Contacts of the helix formed by residues 547 - 561 (chain A) in PDB entry 2IO1
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 547 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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408A TYR* 4.9 2.8 + - - -
542A GLN* 3.2 6.4 - - - +
544A ASN* 3.3 16.4 + - - +
546A SER* 1.3 94.7 + - - +
548A SER* 1.3 65.6 + - - +
549A GLY 3.2 2.9 - - - -
550A MET* 3.0 10.7 + - + +
551A PHE* 2.9 41.7 + - + -
569A GLN* 3.2 18.8 + - - +
572A MET* 3.4 15.5 - - + +
573A PRO* 5.9 0.2 - - - +
576A ARG* 3.3 24.5 + - - +
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Residues in contact with SER 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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478A HIS* 3.2 26.8 + - - -
479A TRP* 3.0 25.1 + - - +
496A SER* 3.6 6.4 + - - -
542A GLN* 3.3 14.4 + - - -
546A SER 3.5 1.4 + - - -
547A ASP* 1.3 76.8 - - - +
549A GLY* 1.3 64.5 + - - +
551A PHE* 3.7 2.0 - - - +
552A THR* 2.9 27.4 + - - -
92B GLY 3.2 28.5 + - - -
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Residues in contact with GLY 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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411A LEU* 3.9 18.8 - - - +
416A ILE* 4.3 3.0 - - - +
479A TRP* 3.4 30.3 - - - -
546A SER 4.8 0.6 + - - -
547A ASP 3.2 1.0 - - - -
548A SER* 1.3 80.5 + - - +
550A MET* 1.3 61.7 + - - +
552A THR* 3.3 4.9 + - - -
553A CYS* 3.1 27.2 + - - -
91B GLY 4.2 3.6 + - - -
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Residues in contact with MET 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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405A LEU* 3.9 16.8 - - - -
411A LEU* 4.0 9.8 - - + +
547A ASP* 3.0 12.8 + - + +
549A GLY* 1.3 73.3 - - - +
551A PHE* 1.3 66.2 + - - +
553A CYS* 3.3 2.9 + - - +
554A LYS* 2.9 30.7 + - + +
572A MET* 3.8 17.7 - - - -
575A PHE* 3.4 33.4 - - + -
576A ARG* 3.6 52.3 - - + +
579A MET* 3.7 29.2 - - + -
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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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496A SER* 3.6 21.5 - - - -
540A PRO* 3.8 19.5 - - + -
541A GLN 3.8 11.2 - - - -
542A GLN* 3.5 32.1 - - + -
547A ASP* 2.9 27.2 + - + -
548A SER 3.7 4.5 - - - +
550A MET* 1.3 76.9 - - - +
552A THR* 1.3 53.7 + - - +
554A LYS* 3.3 1.3 + - - +
555A TYR* 2.8 65.9 + + + -
567A PHE* 3.9 19.3 - + - -
569A GLN* 3.6 25.4 - - - -
572A MET* 3.5 30.7 - - + -
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Residues in contact with THR 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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416A ILE* 5.2 6.3 - - + -
420A MET* 4.3 19.1 - - + -
472A PRO* 5.1 3.4 - - + -
479A TRP* 3.4 29.6 + - + -
480A SER* 3.4 22.7 + - - +
481A LEU* 3.8 12.5 - - + +
548A SER 2.9 15.9 + - - -
549A GLY 3.4 10.3 - - - +
550A MET 3.2 0.2 - - - -
551A PHE* 1.3 76.5 - - - +
553A CYS* 1.3 61.9 + - - +
555A TYR* 3.3 12.8 + - - +
556A ALA* 3.1 23.0 + - - +
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Residues in contact with CYS 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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411A LEU* 4.5 8.7 - - - -
415A VAL 5.3 0.2 - - - -
416A ILE* 3.9 35.0 - - - -
419A TYR* 3.7 35.1 - - + -
420A MET* 5.1 4.0 - - - -
549A GLY 3.1 17.4 + - - -
550A MET 3.3 7.4 + - - +
552A THR* 1.3 76.9 - - - +
554A LYS* 1.3 61.2 + - - +
556A ALA* 3.5 6.5 + - - +
557A ASP* 3.0 26.7 + - - +
579A MET* 4.0 14.1 - - + -
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Residues in contact with LYS 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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419A TYR* 3.1 18.6 + - - +
550A MET* 2.9 23.8 + - + +
553A CYS* 1.3 74.9 - - - +
555A TYR* 1.3 68.2 + - - +
