Contacts of the helix formed by residues 542 - 555 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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541A HIS* 1.3 80.0 - - - +
543A ALA* 1.3 64.6 + - - +
544A SER* 2.9 30.7 + - - -
545A THR* 2.7 28.5 + - - -
546A ASN* 3.0 20.1 + - - -
30B LEU* 5.2 4.9 - - + -
33B PHE* 4.2 13.7 - - + -
61B LYS* 4.2 0.2 - - - -
437B GLU* 3.7 11.5 + - - +
440B MET* 3.5 33.3 - - + +
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Residues in contact with ALA 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541A HIS 3.8 0.2 + - - -
542A ASP* 1.3 75.4 - - - +
544A SER* 1.3 57.2 + - - +
546A ASN* 3.8 10.1 - - - +
547A GLY* 2.9 22.2 + - - -
33B PHE* 3.9 15.8 - - + +
36B ASP 5.4 0.7 - - - +
37B ALA* 4.1 21.1 - - - +
39B ARG* 5.2 0.4 - - + +
40B PHE* 3.4 26.4 - - + +
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Residues in contact with SER 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A ASP* 2.9 11.4 + - - -
543A ALA* 1.3 74.3 - - - +
545A THR* 1.3 60.4 + - - -
547A GLY* 3.1 1.0 + - - -
548A LEU* 2.8 32.3 + - - +
33B PHE* 3.5 13.5 - - - -
40B PHE* 3.9 6.5 - - - -
58B ASP* 2.5 28.2 + - - +
60B SER* 3.2 20.1 + - - -
61B LYS* 2.8 29.1 + - - +
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Residues in contact with THR 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A ILE* 4.3 8.5 - - + -
541A HIS* 3.5 34.1 - - + +
542A ASP* 2.7 29.9 + - - -
544A SER* 1.3 76.2 + - - +
546A ASN* 1.3 62.9 + - - +
548A LEU* 3.4 10.0 + - - +
549A ILE* 3.0 38.0 + - + +
61B LYS* 3.8 8.0 + - - +
433B LEU* 4.6 8.0 + - + +
437B GLU* 3.6 23.0 - - + +
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Residues in contact with ASN 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A ILE* 3.6 18.9 + - - +
539A THR* 3.4 19.4 + - - +
540A SER 3.4 4.9 + - - -
541A HIS* 2.9 49.9 + - - +
542A ASP 3.0 16.9 + - - +
543A ALA* 3.8 8.1 - - - +
545A THR* 1.3 77.5 - - - +
547A GLY* 1.3 57.9 + - - +
549A ILE* 3.3 6.7 + - - +
550A ASN* 2.9 37.0 + - - +
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Residues in contact with GLY 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A ALA 2.9 17.2 + - - -
544A SER 3.1 2.9 + - - -
546A ASN* 1.3 77.2 - - - +
548A LEU* 1.3 61.3 + - - +
550A ASN* 3.5 4.8 + - - +
551A PHE* 3.1 24.4 + - - +
40B PHE* 3.7 30.7 - - - -
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Residues in contact with LEU 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A SER 2.8 20.3 + - - +
545A THR* 3.8 2.9 - - - +
547A GLY* 1.3 71.2 - - - +
549A ILE* 1.3 66.7 + - - +
551A PHE* 3.4 5.2 + - - +
552A LEU* 2.9 32.2 + - + +
40B PHE* 5.1 0.2 - - + -
56B LEU* 3.9 14.1 - - + -
58B ASP* 3.5 20.0 - - + +
61B LYS* 3.4 28.9 - - - +
432B PHE* 4.9 2.0 - - + -
433B LEU* 3.5 22.9 - - + -
436B THR* 4.7 2.5 - - - +
479B SER* 3.8 24.9 - - - +
481B VAL* 3.8 26.4 - - + +
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Residues in contact with ILE 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528A ILE* 4.5 9.9 - - + -
