Contacts of the helix formed by residues 502 - 516 (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 ASN 502 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406B ASP* 4.1 7.3 - - - +
463B TRP* 3.6 51.9 + - + -
500B ILE* 4.0 4.3 - - - +
501B SER* 1.3 83.2 + - - +
503B VAL* 1.3 66.1 + - - +
504B GLN* 2.6 47.1 - - - +
505B LEU* 3.5 4.7 + - + +
506B ALA* 3.0 21.7 + - - +
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Residues in contact with VAL 503 (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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502B ASN* 1.3 74.1 + - - +
504B GLN* 1.3 65.9 + - - +
506B ALA* 3.1 6.4 + - - +
507B ASP* 3.0 31.9 + - - +
542B GLU* 3.7 48.0 - - + +
543B LEU* 3.8 11.0 - - + -
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Residues in contact with GLN 504 (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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403B PHE* 3.0 37.6 - - + -
424B ARG* 3.2 17.0 - - - +
463B TRP* 3.6 21.3 - - + -
467B GLU* 3.4 10.9 + - - -
502B ASN* 2.6 26.2 - - - +
503B VAL* 1.3 74.8 - - - +
505B LEU* 1.3 57.1 + - - +
507B ASP* 3.4 10.0 + - - +
508B THR* 3.0 29.6 + - - -
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Residues in contact with LEU 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B TRP* 4.0 23.5 - - + -
466B THR* 4.2 11.4 - - + -
467B GLU* 3.5 40.8 - - + +
470B LEU* 4.5 15.5 - - + -
498B ILE* 3.9 15.0 - - + -
499B SER 3.5 24.2 - - - +
500B ILE* 4.2 8.3 - - - -
501B SER 4.4 0.7 - - - +
502B ASN* 3.5 17.9 + - + +
503B VAL 3.3 0.2 - - - -
504B GLN* 1.3 76.8 - - - +
506B ALA* 1.3 67.4 + - - +
508B THR* 4.8 0.4 - - - -
509B VAL* 3.1 27.3 + - + +
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Residues in contact with ALA 506 (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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500B ILE* 3.9 21.0 - - + +
502B ASN 3.0 15.2 + - - +
503B VAL* 3.1 6.5 + - - +
505B LEU* 1.3 79.2 - - - +
507B ASP* 1.3 62.5 + - - +
509B VAL* 3.4 6.5 + - - +
510B MET* 3.1 25.0 + - - +
543B LEU* 3.2 39.0 - - + -
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Residues in contact with ASP 507 (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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503B VAL* 3.0 27.8 + - - +
504B GLN* 3.9 11.5 - - - +
506B ALA* 1.3 73.7 - - - +
508B THR* 1.3 56.6 + - - +
510B MET* 2.9 3.6 + - - +
511B PHE* 2.7 56.4 + - + -
542B GLU 4.9 1.4 - - - +
543B LEU* 3.8 14.9 - - - +
546B SER* 2.9 30.8 + - - -
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Residues in contact with THR 508 (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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424B ARG* 5.0 0.3 + - - -
467B GLU* 2.5 34.8 + - - +
470B LEU* 3.8 28.7 - - + -
471B TYR* 3.9 11.5 - - - +
474B GLN* 3.6 20.9 + - - +
504B GLN* 3.0 16.4 + - - -
505B LEU 3.8 4.9 - - - -
507B ASP* 1.3 75.8 - - - +
509B VAL* 1.3 58.2 + - - +
511B PHE* 3.8 3.6 - - - +
512B THR* 2.8 36.0 + - - +
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Residues in contact with VAL 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B LEU* 3.4 25.8 - - + -
495B ILE* 4.0 25.5 - - + +
498B ILE* 4.7 7.6 - - + -
500B ILE* 4.5 23.8 - - + -
505B LEU* 3.1 23.9 + - + +
506B ALA* 3.5 9.9 - - - +
508B THR* 1.3 77.0 - - - +
510B MET* 1.3 68.0 + - - +
512B THR* 3.4 2.6 + - - +
513B ILE* 3.2 33.9 + - + +
533B LEU* 4.8 7.0 - - + -
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Residues in contact with MET 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B ALA 3.1 11.6 + - - +
