Contacts of the helix formed by residues 439 - 456 (chain B) in PDB entry 2XWU
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 GLY 439 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435B TYR* 2.7 47.6 + - - -
436B GLU* 4.4 3.0 + - - -
437B MET 3.6 2.0 - - - -
438B LEU* 1.3 71.2 - - - +
440B ALA* 1.3 64.1 + - - -
441B GLU 3.3 0.9 + - - -
442B LEU* 3.3 9.2 + - - +
443B LEU 4.1 0.2 + - - -
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Residues in contact with ALA 440 (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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435B TYR* 4.2 8.7 + - - +
438B LEU 3.7 0.2 + - - -
439B GLY* 1.3 68.7 - - - -
441B GLU* 1.3 59.8 + - - +
442B LEU 3.0 5.8 - - - -
443B LEU* 3.1 18.6 + - + +
444B SER* 3.3 14.1 + - - -
484B TYR* 3.6 41.9 - - + +
487B VAL* 4.7 5.6 - - + +
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Residues in contact with GLU 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B ARG* 3.7 27.8 - - - +
391B PHE* 3.9 11.5 - - + -
438B LEU 3.6 5.1 + - - +
439B GLY 3.2 1.4 - - - -
440B ALA* 1.3 76.8 - - - +
442B LEU* 1.3 57.3 + - - +
444B SER* 3.6 8.9 + - - +
445B ASN* 3.1 26.3 + - - +
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Residues in contact with LEU 442 (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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391B PHE* 4.5 4.0 - - + -
394B VAL* 3.9 34.1 - - + -
431B LEU* 4.3 2.5 - - + +
434B VAL* 4.1 11.2 - - + +
435B TYR* 3.4 32.3 - - + +
438B LEU* 3.9 14.6 + - + +
439B GLY 3.3 12.4 + - - +
440B ALA 3.0 0.4 - - - -
441B GLU* 1.3 77.0 - - - +
443B LEU* 1.3 67.3 + - + +
445B ASN* 3.3 8.8 + - + +
446B LEU* 3.1 30.4 + - + +
476B ILE* 3.3 33.2 - - + -
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Residues in contact with LEU 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B TYR* 4.1 16.8 - - + +
440B ALA* 3.1 11.7 + - - +
442B LEU* 1.3 82.7 - - + +
444B SER* 1.3 57.0 + - - +
446B LEU* 3.2 23.2 + - + +
447B TYR* 3.0 26.3 + - - +
473B PHE* 4.6 9.0 - - + -
476B ILE* 4.4 12.8 - - + -
480B ILE* 3.4 43.5 - - + -
484B TYR 4.8 10.8 - - - +
487B VAL* 4.0 17.3 - - + +
488B VAL* 4.0 17.3 - - + -
491B LEU* 4.0 8.2 - - + +
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Residues in contact with SER 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B ALA 3.3 9.6 + - - -
441B GLU* 3.9 10.3 - - - -
442B LEU 3.3 0.2 - - - -
443B LEU* 1.3 76.6 - - - +
445B ASN* 1.3 64.0 + - - +
447B TYR* 3.3 4.8 + - - +
448B ASP* 3.1 32.7 + - - +
487B VAL* 3.7 25.6 - - - +
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Residues in contact with ASN 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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391B PHE* 4.3 20.9 + - + -
394B VAL* 4.4 13.3 - - - +
395B ASP* 5.4 1.4 - - - +
441B GLU 3.1 15.2 + - - +
442B LEU* 3.3 14.9 + - - +
444B SER* 1.3 78.2 - - - +
446B LEU* 1.3 63.7 + - - +
448B ASP* 3.5 8.3 + - - +
449B LYS* 3.0 69.1 + - - +
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Residues in contact with LEU 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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394B VAL* 5.0 2.5 - - + -
398B LEU* 4.1 25.8 - - + -
442B LEU* 3.1 24.0 + - + +
443B LEU* 3.4 23.8 - - + +
445B ASN* 1.3 81.7 - - - +
447B TYR* 1.3 66.2 + - - +
449B LYS* 3.1 9.3 + - + +
450B LEU* 2.9 25.7 + - - +
469B LEU* 4.5 13.5 - - + +
472B GLY* 4.2 5.4 - - - +
473B PHE* 4.0 35.7 - - + +
476B ILE* 4.6 11.0 - - + -
491B LEU* 4.4 9.0 - - + -
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Residues in contact with TYR 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B LEU 3.0 13.1 + - - +
444B SER* 3.5 11.9 - - - +
