Contacts of the helix formed by residues 542 - 555 (chain B) in PDB entry 4WMJ
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 542 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A LEU* 5.4 3.6 - - + -
33A PHE* 4.3 14.8 - - + -
61A LYS* 4.1 1.1 - - - -
437A GLU* 3.7 12.2 + - - +
440A MET* 3.5 32.8 - - + +
441A LYS* 5.9 0.3 - - - +
541B HIS* 1.3 79.2 - - - +
543B ALA* 1.3 63.7 + - - +
544B SER* 2.8 32.7 + - - -
545B THR* 2.7 28.8 + - - -
546B ASN* 3.0 18.0 + - - -
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Residues in contact with ALA 543 (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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33A PHE* 4.0 16.2 - - + +
36A ASP 5.3 0.7 - - - +
37A ALA* 4.3 18.6 - - - +
39A ARG* 5.1 0.7 - - + +
40A PHE* 3.4 31.1 - - + +
541B HIS 3.8 0.6 + - - -
542B ASP* 1.3 72.0 - - - +
544B SER* 1.3 57.9 + - - +
546B ASN* 3.8 9.8 - - - +
547B GLY* 2.9 22.0 + - - -
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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
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33A PHE* 3.7 12.9 - - - -
40A PHE* 3.8 6.5 - - - -
58A ASP* 2.5 24.3 + - - +
60A SER* 3.2 20.2 + - - -
61A LYS* 2.7 29.4 + - - +
542B ASP* 2.8 16.4 + - - -
543B ALA* 1.3 71.9 - - - +
545B THR* 1.3 65.3 + - - -
547B GLY* 3.1 1.6 + - - -
548B LEU* 2.8 26.9 + - - +
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Residues in contact with THR 545 (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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61A LYS* 3.7 11.6 + - - +
433A LEU* 4.7 8.3 + - + +
437A GLU* 3.5 20.3 - - + +
528B ILE* 4.3 10.1 - - + -
541B HIS* 3.6 34.1 - - + +
542B ASP* 2.7 32.0 + - - -
544B SER* 1.3 72.2 + - - +
546B ASN* 1.3 62.7 + - - +
548B LEU* 3.4 5.4 + - - +
549B ILE* 2.9 38.6 + - + +
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Residues in contact with ASN 546 (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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538B ILE* 3.5 21.1 - - - +
539B THR* 3.4 19.2 + - - +
540B SER 3.5 4.3 + - - -
541B HIS* 2.9 47.3 + - - +
542B ASP 3.0 17.3 + - - +
543B ALA* 3.8 7.4 - - - +
545B THR* 1.3 78.6 - - - +
547B GLY* 1.3 57.2 + - - +
549B ILE* 3.2 7.4 + - - +
550B ASN* 2.9 36.1 + - - +
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Residues in contact with GLY 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE* 3.7 30.9 - - - -
543B ALA 2.9 16.3 + - - -
544B SER 3.5 3.1 - - - -
546B ASN* 1.3 75.9 - - - +
548B LEU* 1.3 56.7 + - - +
550B ASN* 3.9 4.5 - - - +
551B PHE* 3.0 29.6 + - - +
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Residues in contact with LEU 548 (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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56A LEU* 3.8 15.9 - - + -
58A ASP* 3.4 26.0 - - + +
61A LYS* 3.4 24.0 - - - +
432A PHE* 4.9 2.2 - - + -
433A LEU* 3.4 26.0 - - + +
436A THR* 4.7 2.5 - - - +
479A SER* 3.8 24.9 - - - +
481A VAL* 3.8 26.9 - - + +
544B SER 2.8 17.1 + - - +
545B THR* 3.8 2.2 - - - +
547B GLY* 1.3 70.2 - - - +
549B ILE* 1.3 67.4 + - - +
551B PHE* 3.4 4.5 + - - +
552B LEU* 3.0 29.7 + - + +
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Residues in contact with ILE 549 (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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433A LEU* 3.8 19.7 - - + -
