Contacts of the helix formed by residues 448 - 464 (chain B) in PDB entry 4Y5U
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 TRP 448 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446B VAL 3.7 1.6 + - - -
447B PRO* 1.3 71.4 - - - +
449B GLU* 1.3 56.8 + - - +
450B LYS 3.4 0.2 - - - -
451B MET* 3.2 27.8 + - + +
452B CYS* 3.0 49.8 + - - -
455B LEU* 4.8 6.7 - - + -
474B PHE* 3.8 7.7 + - - +
477B LEU* 4.1 13.0 - - + -
478B ALA* 3.6 39.6 - - + +
481B ILE* 3.9 27.1 - - + -
482B PHE* 4.0 15.3 - + + -
492B PHE* 3.2 25.8 + - - +
493B GLN* 5.3 1.8 - - - +
495B ARG 3.1 22.9 + - - +
497B VAL* 3.6 22.7 - - + -
514B PHE* 4.6 9.2 - + - -
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Residues in contact with GLU 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B PRO* 4.4 7.4 - - + +
448B TRP* 1.3 80.7 - - - +
450B LYS* 1.3 60.1 + - + +
451B MET 3.4 0.2 - - - -
452B CYS* 3.7 8.7 + - + +
453B GLU* 3.6 21.1 + - - +
493B GLN* 4.2 23.3 + - + +
494B HIS* 4.6 10.7 + - - -
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Residues in contact with LYS 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B PHE* 3.9 18.5 - - + -
447B PRO* 3.3 37.3 + - + +
449B GLU* 1.3 75.6 - - + +
451B MET* 1.3 63.2 + - - +
452B CYS 3.4 0.2 - - - -
453B GLU* 3.3 32.0 - - - +
454B THR* 3.4 14.6 + - - -
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Residues in contact with MET 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B LEU* 4.9 3.1 - - + -
428B TRP* 3.3 39.3 - - + -
432B PHE* 3.8 19.9 - - + -
446B VAL* 4.9 0.2 - - + -
447B PRO 3.2 2.3 + - - +
448B TRP* 3.2 32.7 + - + +
450B LYS* 1.3 78.6 - - - +
452B CYS* 1.3 61.7 + - - +
453B GLU 3.2 0.2 - - - -
454B THR* 3.2 6.5 + - - -
455B LEU* 3.1 39.9 + - + +
497B VAL* 3.8 22.4 - - + -
502B PHE* 3.6 34.3 - - + -
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Residues in contact with CYS 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B TRP* 3.0 61.1 + - - +
449B GLU* 3.8 9.6 - - + +
451B MET* 1.3 75.1 - - - +
453B GLU* 1.3 61.4 + - - +
455B LEU* 3.8 6.1 - - - +
456B ASN* 3.2 16.8 + - - +
474B PHE* 3.2 54.3 - - + -
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Residues in contact with GLU 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B LEU* 5.7 5.2 - - - +
449B GLU 3.6 10.0 + - - +
450B LYS* 3.3 38.0 - - - +
452B CYS* 1.3 76.7 - - - +
454B THR* 1.3 67.9 + - - +
455B LEU 3.1 0.2 - - - -
456B ASN* 3.4 7.3 + - - +
457B LEU* 3.1 42.6 + - + +
474B PHE* 5.4 0.4 - - - -
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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
----------------------------------------------------------
210B LEU* 5.5 3.8 - - - +
213B ASN* 4.1 12.4 + - - +
427B LEU* 3.7 30.0 - - + +
431B ALA* 3.3 28.6 - - + +
432B PHE* 4.3 5.5 - - + -
450B LYS 3.4 15.5 + - - -
451B MET* 3.2 11.8 + - - +
453B GLU* 1.3 85.0 + - - +
455B LEU* 1.3 59.3 + - + +
457B LEU* 3.7 8.7 + - - +
458B LYS* 3.2 24.3 + - - +
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Residues in contact with LEU 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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427B LEU* 5.3 5.4 - - + -
448B TRP* 4.8 7.4 - - + -
451B MET* 3.1 37.0 + - - +
452B CYS* 3.8 11.7 - - - +
453B GLU 3.1 0.2 - - - -
454B THR* 1.3 77.2 - - - +
456B ASN* 1.3 58.5 + - - +
457B LEU 3.3 0.2 - - - -
458B LYS* 3.4 6.2 + - + +
459B PHE* 3.1 29.5 + - - +
469B LEU* 3.9 6.0 - - + +
474B PHE* 5.4 0.4 - - + -
477B LEU* 4.4 11.4 - - + -
502B PHE* 4.5 14.6 - - + -
514B PHE* 4.4 17.5 - - + -
515B TRP* 5.1 4.0 - - + -
518B PHE* 3.6 46.2 - - + -
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Residues in contact with ASN 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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452B CYS 3.2 17.8 + - - +
453B GLU* 3.4 8.6 + - - +
455B LEU* 1.3 74.0 - - - +
457B LEU* 1.3 67.2 + - - +
459B PHE* 3.6 2.2 + - - +
