Contacts of the helix formed by residues 444 - 457 (chain B) in PDB entry 1YUC
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 444 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392B TYR* 3.9 6.6 - - - -
442B GLN 3.2 1.3 + - - +
443B PHE* 1.3 75.8 - - - +
445B GLN* 1.3 60.2 + - - +
446B ARG* 3.0 19.2 + - - +
447B GLU* 2.9 37.4 + - - +
448B PHE* 2.9 27.4 + - - +
484B TYR* 2.5 26.9 + - - -
489B TYR* 2.7 28.2 + - - +
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Residues in contact with GLN 445 (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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309B LEU* 3.9 23.9 - - + +
312B GLU* 4.5 17.3 + - - +
315B GLU* 5.1 8.7 + - - +
392B TYR* 3.1 29.3 + - + +
444B ASP* 1.3 75.1 - - - +
446B ARG* 1.3 84.9 + - - +
448B PHE* 3.2 6.8 + - + +
449B VAL* 3.0 26.8 + - + +
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Residues in contact with ARG 446 (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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301B ILE* 4.3 13.3 - - + +
305B ILE* 3.7 23.8 - - + -
309B LEU* 4.1 20.4 - - + -
444B ASP* 3.0 29.1 + - - +
445B GLN* 1.3 101.3 + - - +
447B GLU* 1.3 59.2 + - - +
449B VAL* 2.9 28.0 - - - +
450B CYS* 3.3 13.2 + - - -
484B TYR* 2.9 43.4 + - + +
489B TYR* 4.7 1.4 + - - -
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Residues in contact with GLU 447 (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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443B PHE* 3.3 20.3 - - + -
444B ASP* 2.9 35.6 + - - +
446B ARG* 1.3 73.6 - - - +
448B PHE* 1.3 65.4 + - - +
450B CYS* 3.4 2.3 + - - +
451B LEU* 3.0 28.6 + - - +
481B LEU* 4.0 15.6 - - + +
484B TYR* 3.6 18.3 - - + -
485B THR* 3.7 4.8 - - + +
489B TYR* 3.3 12.8 - - - -
495B LYS* 2.7 40.9 + - - +
499B LEU* 3.8 15.2 - - + +
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Residues in contact with PHE 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B GLU* 3.8 20.6 - - - -
388B LEU* 3.8 20.2 - - + -
389B ASP* 4.3 17.9 - - + -
392B TYR* 3.4 55.6 - + + -
443B PHE* 3.4 20.1 - + + -
444B ASP 2.9 13.3 + - - +
445B GLN* 3.2 17.5 + - + +
447B GLU* 1.3 77.9 - - - +
449B VAL* 1.3 66.3 + - + +
451B LEU* 3.3 4.3 + - - +
452B LYS* 3.1 56.1 + - + +
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Residues in contact with VAL 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B ILE* 4.5 8.5 - - + -
308B LEU* 4.4 22.4 - - + +
309B LEU* 3.8 17.9 - - + -
312B GLU* 3.7 37.9 - - + +
445B GLN* 3.0 14.3 + - + +
446B ARG* 2.9 29.8 - - - +
448B PHE* 1.3 78.0 - - + +
450B CYS* 1.3 65.6 + - - +
452B LYS* 3.2 10.1 + - - +
453B PHE* 3.1 32.7 + - + -
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Residues in contact with CYS 450 (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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305B ILE* 3.7 31.9 - - - -
308B LEU* 4.7 6.1 - - - -
446B ARG 3.3 14.5 + - - -
447B GLU 3.6 7.9 - - - +
448B PHE 3.3 0.4 - - - -
449B VAL* 1.3 85.1 - - - +
451B LEU* 1.3 63.7 + - - +
453B PHE* 3.1 3.3 + - - -
454B LEU* 2.9 25.3 + - - +
477B VAL* 3.6 24.2 - - + +
480B ALA* 5.2 0.7 - - - -
481B LEU* 3.8 34.8 - - + -
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Residues in contact with LEU 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B LEU* 4.0 19.5 - - + -
438B LEU* 5.5 4.5 - - + -
443B PHE* 3.6 28.5 - - + -
447B GLU* 3.0 20.2 + - + +
448B PHE 3.7 4.3 - - - +
450B CYS* 1.3 75.8 - - - +
452B LYS* 1.3 57.7 + - - +