528B ILE* 4.4 12.3 - - + -
531B GLU* 4.0 10.3 - - + +
532B LEU* 4.1 11.7 - - + -
538B ILE* 3.6 31.2 - - + -
541B HIS* 4.0 28.9 - - + +
545B THR* 2.9 29.9 + - + +
546B ASN* 3.5 5.2 - - - +
548B LEU* 1.3 77.7 - - - +
550B ASN* 1.3 57.3 + - - +
552B LEU* 3.3 8.4 + - - +
553B LYS* 2.9 39.8 + - + +
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Residues in contact with ASN 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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536B LYS 4.1 3.4 + - - -
537B LYS* 3.6 28.3 - - + +
538B ILE* 2.9 51.8 + - - +
546B ASN* 2.9 19.2 + - - +
547B GLY* 4.2 5.0 - - - +
549B ILE* 1.3 76.7 - - - +
551B PHE* 1.3 56.4 + - - +
553B LYS* 3.4 8.5 + - - +
554B GLU* 3.0 36.0 + - - +
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Residues in contact with PHE 551 (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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40A PHE* 5.9 0.4 - - + -
46A ARG* 3.7 40.4 - - + +
54A GLU* 3.6 35.9 - - + -
56A LEU* 3.7 35.7 - - + -
481A VAL* 3.7 40.8 - - + -
482A VAL 4.9 2.0 - - - -
547B GLY 3.0 19.6 + - - +
548B LEU 3.7 3.1 - - - +
550B ASN* 1.3 73.1 - - - +
552B LEU* 1.3 65.2 + - - +
554B GLU* 3.2 12.2 + - + +
555B ASN* 2.9 48.4 + - - -
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Residues in contact with LEU 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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412A PRO 4.4 0.2 - - - -
413A ALA* 3.7 26.2 - - + +
429A LEU* 4.0 30.7 - - + -
432A PHE* 4.6 6.7 - - + -
433A LEU* 3.9 34.8 - - + -
481A VAL* 3.6 28.5 - - + -
532B LEU* 5.1 2.9 - - + -
548B LEU* 3.0 19.9 + - + +
549B ILE* 3.5 7.0 - - - +
551B PHE* 1.3 74.6 - - - +
553B LYS* 1.3 57.4 + - + +
555B ASN* 2.8 20.3 + - - +
556B PHE* 3.1 28.5 + - + -
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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
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531B GLU 2.6 27.2 + - - +
532B LEU* 4.1 8.5 - - + +
534B ASP* 2.8 38.9 + - - -
535B GLY 4.5 4.0 - - - -
536B LYS 2.9 21.8 + - - +
538B ILE* 3.9 3.0 - - - +
549B ILE* 2.9 38.3 + - + +
550B ASN* 3.7 11.2 - - - +
551B PHE 3.3 0.2 - - - -
552B LEU* 1.3 74.9 - - - +
554B GLU* 1.3 61.9 + - - +
555B ASN 3.2 1.0 + - - -
556B PHE* 3.5 35.2 + - + +
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Residues in contact with GLU 554 (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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46A ARG* 3.0 39.0 + - - +
54A GLU* 4.7 0.7 - - - +
550B ASN* 3.0 20.1 + - - +
551B PHE* 3.2 17.4 + - - +
552B LEU 3.2 0.2 - - - -
553B LYS* 1.3 78.6 - - - +
555B ASN* 1.3 66.7 + - - +
556B PHE 3.5 1.3 + - - -
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Residues in contact with ASN 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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53A GLY* 5.1 1.0 - - - -
54A GLU* 4.9 7.3 + - - +
413A ALA* 3.5 22.7 - - + +
414A GLN* 2.9 30.9 + - - +
483A LYS* 3.7 34.3 + - + +
551B PHE* 2.9 47.5 + - + +
552B LEU 2.8 5.3 + - - +
554B GLU* 1.3 88.3 - - - +
556B PHE* 1.3 61.7 - - - +
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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