Contacts of the helix formed by residues 543 - 558 (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 LEU 543 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500B ILE* 5.8 2.9 - - + -
503B VAL* 3.8 14.8 - - + -
506B ALA* 3.2 37.9 - - + +
507B ASP* 3.8 16.2 - - - +
510B MET* 5.7 1.8 - - + -
537B ALA* 4.0 27.5 - - + +
540B ASN* 2.8 30.0 + - + +
542B GLU* 1.3 88.6 - - + +
544B SER* 1.3 51.8 + - - +
545B VAL 3.6 1.8 - - - -
546B SER* 4.3 9.4 - - - +
547B SER* 2.6 33.6 + - - -
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Residues in contact with SER 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B ASN 3.5 0.6 + - - -
541B PRO* 3.0 20.3 + - - -
542B GLU 3.6 1.2 - - - -
543B LEU* 1.3 76.3 - - - +
545B VAL* 1.3 66.7 + - - +
547B SER* 3.9 1.1 - - - -
548B VAL* 2.9 31.9 + - - +
581B ILE 4.5 2.0 - - - -
582B HIS* 2.8 40.1 - - - +
583B LYS* 4.4 4.2 + - - +
586B GLN* 3.5 17.2 - - - +
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Residues in contact with VAL 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B PHE* 5.3 7.6 - - + -
543B LEU 3.6 0.4 - - - -
544B SER* 1.3 80.3 - - - +
546B SER* 1.3 60.9 + - - +
549B SER* 3.2 29.6 + - - +
586B GLN* 3.1 35.4 - - - +
589B TRP* 3.7 16.4 - - + -
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Residues in contact with SER 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B ASP* 2.9 29.1 + - - -
510B MET* 3.5 24.6 - - - +
511B PHE* 3.7 25.5 - - - -
543B LEU* 3.7 9.5 + - - +
544B SER 3.4 0.2 - - - -
545B VAL* 1.3 77.5 - - - +
547B SER* 1.3 67.1 + - - +
549B SER* 3.1 17.9 + - - -
550B THR* 3.1 16.6 + - - -
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Residues in contact with SER 547 (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* 3.2 26.9 - - - -
534B VAL* 3.9 2.6 - - - +
537B ALA* 3.8 12.1 - - - -
538B LEU* 3.4 27.7 - - - +
543B LEU 2.6 23.5 + - - -
544B SER* 3.4 6.2 + - - -
546B SER* 1.3 80.9 + - - +
548B VAL* 1.3 61.0 + - - +
550B THR* 3.3 2.6 + - - -
551B LEU* 2.9 28.8 + - - +
582B HIS* 4.3 0.2 + - - -
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Residues in contact with VAL 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B LEU* 4.1 8.5 - - + -
544B SER 2.9 20.4 + - - +
547B SER* 1.3 74.1 + - - +
549B SER* 1.3 65.7 + - - +
551B LEU* 3.5 4.3 + - + +
552B LYS* 3.0 22.0 + - - +
582B HIS* 3.8 30.7 - - + +
586B GLN* 3.5 18.8 - - + +
589B TRP* 3.5 37.6 - - + -
590B LEU* 3.6 17.9 - - + +
593B ALA* 5.9 0.2 - - + -
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Residues in contact with SER 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B PHE* 4.0 10.9 - - - -
545B VAL* 3.2 17.9 + - - +
546B SER* 3.1 14.0 + - - -
548B VAL* 1.3 77.2 - - - +
550B THR* 1.3 66.6 + - - +
552B LYS* 3.1 9.2 + - - +
553B LYS* 2.9 43.3 + - - +
589B TRP* 4.3 14.8 - - - -
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Residues in contact with THR 550 (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* 2.6 33.3 + - - +
511B PHE* 4.3 2.4 - - - -
513B ILE* 3.9 6.1 - - + -
514B GLY* 3.7 12.1 - - - +
534B VAL* 3.6 28.3 - - + -
546B SER 3.1 15.0 + - - -
547B SER 3.8 3.6 - - - -
549B SER* 1.3 83.0 + - - +
551B LEU* 1.3 62.3 + - - +
553B LYS* 3.2 9.7 + - - +
554B ILE* 3.0 35.1 + - + +
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Residues in contact with LEU 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B LEU* 4.5 15.3 - - + -
534B VAL* 4.0 18.6 - - + -
535B LEU* 4.5 4.7 - - + -
538B LEU* 3.8 31.4 - - + -
547B SER 2.9 16.6 + - - +
548B VAL* 3.9 6.7 - - + +
