Contacts of the helix formed by residues 538 - 554 (chain B) in PDB entry 1KOJ
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 538 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A PHE* 4.1 18.5 - - + -
30A ASP* 5.8 1.6 - - - +
56A LYS* 4.4 0.2 - - - -
433A GLU* 3.9 14.1 + - - +
436A MET* 3.7 25.9 - - + +
437A LYS* 5.0 5.9 - - + +
537B HIS* 1.3 82.5 - - - +
539B SER* 1.3 63.3 + - - +
540B SER* 2.9 18.5 + - - -
541B THR* 2.9 42.4 + - - -
542B ASN* 3.0 17.5 + - - -
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Residues in contact with SER 539 (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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29A PHE* 3.6 15.4 - - - +
32A ASP 4.6 1.7 + - - -
33A LYS* 4.0 22.0 + - - -
35A ARG* 4.1 3.5 - - - +
36A PHE* 3.3 38.0 + - - +
537B HIS 3.8 0.4 + - - -
538B ASP* 1.3 73.4 - - - +
540B SER* 1.3 59.6 + - - +
542B ASN* 3.7 9.0 - - - +
543B GLY* 2.8 23.0 + - - -
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Residues in contact with SER 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 3.8 8.2 - - - -
36A PHE* 3.7 10.7 - - - -
53A ASP* 2.6 21.8 + - - +
55A SER* 3.3 19.9 + - - -
56A LYS* 2.7 29.2 + - - +
538B ASP* 2.9 10.3 + - - -
539B SER* 1.3 78.0 + - - +
541B THR* 1.3 61.6 + - - +
543B GLY* 3.1 2.3 + - - -
544B LEU* 2.8 33.8 + - - +
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Residues in contact with THR 541 (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 LYS* 4.2 6.4 + - - +
429A LEU* 4.7 8.5 + - + +
433A GLU* 3.7 20.2 - - + +
524B ILE* 4.0 17.5 - - + -
537B HIS* 3.6 33.0 - - + -
538B ASP* 2.9 22.0 + - - -
540B SER* 1.3 75.9 + - - +
542B ASN* 1.3 63.5 + - - +
544B LEU* 3.8 9.8 - - - +
545B ILE* 3.0 42.5 + - + +
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Residues in contact with ASN 542 (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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534B VAL* 3.5 20.9 + - - +
535B THR* 3.2 18.4 - - + +
536B SER 3.6 5.7 - - - +
537B HIS* 2.8 50.9 - - - +
538B ASP 3.0 17.3 + - - +
539B SER* 3.7 8.8 - - - +
541B THR* 1.3 75.7 - - - +
543B GLY* 1.3 57.6 + - - +
545B ILE* 3.2 6.0 + - - +
546B ASN* 2.8 38.2 + - - +
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Residues in contact with GLY 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE* 3.5 29.6 - - - -
539B SER 2.8 21.5 + - - -
540B SER 3.1 0.4 + - - -
542B ASN* 1.3 74.0 - - - +
544B LEU* 1.3 55.6 + - - +
546B ASN* 3.4 8.4 + - - +
547B PHE* 2.9 29.8 + - - +
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Residues in contact with LEU 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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36A PHE* 4.3 0.4 - - + -
51A LEU* 3.9 21.3 - - + -
53A ASP* 3.5 24.7 - - + +
56A LYS* 3.6 27.6 - - - +
428A PHE* 4.7 2.0 - - + -
429A LEU* 3.4 26.9 - - + +
432A THR* 4.7 2.7 - - - +
475A SER* 3.9 16.6 - - - +
477A VAL* 3.9 21.6 - - + +
540B SER 2.8 21.5 + - - +
541B THR* 3.8 2.7 - - - +
543B GLY* 1.3 72.8 - - - +
545B ILE* 1.3 58.2 + - - +
547B PHE* 3.3 7.0 + - - +
548B ILE* 2.9 33.9 + - - +
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Residues in contact with ILE 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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429A LEU* 3.7 21.3 - - + -
524B ILE* 4.1 16.8 - - + -
527B GLU* 4.9 2.2 - - + +
528B LEU* 4.1 10.3 - - + -
534B VAL* 3.5 35.7 - - + -
537B HIS* 3.9 18.2 - - + +
541B THR* 3.0 42.2 + - + +
542B ASN 3.5 3.8 - - - +
544B LEU* 1.3 77.4 - - - +
546B ASN* 1.3 59.0 + - - +
548B ILE* 3.1 10.3 - - - +
549B LYS* 3.0 40.1 + - - +
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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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533B PRO* 3.0 21.4 - - + +
534B VAL* 2.8 42.4 + - - +
535B THR* 5.3 1.2 - - - +
542B ASN* 2.8 26.6 + - - +
543B GLY* 3.9 6.3 - - - +
545B ILE* 1.3 76.2 - - - +
