Contacts of the helix formed by residues 538 - 558 (chain A) in PDB entry 1OY6
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 THR 538 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535A LEU 4.1 5.7 + - - -
536A ARG 4.5 2.8 + - - -
537A SER* 1.3 83.9 + - - +
539A GLY* 1.3 65.9 + - - +
540A ARG 3.2 1.9 - - - +
541A TYR* 3.5 2.9 + - - +
542A LEU* 2.9 30.9 + - + +
1026A PHE* 3.9 12.9 - - + -
1029A VAL* 4.2 20.2 - - + +
1030A ARG* 3.6 29.8 + - + +
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Residues in contact with GLY 539 (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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538A THR* 1.3 79.7 - - - +
540A ARG* 1.3 62.4 + - - +
542A LEU* 3.7 14.0 - - - +
543A VAL* 3.2 28.8 + - - +
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Residues in contact with ARG 540 (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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533A GLY 5.3 2.4 + - - -
537A SER* 4.0 18.3 + - - -
538A THR 3.2 1.2 - - - +
539A GLY* 1.3 75.8 - - - +
541A TYR* 1.3 99.0 + - + +
543A VAL* 3.3 7.8 + - - +
544A LEU* 3.3 18.8 + - + +
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Residues in contact with TYR 541 (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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533A GLY 5.1 0.7 + - - -
534A ILE* 3.5 32.1 - - + +
537A SER* 3.1 33.7 - - - -
538A THR 3.5 1.8 + - - +
540A ARG* 1.3 105.4 + - + +
542A LEU* 1.3 65.1 + - - +
544A LEU* 3.4 17.3 + - + +
545A TYR* 3.1 22.0 + - - +
1021A PHE* 4.6 26.2 - + + -
1022A VAL* 4.7 8.7 - - + +
1023A PRO* 4.9 4.8 - - + +
1026A PHE* 3.4 37.5 - + + -
1030A ARG* 4.6 1.3 - - - -
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Residues in contact with LEU 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A THR* 2.9 21.3 + - + +
539A GLY* 3.7 15.0 - - - +
541A TYR* 1.3 78.0 - - - +
543A VAL* 1.3 61.9 + - + +
545A TYR* 3.1 14.6 + - + +
546A LEU* 3.1 44.4 + - + +
1030A ARG* 3.5 39.9 - - - +
1031A ARG* 5.3 4.3 - - - +
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Residues in contact with VAL 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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539A GLY 3.2 18.3 + - - +
540A ARG* 3.3 7.6 + - - +
542A LEU* 1.3 86.5 - - + +
544A LEU* 1.3 57.5 + - - +
546A LEU* 3.6 21.9 + - + +
547A ILE* 3.1 34.2 + - + +
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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 ARG* 3.3 11.9 + - + +
541A TYR* 3.6 20.4 - - + +
542A LEU 3.2 0.6 - - - -
543A VAL* 1.3 75.7 - - - +
545A TYR* 1.3 53.6 + - - +
546A LEU 3.2 0.2 - - - -
547A ILE* 3.1 23.8 + - + +
548A ILE* 2.8 50.8 + - + +
1017A LEU* 6.3 1.1 - - + -
1021A PHE* 6.4 2.0 - - + -
1022A VAL* 5.0 7.6 - - + -
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Residues in contact with TYR 545 (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 TYR 3.1 12.6 + - - +
542A LEU* 3.1 16.9 + - + +
544A LEU* 1.3 73.4 - - - +
546A LEU* 1.3 80.6 + - + +
548A ILE* 3.4 15.2 + - + +
549A VAL* 3.3 35.0 + - + +
902A MET 4.3 1.0 + - - -
903A LEU* 3.4 49.4 + - + +
906A PRO* 3.9 13.2 - - + +
907A LEU* 3.5 28.9 - - + -
1022A VAL* 4.3 9.6 - - + +
1023A PRO* 3.6 23.1 - - + -
1030A ARG* 6.0 0.2 - - - +
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Residues in contact with LEU 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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542A LEU* 3.1 29.3 + - + +
543A VAL* 3.6 26.9 - - + +
544A LEU 3.2 0.2 - - - -
545A TYR* 1.3 90.5 - - + +
547A ILE* 1.3 63.5 + - - +
549A VAL* 3.2 8.3 + - - +
550A VAL* 3.1 27.9 + - + +
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Residues in contact with ILE 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 VAL* 3.1 22.1 + - + +
544A LEU* 3.1 29.6 + - + +
546A LEU* 1.3 80.4 - - + +
548A ILE* 1.3 63.4 + - + +
550A VAL* 3.4 11.6 + - + +
551A GLY* 3.4 17.8 + - - -
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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
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544A LEU* 2.8 33.1 + - + +
545A TYR* 3.4 16.4 - - + +
