Contacts of the helix formed by residues 546 - 559 (chain A) in PDB entry 1O1F
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 546 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544A LYS 4.6 3.3 + - - -
545A ALA* 1.3 78.6 + - - +
547A ASP* 1.3 79.5 + - + +
548A THR* 3.0 27.6 - - - +
549A SER* 2.9 16.9 + - - -
550A PHE* 2.8 23.0 + - - +
596A LEU* 3.5 7.3 - - - +
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Residues in contact with ASP 547 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546A THR* 1.3 77.5 - - + +
548A THR* 1.3 53.7 + - - +
550A PHE* 3.0 12.7 - - - +
551A MLY 2.7 36.7 + - - +
592A ILE* 3.7 17.5 - - + +
593A SER* 3.3 8.7 - - - -
594A GLY* 2.9 28.6 + - - -
595A TRP* 4.5 0.8 - - - +
596A LEU* 3.4 32.2 + - - +
597A GLU 4.9 0.2 + - - -
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Residues in contact with THR 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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476 MET* 2.9 6.1 - - - +
546A THR* 3.0 17.4 - - + +
547A ASP* 1.3 80.3 - - - +
549A SER* 1.3 63.0 + - - +
551A MLY 3.3 27.9 + - - +
552A ASN* 2.8 36.5 + - - +
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Residues in contact with SER 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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456 VAL* 2.4 21.9 - - - +
466 GLY* 2.2 31.9 - - - +
476 MET* 2.6 9.0 + - - +
539A GLU* 2.8 24.2 + - - +
544A LYS 5.6 0.2 - - - -
545A ALA* 4.2 1.8 - - - -
546A THR* 2.9 30.4 + - - -
548A THR* 1.3 86.7 - - - +
550A PHE* 1.3 66.4 + - - +
552A ASN 3.0 0.7 + - - -
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Residues in contact with PHE 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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466 GLY* 1.1 63.1 - - - +
532A ILE* 4.4 3.4 - - + -
535A ILE* 3.9 20.9 - - + -
536A LEU* 3.2 53.4 - - + -
539A GLU* 4.1 3.6 - - + -
546A THR 2.8 9.7 + - - +
547A ASP* 3.0 8.3 - - - +
549A SER* 1.3 74.0 + - - +
551A MLY 1.3 53.4 + - - +
553A MLY 3.5 0.2 - - - +
554A LEU* 2.9 29.7 + - + +
592A ILE* 3.0 40.6 - - + -
595A TRP* 4.1 15.9 - + + -
596A LEU* 3.8 18.8 - - + -
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Residues in contact with MLY 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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466 GLY 2.5 10.2 - - - +
547A ASP 2.7 19.4 + - - +
548A THR* 3.5 30.1 + - - +
549A SER 3.1 0.2 + - - -
550A PHE* 1.3 72.0 + - - +
552A ASN* 1.3 69.0 + - - +
554A LEU* 2.7 28.0 + - + +
555A TYR* 3.0 41.2 + - + +
576A GLU* 5.3 4.5 - - - -
577A ALA* 5.0 2.2 - - - -
578A HIS* 3.8 34.3 - - + +
592A ILE* 4.4 18.2 - - + -
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Residues in contact with ASN 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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446 MET* 4.6 1.6 - - + -
466 GLY 2.7 1.6 + - - -
476 MET* 0.7 425.7 - - + +
486 GLY 1.2 53.2 + - - -
506 LYS* 5.9 3.6 - - - +
536 TYR* 6.0 1.6 - - - +
576 GLU* 5.2 9.7 + - - +
548A THR* 2.8 25.9 + - - +
551A MLY 1.3 82.4 + - - -
553A MLY 1.3 6.7 - - - -
555A TYR* 2.9 4.9 + - - -
556A ASP 2.9 0.9 + - - -
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Residues in contact with MLY 553 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1674 GLU 5.2 2.9 - - - -
3554 MET* 5.5 1.6 - - - -
436 VAL* 4.2 17.5 - - + -
446 MET 2.2 26.5 - - - +
456 VAL* 1.1 85.4 - - - +
466 GLY* 1.6 58.1 + - - +
476 MET* 0.9 148.6 + - - +