446B LEU* 1.3 76.4 - - - +
448B ASP* 1.3 64.8 + - - +
451B GLY* 2.8 36.4 + - - -
487B VAL* 4.5 9.9 - - + -
490B GLY* 3.2 41.7 + - - -
491B LEU* 3.6 19.2 - - + +
494B LEU* 3.6 29.6 - - + +
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Residues in contact with ASP 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B SER* 3.1 23.9 + - - +
445B ASN* 3.8 7.6 - - - +
447B TYR* 1.3 85.7 - - - +
449B LYS* 1.3 62.0 + - + +
451B GLY* 5.0 0.7 - - - -
452B ARG* 2.9 33.0 + - - +
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Residues in contact with LYS 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B VAL* 4.1 7.9 + - - +
395B ASP* 2.5 49.5 + - - +
398B LEU* 4.9 3.0 - - - +
445B ASN* 3.0 44.2 + - - +
446B LEU* 3.1 12.9 + - + +
448B ASP* 1.3 76.4 - - + +
450B LEU* 1.3 64.5 + - - +
452B ARG* 3.6 4.8 - - - +
453B LEU* 3.1 23.2 + - - +
465B HIS* 5.9 0.2 - - - -
469B LEU* 4.0 29.6 - - + +
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Residues in contact with LEU 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B LEU 2.9 15.9 + - - +
447B TYR* 4.0 2.9 - - - +
449B LYS* 1.3 74.0 - - - +
451B GLY* 1.3 68.7 + - - +
453B LEU* 3.2 6.0 + - + +
454B LEU* 3.0 40.4 + - + +
466B THR* 4.4 21.5 - - + +
469B LEU* 4.1 30.4 - - + +
470B LEU* 4.0 25.1 - - + -
491B LEU* 4.6 12.8 - - + +
494B LEU* 4.1 25.4 - - + -
495B ILE* 5.4 0.4 - - + +
498B ILE* 4.5 7.6 - - + -
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Residues in contact with GLY 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B TYR* 2.8 25.0 + - - -
448B ASP* 3.9 0.9 - - - -
450B LEU* 1.3 73.9 - - - +
452B ARG* 1.3 60.2 + - - +
454B LEU* 3.3 2.6 + - - +
455B THR* 3.0 31.0 + - - +
494B LEU* 3.5 20.8 - - - +
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Residues in contact with ARG 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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448B ASP 2.9 20.3 + - - +
449B LYS* 3.6 5.8 - - - +
451B GLY* 1.3 76.6 - - - +
453B LEU* 1.3 55.5 + - - +
455B THR* 4.1 3.8 - - - -
456B SER* 2.6 44.2 + - - -
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Residues in contact with LEU 453 (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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449B LYS 3.1 12.9 + - - +
450B LEU* 3.7 5.2 - - + +
452B ARG* 1.3 80.7 - - - +
454B LEU* 1.3 74.3 + - + +
455B THR 3.5 0.3 + - - -
456B SER* 4.1 10.4 + - - -
461B TYR* 5.0 21.2 - - + +
465B HIS* 2.8 44.2 - - + +
466B THR* 3.1 31.2 - - + +
469B LEU* 3.6 12.8 - - + -
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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
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450B LEU* 3.0 30.0 + - + +
451B GLY* 3.8 4.5 - - - +
453B LEU* 1.3 91.5 - - + +
455B THR* 1.3 64.9 + - + +
456B SER 5.3 0.2 - - - -
466B THR* 5.0 2.0 - - - +
494B LEU* 3.5 49.6 - - + +
497B ARG* 4.1 21.8 + - + +
498B ILE* 3.9 30.3 - - + -
499B SER 5.4 0.7 - - - +
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Residues in contact with THR 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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451B GLY* 3.0 19.4 + - - +
452B ARG* 3.7 3.3 + - - -
454B LEU* 1.3 78.8 - - + +
456B SER* 1.3 68.0 + - - +
497B ARG* 3.0 36.8 - - - +
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Residues in contact with SER 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B ARG* 2.6 31.4 + - - -
453B LEU* 4.4 8.7 - - - -
455B THR* 1.3 79.5 + - - +
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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
------------------------------------------------------------
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