Contacts of the helix formed by residues 538 - 552 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537A HIS* 1.3 81.9 - - - +
539A SER* 1.3 59.1 + - - +
540A SER* 2.9 19.2 + - - -
541A THR* 2.8 40.9 + - - -
542A ASN* 2.9 23.4 + - - -
29B PHE* 3.9 17.2 - - + -
30B ASP* 5.9 0.9 - - - +
33B LYS* 4.8 5.6 - - - +
56B LYS* 4.2 1.1 - - - -
433B GLU* 3.6 15.8 + - - +
436B MET* 3.7 27.3 - - + +
437B LYS* 5.0 3.3 - - + +
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Residues in contact with SER 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A HIS 3.8 0.6 + - - -
538A ASP* 1.3 73.8 - - - +
540A SER* 1.3 58.8 + - - +
542A ASN* 3.7 9.0 - - - +
543A GLY* 2.8 22.7 + - - -
29B PHE* 3.6 14.9 + - - +
32B ASP 4.5 1.2 + - - -
33B LYS* 4.0 34.8 + - - +
35B ARG* 4.0 4.3 + - - +
36B PHE* 3.4 35.9 + - - +
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Residues in contact with SER 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A ASP* 2.9 10.8 + - - -
539A SER* 1.3 77.6 + - - +
541A THR* 1.3 67.2 + - - +
543A GLY* 3.1 1.6 + - - -
544A LEU* 2.9 26.4 + - - +
29B PHE* 3.5 10.7 - - - -
36B PHE* 3.9 11.0 - - - -
53B ASP* 2.7 20.6 + - - +
55B SER* 3.2 20.3 + - - -
56B LYS* 2.9 25.3 + - - +
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Residues in contact with THR 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A ILE* 3.9 17.9 - - + -
537A HIS* 3.6 27.4 - - + +
538A ASP* 2.8 35.3 + - - -
540A SER* 1.3 72.8 + - - +
542A ASN* 1.3 62.6 + - - +
544A LEU* 3.4 9.6 + - - +
545A ILE* 3.1 35.5 + - + +
56B LYS* 4.1 6.9 + - - -
429B LEU* 4.7 8.6 + - + +
433B GLU* 3.4 19.5 - - + +
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Residues in contact with ASN 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A VAL* 3.5 23.6 + - - +
535A THR* 3.3 15.1 - - - +
536A SER 3.7 2.6 - - - +
537A HIS* 2.7 54.1 - - - +
538A ASP 2.9 15.7 + - - +
539A SER* 3.7 8.1 - - - +
541A THR* 1.3 76.5 - - - +
543A GLY* 1.3 62.5 + - - +
545A ILE* 3.3 5.8 + - - +
546A ASN* 3.0 33.0 + - - +
33B LYS* 5.8 0.2 + - - -
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Residues in contact with GLY 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A SER 2.8 19.4 + - - -
540A SER 3.1 1.8 + - - -
542A ASN* 1.3 78.2 - - - +
544A LEU* 1.3 60.0 + - - +
546A ASN* 3.4 7.5 + - - +
547A PHE* 3.0 23.9 + - - +
36B PHE* 3.8 30.6 - - - -
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Residues in contact with LEU 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A SER 2.9 15.0 + - - +
541A THR* 3.8 2.9 - - - +
543A GLY* 1.3 73.2 - - - +
545A ILE* 1.3 67.5 + - - +
547A PHE* 3.2 6.2 + - - +
548A ILE* 3.1 29.6 + - + +
36B PHE* 4.9 0.2 - - + -
51B LEU* 3.9 17.0 - - + -
53B ASP* 3.5 25.4 - - + +
56B LYS* 3.6 23.1 - - - +
428B PHE* 4.9 1.6 - - + -
429B LEU* 3.4 25.1 - - + -
432B THR* 4.7 2.5 - - - +
475B SER* 3.8 22.0 - - - +
477B VAL* 3.8 27.4 - - + -
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Residues in contact with ILE 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A ILE* 4.3 15.0 - - + -
527A GLU* 4.6 3.8 - - + +
528A LEU* 4.1 15.4 - - + +
534A VAL* 3.7 31.2 - - + -
537A HIS* 4.1 20.6 - - + +
541A THR* 3.1 37.0 + - + +
542A ASN 3.7 4.0 - - - +
544A LEU* 1.3 76.3 - - - +
546A ASN* 1.3 61.8 + - - +
548A ILE* 3.2 11.3 + - - +
549A LYS* 3.1 31.7 + - - +