486 GLY* 2.5 12.5 + - - -
535A ILE* 3.9 17.3 - - + +
538A GLU* 4.3 17.0 - - - +
539A GLU* 3.0 12.1 + - - +
542A PHE* 3.3 32.5 - - - -
550A PHE 3.5 0.4 - - - +
552A ASN 1.3 6.1 - - - -
554A LEU* 1.3 53.4 + - - +
557A GLU* 3.6 11.4 + - - +
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Residues in contact with LEU 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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466 GLY 2.5 7.5 + - - -
532A ILE* 4.1 22.9 - - + -
535A ILE* 3.4 36.3 - - + -
550A PHE* 2.9 33.3 + - + +
551A MLY 2.8 14.4 - - + +
553A MLY 1.3 75.5 + - - +
555A TYR* 1.3 62.5 + - + +
558A HIS* 3.1 30.8 + - + +
565A PHE* 4.1 17.3 - - + -
579A PHE* 3.9 31.2 - - + -
592A ILE* 4.4 4.9 - - + -
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Residues in contact with TYR 555 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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476 MET* 4.2 8.7 - - + -
486 GLY* 2.3 15.5 - - - +
496 GLN 3.4 3.8 - - - +
506 LYS* 5.3 6.7 - - + -
551A MLY 3.0 52.6 + - + +
552A ASN* 2.9 3.9 + - - +
554A LEU* 1.3 70.2 - - + +
556A ASP* 1.3 56.8 + - - +
557A GLU 2.7 12.6 + - - -
558A HIS 2.7 0.5 + - - -
559A LEU* 2.7 59.9 + - + +
565A PHE* 3.8 17.5 - + - -
567A LYS* 4.4 12.7 - - + +
568A PRO* 4.5 4.3 - - - +
578A HIS* 2.9 32.5 + - - -
579A PHE* 4.9 0.4 - - + -
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Residues in contact with ASP 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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426 GLY 4.4 1.4 - - - +
436 VAL* 3.5 14.0 - - + -
446 MET* 3.6 20.1 + - - +
476 MET* 3.5 11.0 - - - +
486 GLY* 0.9 202.1 + - - +
496 GLN* 1.0 142.4 - - - +
506 LYS* 2.7 36.5 + - - +
536 TYR* 4.1 9.1 + - - -
552A ASN 3.6 4.3 - - - +
555A TYR* 1.3 66.7 - - - +
557A GLU* 1.3 46.3 + - - -
559A LEU 5.0 1.4 - - - +
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Residues in contact with GLU 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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436 VAL* 4.9 9.7 - - + +
476 MET 4.9 0.4 - - - +
486 GLY* 2.1 19.6 - - - -
496 GLN* 2.0 8.8 - - - +
530A MET* 3.6 41.0 - - - +
535A ILE* 4.2 5.2 - - + -
553A MLY 3.6 15.0 - - - +
554A LEU 4.2 0.9 - - - +
555A TYR 2.7 0.4 + - - -
556A ASP 1.3 69.2 - - - -
558A HIS* 1.3 82.6 + - + +
559A LEU 5.2 0.2 - - - -
561A LYS* 4.2 31.6 + - - +
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Residues in contact with HIS 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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525A LEU* 3.6 26.0 - - + +
530A MET* 2.7 31.3 + - + -
531A GLY* 3.6 16.3 - - - -
532A ILE* 4.1 6.0 + - + -
535A ILE* 3.8 8.7 - - + +
554A LEU* 3.1 27.1 + - + +
555A TYR 2.7 4.8 + - - -
557A GLU* 1.3 89.7 + - + +
559A LEU* 1.3 63.5 + - - +
561A LYS* 3.1 2.8 + - - -
562A SER* 2.8 41.4 + - - +
565A PHE* 3.7 24.9 - + + -
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Residues in contact with LEU 559 (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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496 GLN* 4.3 10.2 - - - +
516 ASP* 5.7 5.2 - - - +
555A TYR* 2.7 54.7 + - + +
556A ASP 5.0 1.2 - - - +
557A GLU 5.2 0.2 - - - -
558A HIS* 1.3 72.8 + - - +
560A GLY* 1.3 68.0 + - - +
561A LYS* 3.0 8.4 + - - +
565A PHE* 3.6 21.1 - - + +
566A GLN* 5.4 0.9 - - - -
567A LYS* 4.2 33.7 - - + +
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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