531A GLU* 3.9 6.5 - - + +
532A LEU* 3.9 11.4 - - + +
538A ILE* 3.7 44.4 - - + -
541A HIS* 3.9 20.9 - - + +
545A THR* 3.0 27.5 + - + +
546A ASN* 3.7 4.3 - - - +
548A LEU* 1.3 75.0 - - - +
550A ASN* 1.3 58.4 + - - +
552A LEU* 3.2 10.0 + - - +
553A LYS* 3.0 40.1 + - - +
433B LEU* 3.7 22.4 - - + -
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Residues in contact with ASN 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536A LYS 4.0 4.2 + - - -
537A LYS* 3.5 26.9 - - + +
538A ILE* 2.9 49.9 + - - +
546A ASN* 2.9 24.3 + - - +
547A GLY* 3.5 4.5 + - - +
549A ILE* 1.3 72.9 - - - +
551A PHE* 1.3 59.0 + - - +
553A LYS* 3.3 8.6 + - - +
554A GLU* 2.9 37.8 + - - +
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Residues in contact with PHE 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A GLY 3.1 17.8 + - - +
548A LEU 3.7 3.8 - - - +
550A ASN* 1.3 73.4 - - - +
552A LEU* 1.3 65.5 + - - +
554A GLU* 3.2 14.2 + - - +
555A ASN* 3.0 45.9 + - - -
40B PHE* 5.7 0.9 - - + -
46B ARG* 3.7 26.5 - - - +
54B GLU* 3.5 50.3 - - + -
56B LEU* 3.5 40.6 - - + -
481B VAL* 3.6 34.3 - - + -
482B VAL 5.0 1.6 - - - -
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Residues in contact with LEU 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A LEU* 5.2 2.5 - - + -
548A LEU* 2.9 22.0 + - + +
549A ILE* 3.2 5.1 + - - +
551A PHE* 1.3 78.0 - - - +
553A LYS* 1.3 57.2 + - - +
555A ASN* 2.9 18.4 + - - +
556A PHE* 3.0 30.6 + - + -
411B ALA 5.4 0.2 - - - +
412B PRO 4.4 0.7 - - - -
413B ALA* 3.7 25.9 - - - +
429B LEU* 4.1 28.9 - - + -
432B PHE* 4.7 7.0 - - + -
433B LEU* 3.9 35.7 - - + -
481B VAL* 3.6 28.9 - - + -
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Residues in contact with LYS 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531A GLU 2.6 30.9 + - - -
532A LEU* 4.3 4.3 - - + +
534A ASP* 2.8 37.8 + - - +
535A GLY* 3.9 15.3 - - - +
536A LYS 2.7 30.0 + - - +
538A ILE* 3.6 5.4 - - - +
549A ILE* 3.0 31.9 + - + +
550A ASN* 3.5 15.5 - - - +
551A PHE 3.3 0.2 - - - -
552A LEU* 1.3 76.6 - - - +
554A GLU* 1.3 62.1 + - - +
555A ASN 3.1 0.9 + - - -
556A PHE* 3.5 28.3 + - + +
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Residues in contact with GLU 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550A ASN* 2.9 22.7 + - + +
551A PHE* 3.4 13.5 - - - +
553A LYS* 1.3 75.6 - - - +
555A ASN* 1.3 66.4 + - - +
556A PHE 3.6 0.2 - - - -
46B ARG* 3.1 40.9 + - - -
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Residues in contact with ASN 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551A PHE* 3.0 52.2 + - + +
552A LEU 2.9 5.8 + - - +
554A GLU* 1.3 88.0 + - - +
556A PHE* 1.3 67.0 + - - +
53B GLY* 5.1 1.0 - - - -
54B GLU* 5.1 5.9 + - - +
413B ALA* 3.4 23.6 - - + +
414B GLN* 3.0 23.8 + - - +
483B LYS* 3.7 31.8 - - + +
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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