546A LEU 3.2 0.6 - - - -
547A ILE* 1.3 76.3 - - + +
549A VAL* 1.3 62.3 + - + +
551A GLY* 3.6 0.7 + - - -
552A MET* 2.9 26.1 + - + +
906A PRO 4.4 8.7 - - - +
907A LEU* 5.5 1.3 - - + -
910A ILE* 4.0 33.3 - - + +
1017A LEU* 4.4 18.2 - - + -
1022A VAL* 3.4 33.7 - - + -
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Residues in contact with VAL 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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545A TYR* 3.4 29.4 - - + +
546A LEU* 3.2 9.4 + - - +
548A ILE* 1.3 77.8 - - + +
550A VAL* 1.3 63.3 + - - +
552A MET* 3.7 15.0 - - + -
553A ALA* 3.3 20.1 + - + +
906A PRO* 3.9 32.5 - - + -
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Residues in contact with VAL 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 LEU* 3.1 21.7 + - + +
547A ILE* 3.6 13.7 - - + +
548A ILE 3.2 0.2 - - - -
549A VAL* 1.3 75.3 - - - +
551A GLY* 1.3 66.7 + - - +
553A ALA* 3.4 14.1 + - - +
554A TYR* 3.4 11.6 + - - +
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Residues in contact with GLY 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 ILE 3.4 8.7 + - - -
548A ILE 4.0 1.6 - - - -
550A VAL* 1.3 77.5 - - - +
552A MET* 1.3 60.0 + - - +
554A TYR* 3.0 9.9 + - - +
555A LEU* 2.8 39.0 + - - +
910A ILE* 4.2 2.0 - - - -
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Residues in contact with MET 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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548A ILE 2.9 20.3 + - - +
549A VAL* 3.7 16.8 - - + +
551A GLY* 1.3 74.5 - - - +
553A ALA* 1.3 69.8 + - + +
555A LEU* 3.3 2.2 + - - -
556A PHE* 3.3 33.6 + - + +
906A PRO* 3.9 25.8 - - + +
909A VAL* 4.0 17.9 - - + -
910A ILE* 3.4 39.5 - - + +
913A LEU* 3.4 16.0 - - + +
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Residues in contact with ALA 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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549A VAL* 3.3 13.0 + - + +
550A VAL* 3.5 10.8 - - - +
551A GLY 3.2 0.6 - - - -
552A MET* 1.3 87.5 - - + +
554A TYR* 1.3 57.6 + - - +
556A PHE* 3.1 6.2 + - - +
557A VAL* 2.9 40.1 + - + +
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Residues in contact with TYR 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 VAL 3.4 8.7 + - - +
551A GLY* 3.0 11.7 + - - +
553A ALA* 1.3 73.9 - - - +
555A LEU* 1.3 69.8 + - + +
556A PHE 3.1 5.9 + - - -
557A VAL* 4.1 5.4 - - + +
558A ARG* 3.6 59.5 + - + +
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Residues in contact with LEU 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 GLY* 2.8 23.3 + - - +
552A MET 3.7 6.1 - - - +
553A ALA 3.3 0.4 - - - -
554A TYR* 1.3 86.6 - - + +
556A PHE* 1.3 55.4 + - - +
558A ARG* 5.6 0.2 - - - -
559A LEU* 3.4 21.5 + - - +
910A ILE* 3.6 34.8 - - + +
913A LEU* 3.4 20.1 - - + +
914A LEU* 4.0 26.9 - - + -
917A THR* 3.6 20.6 + - + +
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Residues in contact with PHE 556 (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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552A MET* 3.3 24.7 - - + +
553A ALA* 3.5 7.4 - - - +
554A TYR 3.1 0.4 - - - -
555A LEU* 1.3 78.8 - - - +
557A VAL* 1.3 73.4 + - + +
558A ARG 3.5 0.9 - - - -
559A LEU* 3.8 14.8 + - - +
909A VAL* 5.5 3.8 - - + -
913A LEU* 3.5 26.7 - - + -
923A ASN* 5.2 9.4 - - - -
927A PHE* 6.1 0.4 - + - -
928A GLN* 6.1 4.0 - - - -
931A LEU* 5.1 15.0 - - + -
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Residues in contact with VAL 557 (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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553A ALA* 2.9 27.4 + - + +
554A TYR* 3.9 4.9 + - + +
556A PHE* 1.3 88.7 - - + +
558A ARG* 1.3 74.8 + - + +
559A LEU 3.5 5.2 + - - +
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Residues in contact with ARG 558 (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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554A TYR* 3.6 57.8 + - + +
557A VAL* 1.3 87.0 - - + +
559A LEU* 1.3 63.8 + - - +
560A PRO* 3.2 9.7 - - - +
917A THR* 6.3 0.7 - - - -
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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