547B PHE* 1.3 59.9 + - - +
549B LYS* 3.4 7.1 + - - +
550B GLN* 3.0 29.1 + - - +
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Residues in contact with PHE 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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42A THR* 4.1 16.4 - - + -
49A HIS* 3.9 26.2 - - + -
51A LEU* 3.5 40.2 - - + -
409A VAL* 4.2 5.6 - - + -
477A VAL* 3.6 43.1 - - + -
478A PHE* 4.5 0.9 - - - -
479A THR 5.0 0.2 - - - -
543B GLY 2.9 17.9 + - - +
544B LEU 3.6 3.6 - - - +
545B ILE 3.3 0.2 - - - -
546B ASN* 1.3 77.0 - - - +
548B ILE* 1.3 57.4 + - - +
550B GLN* 3.7 16.9 - - - +
551B GLN* 3.0 54.4 + - + +
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Residues in contact with ILE 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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407A ILE* 5.4 0.4 - - + -
409A VAL* 3.4 34.6 - - + +
425A LEU* 3.8 40.4 - - + -
428A PHE* 6.5 0.4 - - + -
429A LEU* 5.0 11.4 - - + -
477A VAL* 3.7 18.4 - - + -
528B LEU* 4.4 12.1 - - + -
544B LEU* 2.9 23.2 + - + +
545B ILE* 3.1 13.5 - - - +
547B PHE* 1.3 76.1 - - - +
549B LYS* 1.3 68.4 + - - +
551B GLN 3.4 0.2 + - - -
552B ARG* 3.0 35.1 + - - +
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Residues in contact with LYS 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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527B GLU 2.7 29.5 + - - -
528B LEU* 3.6 7.9 - - - +
530B GLY* 2.7 33.2 + - - +
531B SER* 4.1 17.3 + - - +
532B SER* 3.0 28.3 + - - +
533B PRO* 5.0 0.2 - - + -
534B VAL* 3.9 3.8 - - - +
545B ILE* 3.0 31.0 + - + +
546B ASN* 4.0 9.4 - - - +
548B ILE* 1.3 75.7 - - + +
550B GLN* 1.3 63.6 + - - +
552B ARG* 3.2 38.7 + - - +
553B GLU* 4.2 10.2 + - - +
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Residues in contact with GLN 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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42A THR* 5.8 1.2 - - - +
49A HIS* 5.0 6.1 + - - -
546B ASN 3.0 19.2 + - - +
547B PHE* 3.7 17.6 - - - +
549B LYS* 1.3 80.2 - - - +
551B GLN* 1.3 85.7 + - - +
552B ARG 3.2 1.0 + - - -
553B GLU* 3.5 21.2 + - - +
554B ALA 4.1 1.7 + - - -
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Residues in contact with GLN 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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48A GLY* 5.3 0.4 - - - -
49A HIS* 3.3 29.5 + - - -
409A VAL* 3.9 20.0 - - + +
410A GLN* 2.9 22.2 + - - -
479A THR* 2.8 27.2 + - + +
547B PHE* 3.0 43.1 + - + +
548B ILE 3.8 0.2 - - - -
550B GLN* 1.3 91.6 + - - +
552B ARG* 1.3 63.9 + - - +
553B GLU 3.0 3.2 + - - -
554B ALA* 3.0 31.6 + - - +
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Residues in contact with ARG 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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409A VAL* 4.0 9.2 - - + -
410A GLN* 3.9 14.1 + - + +
528B LEU* 2.5 27.6 + - - +
529B ASP* 3.2 23.8 + - - +
530B GLY 3.7 5.3 + - - -
531B SER* 4.9 5.1 - - - +
548B ILE* 3.0 21.3 + - + +
549B LYS* 3.2 41.3 - - - +
550B GLN 3.2 0.4 - - - -
551B GLN* 1.3 78.1 - - - +
553B GLU* 1.3 63.9 + - + +
554B ALA 4.5 0.2 - - - +
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Residues in contact with GLU 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 SER* 4.5 12.1 + - - -
549B LYS 4.4 10.5 - - - +
550B GLN* 3.8 13.4 - - - +
551B GLN 3.0 0.4 - - - -
552B ARG* 1.3 81.2 - - + +
554B ALA* 1.3 71.3 + - - +
555B LYS* 3.3 5.9 + - - +
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Residues in contact with ALA 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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410A GLN* 2.8 24.8 + - - +
479A THR* 3.6 11.0 - - + -
550B GLN 4.1 2.2 + - - +
551B GLN* 3.0 43.8 + - - +
552B ARG 4.5 0.2 - - - +
553B GLU* 1.3 82.5 - - - +
555B LYS* 1.3 59.2 + - - +
556B ILE* 3.7 2.5 + - + +
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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