507B ASP 2.9 7.6 + - - +
509B VAL* 1.3 86.4 - - - +
511B PHE* 1.3 55.4 + - - +
513B ILE* 3.3 6.6 + - - +
514B GLY 3.0 14.0 + - - -
533B LEU* 4.4 3.6 - - - +
534B VAL* 3.5 39.5 - - + -
537B ALA* 3.5 22.4 - - + -
543B LEU* 5.7 2.2 - - + -
546B SER* 3.5 32.1 - - - +
547B SER* 3.2 36.3 - - - -
550B THR* 2.6 23.5 + - - +
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Residues in contact with PHE 511 (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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474B GLN* 3.1 32.5 - - - +
507B ASP* 2.7 48.2 + - + +
508B THR* 3.8 3.1 - - - +
510B MET* 1.3 70.9 - - - +
512B THR* 1.3 54.8 + - - +
514B GLY* 3.2 1.8 + - - -
515B ALA* 2.8 34.3 + - - +
545B VAL* 5.3 7.9 - - + -
546B SER* 3.7 24.0 - - - -
549B SER* 4.0 17.7 - - - -
550B THR* 4.3 2.9 - - - -
553B LYS* 5.2 7.8 + - - +
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Residues in contact with THR 512 (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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470B LEU* 3.7 16.5 + - + +
473B PHE* 3.9 22.2 - - + -
474B GLN* 3.4 27.9 - - - +
477B ALA* 5.5 1.1 - - + -
495B ILE* 3.9 14.6 - - + -
508B THR 2.8 22.4 + - - -
509B VAL* 3.6 6.7 - - - -
511B PHE* 1.3 76.0 - - - +
513B ILE* 1.3 63.0 + - - +
515B ALA* 3.1 7.1 + - - +
516B LEU* 3.0 40.2 + - + +
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Residues in contact with ILE 513 (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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495B ILE* 4.6 14.6 - - + -
509B VAL* 3.2 30.8 + - + +
510B MET* 3.6 8.7 - - - +
512B THR* 1.3 76.1 - - - +
514B GLY* 1.3 60.7 + - - +
516B LEU* 3.4 11.5 + - + +
517B SER* 3.4 16.3 + - - -
520B LEU* 4.3 3.1 - - + +
530B VAL* 3.8 43.1 - - + +
533B LEU* 4.3 15.5 - - + -
534B VAL* 4.0 11.9 - - + -
550B THR* 3.9 5.2 - - + -
554B ILE* 3.6 25.9 - - + +
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Residues in contact with GLY 514 (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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510B MET 3.0 10.7 + - - -
511B PHE 3.2 3.3 + - - -
512B THR 3.1 0.2 - - - -
513B ILE* 1.3 74.7 - - - +
515B ALA* 1.3 60.8 + - - +
517B SER* 2.6 35.7 + - - -
550B THR* 3.7 19.9 + - - -
553B LYS* 3.8 23.0 - - - +
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Residues in contact with ALA 515 (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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474B GLN* 4.5 9.6 - - + +
477B ALA* 3.6 23.0 - - + +
478B GLU* 3.9 38.5 + - + +
511B PHE 2.8 13.9 + - - +
512B THR* 3.1 11.6 + - - +
514B GLY* 1.3 78.4 - - - +
516B LEU* 1.3 57.5 + - - +
517B SER 3.1 3.0 + - - -
518B GLU* 4.4 7.1 + - - +
519B TRP 5.3 0.3 + - - -
553B LYS* 5.7 0.7 - - - +
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Residues in contact with LEU 516 (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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473B PHE* 3.9 29.2 - - + -
477B ALA* 4.1 20.2 - - + +
480B ILE* 5.4 1.6 - - + -
488B VAL* 4.2 19.3 - - + -
492B ILE* 4.4 15.3 - - + -
495B ILE* 4.8 4.7 - - + -
512B THR* 3.0 38.2 + - + +
513B ILE* 3.4 11.0 + - + +
514B GLY 3.1 0.4 - - - -
515B ALA* 1.3 74.4 - - - +
517B SER* 1.3 63.8 + - - +
518B GLU 3.3 1.8 - - - -
519B TRP* 3.1 16.7 + - + +
520B LEU* 2.9 34.4 + - + +
530B VAL* 5.9 2.9 - - + -
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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