429B LEU* 3.5 22.0 - - + -
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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
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532A SER 4.7 0.2 - - - +
533A PRO* 3.2 21.2 - - + +
534A VAL 2.9 39.1 + - - +
535A THR* 5.8 0.2 - - - +
542A ASN* 3.0 27.2 + - - +
543A GLY* 3.9 6.4 - - - +
544A LEU 3.3 0.2 - - - -
545A ILE* 1.3 80.5 - - - +
547A PHE* 1.3 62.5 + - - +
549A LYS* 3.5 7.3 + - - +
550A GLN* 3.1 23.2 + - - +
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Residues in contact with PHE 547 (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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543A GLY 3.0 17.6 + - - +
544A LEU 3.2 5.4 + - - +
546A ASN* 1.3 76.3 - - - +
548A ILE* 1.3 60.7 + - - +
550A GLN* 3.4 16.3 + - - +
551A GLN* 3.0 54.9 + - + +
36B PHE* 5.9 0.2 - - + -
42B THR* 4.4 12.6 - - + -
49B HIS* 3.9 26.2 - - + -
51B LEU* 3.5 39.5 - - + -
409B VAL* 4.3 4.7 - - + -
477B VAL* 3.5 45.8 - - + -
478B PHE* 4.5 1.1 - - - -
479B THR* 5.0 0.2 - - - -
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Residues in contact with ILE 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A LEU* 5.1 8.7 - - + -
544A LEU* 3.1 16.3 + - + +
545A ILE* 3.4 7.2 - - - +
547A PHE* 1.3 74.6 - - - +
549A LYS* 1.3 61.2 + - + +
552A ARG* 2.8 37.6 + - + +
409B VAL* 3.6 27.5 - - + +
425B LEU* 3.5 45.8 - - + -
428B PHE* 5.4 2.9 - - + -
429B LEU* 4.2 30.3 - - + -
477B VAL* 4.5 11.4 - - + -
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Residues in contact with LYS 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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527A GLU 3.0 28.4 + - - -
528A LEU* 3.6 16.8 - - + +
529A ASP 3.4 15.4 + - - -
530A GLY 3.6 11.8 + - - +
531A SER* 3.9 16.2 - - - +
532A SER* 2.7 35.7 + - - +
533A PRO* 4.9 0.4 - - + -
534A VAL* 4.5 2.3 - - - +
545A ILE* 3.1 27.4 + - + +
546A ASN* 3.8 11.9 - - - +
547A PHE 3.3 0.2 - - - -
548A ILE* 1.3 76.8 - - + +
550A GLN* 1.3 59.2 + - - +
552A ARG* 2.5 39.9 - - - +
553A GLU* 5.7 0.3 - - - +
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Residues in contact with GLN 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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546A ASN 3.1 17.5 + - - +
547A PHE* 3.7 18.5 - - - +
549A LYS* 1.3 79.8 - - - +
551A GLN* 1.3 86.2 + - - +
553A GLU* 4.5 2.4 + - - +
554A ALA* 4.4 9.4 + - - +
49B HIS* 4.9 6.7 + - - -
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Residues in contact with GLN 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 PHE* 3.0 41.8 + - + +
550A GLN* 1.3 101.7 + - - +
552A ARG* 1.3 66.8 + - - +
553A GLU 3.1 3.4 - - - -
554A ALA* 2.9 22.4 + - - +
49B HIS* 3.6 30.8 + - - -
409B VAL* 3.8 19.0 - - + +
410B GLN* 2.8 17.5 - - - +
479B THR* 2.6 32.7 + - + +
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Residues in contact with ARG 552 (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 LEU 2.8 21.9 + - - -
529A ASP* 4.9 3.4 + - - +
530A GLY 2.5 36.3 + - - +
531A SER* 6.0 0.7 - - - +
548A ILE* 2.8 15.2 + - + +
549A LYS* 2.5 51.0 - - - +
551A GLN* 1.3 71.7 - - - +
553A GLU* 1.3 78.2 + - + +
409B VAL* 3.3 17.5 - - + +
410B GLN* 3.2 20.0 - - - +
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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