550B THR* 1.3 77.4 - - - +
552B LYS* 1.3 58.2 + - - +
554B ILE* 3.5 6.0 + - + +
555B CYS* 2.8 49.3 + - - +
569B ILE* 4.3 17.5 - - + -
573B SER* 4.3 12.6 - - - +
590B LEU* 5.0 6.7 - - + -
593B ALA* 4.5 11.7 - - + -
594B LEU* 6.0 1.3 - - + -
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Residues in contact with LYS 552 (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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548B VAL 3.0 14.5 + - - +
549B SER* 3.4 11.4 - - - +
551B LEU* 1.3 78.4 - - - +
553B LYS* 1.3 57.6 + - + +
555B CYS* 3.3 1.7 + - - +
556B ARG* 2.9 30.8 + - + +
589B TRP* 4.3 32.0 - - + +
592B GLN* 2.4 40.0 + - - +
593B ALA* 3.8 19.5 - - + +
596B PHE* 4.3 15.2 - - + -
650B THR* 5.6 0.2 - - - -
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Residues in contact with LYS 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B GLU* 5.8 3.6 - - - -
511B PHE* 5.2 8.5 + - - +
514B GLY* 3.8 25.3 - - - +
515B ALA* 6.1 0.4 - - - +
517B SER* 3.1 16.8 - - - +
549B SER* 2.9 40.3 + - - +
550B THR* 3.7 9.8 + - - +
552B LYS* 1.3 77.5 - - + +
554B ILE* 1.3 58.7 + - - +
556B ARG* 3.1 7.1 + - - +
557B GLU* 3.0 35.1 + - + +
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Residues in contact with ILE 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B ILE* 3.6 31.6 - - + +
517B SER* 3.8 14.6 - - - +
520B LEU* 4.6 14.8 - - + -
527B ILE* 5.6 4.3 - - + -
530B VAL* 4.7 6.7 - - + -
531B LEU* 5.0 14.4 - - + -
534B VAL* 4.4 9.0 - - + -
550B THR* 3.0 25.8 + - + +
551B LEU* 3.9 8.3 - - + +
553B LYS* 1.3 74.6 - - - +
555B CYS* 1.3 57.9 + - - +
558B CYS* 2.8 43.9 + - + +
562B LEU* 3.6 22.2 - - + +
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Residues in contact with CYS 555 (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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551B LEU* 2.8 43.1 + - - +
552B LYS 3.7 3.8 - - - +
553B LYS 3.2 0.2 - - - -
554B ILE* 1.3 77.9 - - - +
556B ARG* 1.3 58.8 + - - +
559B LYS* 3.5 18.2 + - - +
562B LEU* 4.0 11.4 - - - -
569B ILE* 4.6 8.5 - - - -
593B ALA* 3.5 32.1 - - - +
594B LEU* 5.4 0.9 - - - -
596B PHE* 3.3 15.7 - - + +
597B LEU* 4.2 24.1 + - - +
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Residues in contact with ARG 556 (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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552B LYS* 2.9 19.4 + - - +
553B LYS* 3.1 6.7 + - - +
555B CYS* 1.3 78.6 - - - +
557B GLU* 1.3 77.0 + - - +
559B LYS* 4.3 17.9 + - - +
596B PHE* 3.6 39.4 - - + -
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Residues in contact with GLU 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B SER* 3.6 37.5 - - - +
518B GLU* 3.8 27.2 - - - +
521B ALA* 3.2 20.7 - - + +
553B LYS* 3.0 21.1 + - + +
556B ARG* 1.3 96.5 + - - +
558B CYS* 1.3 63.5 + - - +
559B LYS* 3.5 1.4 + - - +
560B TYR* 5.3 2.6 + - - -
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Residues in contact with CYS 558 (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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517B SER 3.9 11.7 - - - -
520B LEU* 4.2 10.1 - - - -
521B ALA* 3.9 17.7 - - - +
527B ILE* 4.0 14.4 - - + -
554B ILE* 2.8 33.9 + - - +
557B GLU* 1.3 85.2 - - - +
559B LYS* 1.3 67.1 + - - +
560B TYR 3.0 3.4 - - - -
561B ASP* 2.7 20.8 + - + +
562B LEU* 2.9 26.6 + - + -
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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
------------------------------------------------------------
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