460B MET* 3.3 40.0 + - - +
468B GLY* 3.3 8.1 - - - -
469B LEU* 2.8 44.4 + - + +
474B PHE* 4.1 10.1 - - + -
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Residues in contact with LEU 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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210B LEU* 6.4 1.6 - - + -
213B ASN* 3.8 6.6 - - + +
214B GLY 3.7 24.6 - - - +
215B ALA* 4.2 19.3 - - + +
216B PRO* 4.5 13.7 - - + -
453B GLU* 3.1 33.1 + - + +
454B THR* 3.9 6.7 - - - +
455B LEU 3.3 0.2 - - - -
456B ASN* 1.3 82.8 - - - +
458B LYS* 1.3 58.5 - - - +
460B MET* 3.6 23.0 - - + +
461B ALA* 3.3 23.2 + - - +
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Residues in contact with LYS 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B GLY 4.9 4.6 + - - -
213B ASN* 3.8 25.6 + - - +
423B LYS* 6.3 3.1 - - - -
427B LEU* 3.5 30.9 - - + +
454B THR 3.2 18.6 + - - +
455B LEU* 3.5 10.3 - - + +
457B LEU* 1.3 75.4 - - - +
459B PHE* 1.3 57.8 + - - +
461B ALA* 3.4 3.7 + - - +
462B GLU* 3.0 69.2 + - - +
515B TRP* 4.7 11.7 - - + -
518B PHE* 4.8 6.1 - - + -
522B LEU* 4.4 13.7 - - + -
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Residues in contact with PHE 459 (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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455B LEU 3.1 16.7 + - - +
456B ASN 4.0 4.0 - - - +
457B LEU 3.4 0.2 - - - -
458B LYS* 1.3 73.6 - - - +
460B MET* 1.3 63.9 + - + +
463B VAL* 3.1 34.7 + - + +
465B THR* 4.0 7.2 - - + -
467B ARG 4.4 4.0 - - - -
468B GLY* 5.2 0.4 - - - -
469B LEU* 3.9 24.0 - - + -
518B PHE* 4.5 7.2 - + + -
521B VAL* 4.4 13.7 - - + -
522B LEU* 3.6 22.9 - - + -
525B THR* 3.9 16.6 - - + -
533B TRP* 3.4 49.8 - + - -
541B PHE* 4.2 22.0 - + - -
563B PHE* 5.0 0.9 - + - -
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Residues in contact with MET 460 (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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214B GLY 5.8 0.9 - - - +
456B ASN* 3.3 29.9 + - - +
457B LEU* 3.6 30.3 - - + +
459B PHE* 1.3 79.7 - - - +
461B ALA* 1.3 60.4 + - - +
464B GLY* 3.3 3.6 + - - -
465B THR* 3.2 43.1 + - - +
466B ASN* 4.0 17.0 - - - +
467B ARG 3.8 13.7 - - - +
468B GLY* 4.0 18.4 - - - -
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Residues in contact with ALA 461 (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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213B ASN 4.5 1.1 - - - +
214B GLY* 3.8 23.8 + - - +
457B LEU 3.3 16.8 + - - +
458B LYS* 3.7 7.2 - - - +
460B MET* 1.3 79.4 - - - +
462B GLU* 1.3 71.4 + - + +
464B GLY* 3.9 5.4 + - - -
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Residues in contact with GLU 462 (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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423B LYS* 5.2 8.3 + - - -
458B LYS* 3.0 49.9 + - - +
461B ALA* 1.3 80.5 - - - +
463B VAL* 1.3 67.8 + - + +
464B GLY 3.2 0.4 + - - -
522B LEU* 4.1 26.8 - - + +
526B LYS* 3.2 40.4 + - - +
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Residues in contact with VAL 463 (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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459B PHE* 3.1 32.2 + - + +
462B GLU* 1.3 79.8 - - - +
464B GLY* 1.3 55.9 + - - +
465B THR* 3.7 19.5 - - + -
522B LEU* 3.6 32.5 - - + +
525B THR* 3.5 40.8 - - + +
526B LYS* 4.0 11.2 - - - +
530B ARG* 3.4 28.6 + - + +
533B TRP* 4.9 1.3 - - + -
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Residues in contact with GLY 464 (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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460B MET 3.3 9.9 + - - -
461B ALA 3.9 5.1 + - - -
462B GLU 3.2 3.8 - - - -
463B VAL* 1.3 80.2 - - - +
465B THR* 1.3 59.7 + - - +
466B ASN* 5.7 0.8 + - - -
530B ARG* 2.9 35.1 + - - +
534B SER* 5.3 0.2 + - - -
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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