454B LEU* 3.2 11.1 + - + +
455B VAL* 2.8 34.7 + - - +
481B LEU* 4.3 9.6 - - + -
499B LEU* 4.8 19.7 - - + +
500B LEU* 4.0 27.1 - - + -
502B ARG* 5.6 1.3 - - + -
503B LEU* 4.2 20.8 - - + +
506B ILE* 5.0 4.3 - - + -
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Residues in contact with LYS 452 (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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312B GLU* 2.7 33.7 + - - -
313B PRO* 5.1 2.4 - - - +
359B TRP* 3.4 47.6 - - + +
385B LEU* 4.0 11.0 - - + +
388B LEU* 3.7 20.2 - - + -
389B ASP* 5.9 0.2 + - - -
448B PHE* 3.1 49.5 + - + +
449B VAL* 3.2 10.7 + - - +
451B LEU* 1.3 75.0 - - - +
453B PHE* 1.3 59.0 + - - +
455B VAL* 3.3 2.3 + - - +
456B LEU* 2.9 29.5 + - - +
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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
----------------------------------------------------------
308B LEU* 3.7 47.1 - - + -
311B CYS* 4.2 7.6 - - - -
359B TRP* 3.6 33.7 - + - -
363B SER* 3.3 37.2 - - - -
365B PHE* 4.3 9.0 - + - -
449B VAL* 3.1 26.4 + - + -
450B CYS 3.1 8.1 + - - +
452B LYS* 1.3 78.7 - - - +
454B LEU* 1.3 57.6 + - - +
456B LEU* 4.5 1.6 - - + -
457B PHE* 3.0 59.8 + + + +
473B VAL* 4.4 2.0 - - + +
477B VAL* 4.2 16.4 - - + -
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Residues in contact with LEU 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B CYS 2.9 17.7 + - - +
451B LEU* 3.2 16.8 + - + +
453B PHE* 1.3 78.2 - - - +
455B VAL* 1.3 61.2 + - - +
457B PHE 3.8 5.2 - - - +
458B SER* 4.2 0.7 + - - -
473B VAL* 5.4 0.4 - - + -
474B GLN* 3.0 34.9 - - - +
477B VAL* 3.5 29.6 - - + -
478B ASN* 3.6 32.5 - - - +
481B LEU* 4.4 7.4 - - + -
500B LEU* 3.7 29.2 - - + -
503B LEU* 4.6 6.3 - - + -
5003B GOL 4.0 18.6 - - - +
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Residues in contact with VAL 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B CYS* 3.6 13.7 - - + +
384B GLU* 3.7 37.1 - - + +
385B LEU* 3.6 21.5 - - + +
388B LEU* 4.3 11.4 - - + -
451B LEU 2.8 22.2 + - - +
452B LYS 3.7 4.0 - - - +
454B LEU* 1.3 78.6 - - - +
456B LEU* 1.3 62.6 - - - +
458B SER* 3.9 11.8 - - - -
503B LEU* 3.8 24.0 - - + -
506B ILE* 5.4 5.4 - - + -
5003B GOL 4.1 13.2 + - - +
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Residues in contact with LEU 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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359B TRP* 3.8 27.8 - - + -
360B ALA* 4.0 8.5 - - + -
363B SER* 6.2 0.4 - - - -
366B PHE* 3.8 27.6 - - + -
377B LEU* 3.6 25.3 - - + +
378B LEU* 3.8 21.1 - - + -
380B ASN* 5.4 0.3 - - - +
381B CYS* 3.6 24.2 - - - -
385B LEU* 4.4 2.4 - - + +
452B LYS 2.9 17.2 + - - +
453B PHE* 4.0 3.6 - - + +
455B VAL* 1.3 79.7 - - - +
457B PHE* 1.3 81.8 + - + +
458B SER* 2.9 9.5 + - - -
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Residues in contact with PHE 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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365B PHE* 3.6 8.7 - - + -
366B PHE* 3.5 38.6 - + + -
369B LEU* 3.9 12.8 - - + -
377B LEU* 4.0 12.3 - - + -
453B PHE* 3.0 48.1 + + - +
454B LEU 3.9 1.6 - - - -
456B LEU* 1.3 85.1 - - + +
458B SER* 1.3 56.6 + - - +
469B LEU* 3.7 26.9 - - + -
470B VAL* 3.3 24.3 - - + +
473B VAL* 3.7 30.5 - - + -
474B GLN* 2.7 29.5 - - - +
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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
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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