Contacts of the helix formed by residues 547 - 559 (chain H) in PDB entry 2A07
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 547 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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543H ARG 5.3 3.8 - - - +
544H ASN* 3.4 20.9 + - - +
546H ALA* 1.3 87.0 - - + +
548H TRP* 1.3 65.7 + - - +
549H LYS* 3.1 4.6 + - - -
550H ASN* 3.2 10.4 + - - +
551H ALA* 3.0 22.1 + - - +
509I TYR* 3.4 15.2 + - - -
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Residues in contact with TRP 548 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544H ASN 3.3 12.7 + - - +
545H ALA 3.4 26.0 + - - -
546H ALA* 3.8 0.6 - - - -
547H THR* 1.3 75.7 + - - +
549H LYS* 1.3 112.0 + - + +
551H ALA* 3.7 0.2 - - - +
552H VAL* 2.8 37.9 + - + +
509I TYR* 3.7 25.8 - - + -
531I TYR* 3.5 34.3 - + - -
534I PHE* 3.4 30.1 - + + -
535I THR* 3.5 22.9 - - + -
538I PHE* 3.6 40.8 - + + +
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Residues in contact with LYS 549 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546H ALA 5.3 2.0 + - - +
547H THR 3.1 1.6 + - - -
548H TRP* 1.3 123.1 - - + +
550H ASN* 1.3 66.5 + - - +
552H VAL* 3.6 2.3 - - - +
553H ARG* 3.2 28.3 + - - +
531I TYR* 3.9 38.5 + - + +
535I THR* 4.6 4.4 + - - -
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Residues in contact with ASN 550 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547H THR* 3.2 10.0 + - - +
549H LYS* 1.3 79.9 - - - +
551H ALA* 1.3 60.1 + - - +
553H ARG* 3.2 32.6 + - - +
554H HIS* 2.9 30.2 + - - +
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Residues in contact with ALA 551 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547H THR* 3.0 16.6 + - - +
548H TRP 3.7 0.2 - - - +
550H ASN* 1.3 77.4 - - - +
552H VAL* 1.3 55.5 - - - +
554H HIS* 3.4 6.1 + - - +
555H ASN* 2.9 38.0 + - - +
509I TYR* 3.2 47.1 - - + +
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Residues in contact with VAL 552 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548H TRP* 2.8 29.3 + - + +
549H LYS 3.6 4.9 - - - +
550H ASN 3.2 0.2 - - - -
551H ALA* 1.3 73.8 - - - +
553H ARG* 1.3 66.2 + - - +
555H ASN* 3.3 1.7 + - - +
556H LEU* 2.9 46.3 + - + +
509I TYR* 4.4 4.3 - - + -
513I ILE* 4.1 13.0 - - + +
527I LEU* 4.5 0.2 - - + -
530I ILE* 4.1 19.5 - - + -
531I TYR* 4.3 14.1 - - + -
534I PHE* 3.6 41.7 - - + -
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Residues in contact with ARG 553 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549H LYS 3.2 8.6 + - - +
550H ASN* 3.2 31.6 + - - +
552H VAL* 1.3 78.0 - - - +
554H HIS* 1.3 61.9 + - - +
556H LEU* 3.4 8.8 + - - +
557H SER* 3.2 23.7 + - - -
527I LEU* 4.5 14.6 - - + -
531I TYR* 3.1 30.2 + - + +
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Residues in contact with HIS 554 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550H ASN 2.9 17.5 + - - +
551H ALA* 3.5 7.0 - - - +
553H ARG* 1.3 76.5 - - - +
555H ASN* 1.3 66.2 + - - +
557H SER* 3.2 9.3 + - - -
558H LEU* 2.8 59.7 + - + +
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Residues in contact with ASN 555 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551H ALA* 2.9 29.4 + - - +
552H VAL 3.3 3.6 + - - +
554H HIS* 1.3 85.3 - - - +
556H LEU* 1.3 64.3 + - - +
558H LEU* 4.3 2.2 - - - -
559H HIS* 3.0 59.8 + - + +
562H PHE* 3.7 4.6 - - + -
509I TYR* 3.6 27.0 + - + +
510I ALA* 3.9 13.2 + - - +
513I ILE* 3.9 15.5 - - + -
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Residues in contact with LEU 556 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552H VAL* 2.9 34.9 + - + +
553H ARG* 3.7 7.2 - - - +
554H HIS 3.3 0.2 - - - -
555H ASN* 1.3 78.9 - - - +
557H SER* 1.3 52.5 + - - +
559H HIS 3.6 1.7 - - - +
562H PHE* 3.8 12.5 - - + +
573H TRP* 3.6 57.2 - - + +
602H MG 2.6 29.8 - - - -
513I ILE* 3.9 31.0 - - + -
527I LEU* 3.6 31.2 - - + -
530I ILE* 4.4 5.6 - - + -
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Residues in contact with SER 557 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553H ARG 3.2 14.5 + - - -
554H HIS* 3.2 11.3 + - - -
556H LEU* 1.3 79.5 - - - +
558H LEU* 1.3 62.5 + - - +
573H TRP* 4.9 7.0 - - - -
602H MG 4.1 5.8 - - - -
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Residues in contact with LEU 558 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554H HIS* 2.8 46.8 + - + +
555H ASN* 3.3 3.6 + - - +
557H SER* 1.3 80.1 + - - +
559H HIS* 1.3 88.4 + - + +
560H LYS* 3.6 7.6 + - - +
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Residues in contact with HIS 559 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555H ASN* 3.0 53.6 + - + +
556H LEU 3.6 2.4 - - - +
558H LEU* 1.3 97.5 - - + +
560H LYS* 1.3 60.0 + - - +
561H CYS* 3.7 20.2 - - - -
562H PHE* 3.2 16.5 + + + +
583H ARG* 3.0 29.4 + - - -
602H MG 2.5 23.7 - - - -
510I ALA* 4.7 0.6 - - + +
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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