ALA* 3.8 18.8 - - - -
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Residues in contact with LYS 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406B GLU* 4.8 11.1 + - - +
453B PHE 3.4 7.1 + - - -
454B THR 3.4 16.4 + - - +
455B TYR* 3.2 11.8 - - - +
456B GLY* 1.3 81.9 - - - +
458B ILE* 1.3 67.2 + - - +
459B ASP* 3.8 2.0 - - - -
460B LEU* 3.8 36.9 - - + +
465B LYS* 4.4 0.5 - - - -
471B LEU* 5.4 7.1 - - + +
472B CYS* 3.9 10.4 - - - -
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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