557A ASP* 2.8 28.5 + - - -
558A TYR* 3.1 30.7 + - + -
567A PHE* 3.5 27.6 - - + -
572A MET* 4.4 2.7 - - + -
575A PHE* 3.6 52.4 - - + -
579A MET* 4.1 15.2 - - + +
582A GLU* 5.2 5.7 + - - -
589A LEU* 6.0 0.4 + - - -
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Residues in contact with TYR 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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481A LEU* 4.0 8.3 - - + -
494A LEU* 3.8 41.7 - - + -
495A ASP* 3.9 6.4 + - - -
496A SER* 3.4 30.3 + - - -
539A ILE* 4.4 9.1 - - + +
540A PRO* 2.5 40.2 + - + -
541A GLN* 3.8 4.2 + - - -
551A PHE* 2.8 35.8 + + + +
552A THR* 3.6 11.2 - - - +
554A LYS* 1.3 77.7 - - - +
556A ALA* 1.3 65.9 + - - +
558A TYR* 3.1 1.7 + - - +
559A ILE* 2.8 26.1 + - - +
565A ILE* 3.9 15.6 - - + +
567A PHE* 3.5 24.9 - + - -
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Residues in contact with ALA 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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420A MET* 3.9 12.8 - - + -
423A LEU* 3.8 11.3 - - + +
470A LEU* 3.5 26.4 - - + +
481A LEU* 3.6 15.3 - - + +
552A THR 3.1 14.8 + - - +
553A CYS 3.6 4.7 - - - +
555A TYR* 1.3 81.0 - - - +
557A ASP* 1.3 56.8 + - - +
559A ILE* 4.6 2.9 - - - +
560A SER* 2.9 32.2 + - - -
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Residues in contact with ASP 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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419A TYR* 3.6 11.7 + - - +
423A LEU* 3.7 15.3 - - + +
426A ARG* 2.9 24.0 + - - -
553A CYS 3.0 17.1 + - - +
554A LYS* 2.8 31.7 + - - +
555A TYR 3.1 0.2 - - - -
556A ALA* 1.3 76.9 - - - +
558A TYR* 1.3 66.3 + - - +
560A SER* 2.5 24.0 + - - -
561A ARG* 2.7 34.8 + - - -
588A LEU* 5.6 0.9 - - - -
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Residues in contact with TYR 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 LYS* 3.3 24.5 - - - +
555A TYR 3.1 1.6 + - - -
557A ASP* 1.3 88.3 - - - +
559A ILE* 1.3 61.6 + - - +
561A ARG* 3.2 21.7 + - - +
563A LYS* 2.9 65.3 + - + +
564A PRO 3.6 21.5 - - - -
565A ILE* 3.5 26.2 - - + -
566A THR* 4.2 10.5 - - - -
567A PHE* 3.9 27.2 - + - +
571A GLN* 5.8 0.3 + - - -
575A PHE* 4.1 15.1 - + - -
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Residues in contact with ILE 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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468A ILE* 3.5 16.1 - - + +
470A LEU* 4.4 11.7 - - + -
481A LEU* 5.3 0.4 - - + -
483A VAL* 3.8 40.2 - - + -
492A LYS* 5.2 6.7 - - + +
494A LEU* 3.3 35.7 - - + -
534A MET* 5.9 1.6 - - + -
555A TYR* 2.8 23.6 + - + +
556A ALA* 4.2 2.0 - - - +
558A TYR* 1.3 70.3 - - - +
560A SER* 1.3 65.4 + - - +
562A ASP* 3.3 13.2 + - - +
563A LYS 4.8 3.8 - - - +
565A ILE* 4.0 15.5 - - + -
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Residues in contact with SER 560 (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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423A LEU* 4.3 2.6 - - - +
426A ARG* 2.7 22.6 + - - -
427A ASN* 3.0 32.9 + - - +
433A PRO* 3.6 13.7 - - - +
435A LEU* 3.9 23.8 - - - -
468A ILE* 3.9 10.6 - - - +
470A LEU* 4.9 0.9 - - - -
556A ALA 2.9 16.1 + - - -
557A ASP* 2.5 24.3 + - - -
559A ILE* 1.3 79.7 - - - +
561A ARG* 1.3 55.7 + - - +
562A ASP 3.4 0.8 + - - -
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Residues in contact with ARG 561 (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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426A ARG* 2.9 41.5 - - - +
432A TYR* 3.5 51.7 + - + -
433A PRO* 5.2 0.2 - - - -
557A ASP* 2.7 46.2 + - - -
558A TYR* 3.2 21.4 + - - +
560A SER* 1.3 78.5 + - - +
562A ASP* 1.3 69.7 + - - +
563A LYS* 3.1 41.6 + - + +
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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