Contacts of the helix formed by residues 543 - 551 (chain A) in PDB entry 6A5T
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 GLU 543 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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541A PHE 5.2 3.1 - - - +
542A ILE* 1.3 82.4 - - - +
544A TYR* 1.3 65.9 + - - +
545A GLU* 4.4 15.8 - - + +
546A GLN* 4.1 7.5 + - + +
547A VAL* 3.1 19.1 + - - +
571A PRO 4.8 7.4 - - - -
572A LEU* 4.8 8.3 - - + -
573A TRP* 3.8 2.8 - - - -
1079B LYS* 3.1 30.8 + - - -
188C HIS* 4.0 19.8 + - - -
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Residues in contact with TYR 544 (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 GLU* 1.3 74.6 - - - +
545A GLU* 1.3 77.0 + - + +
547A VAL* 3.0 8.9 + - + +
548A MET* 3.0 52.7 + - + +
561A VAL* 5.6 6.7 - - + -
570A LYS* 6.3 4.0 - - - +
571A PRO* 4.6 9.9 + - + +
573A TRP* 3.2 39.8 - + + -
78H TRP* 4.3 7.6 - + - -
80H PRO* 4.0 29.3 - - + +
51K ALA* 6.0 2.9 - - + -
57K THR 2.9 26.5 + - - -
58K PHE* 4.3 2.9 - - - -
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Residues in contact with GLU 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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543A GLU* 3.5 12.7 - - + +
544A TYR* 1.3 84.8 - - + +
546A GLN* 1.3 67.1 + - - +
547A VAL 2.8 0.2 + - - -
548A MET* 2.8 33.3 + - + +
549A ASN* 3.6 5.9 + - - -
1079B LYS* 5.3 4.7 + - - +
224C LYS* 6.1 0.9 - - - -
47K ARG* 4.3 23.7 + - - +
48K GLU* 4.9 11.3 - - - +
51K ALA* 4.6 16.0 - - + +
52K LEU* 5.3 6.4 - - - +
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Residues in contact with GLN 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 ILE* 3.9 21.4 - - + +
543A GLU* 4.1 10.4 + - + +
544A TYR 3.4 0.4 - - - -
545A GLU* 1.3 77.6 - - - +
547A VAL* 1.3 57.7 + - - +
549A ASN* 3.3 13.1 + - - +
550A MET* 3.0 35.6 + - + +
656A TYR* 5.0 0.4 - - + -
657A TRP* 3.6 26.0 - - - +
660A HIS* 3.5 40.0 + - + +
661A ASN 4.9 0.2 - - - +
1079B LYS* 3.3 28.3 + - - +
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Residues in contact with VAL 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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542A ILE* 3.3 29.2 - - + +
543A GLU 3.1 20.6 + - - +
544A TYR* 3.0 5.0 + - + +
545A GLU 2.8 1.6 + - - -
546A GLN* 1.3 74.3 - - - +
548A MET* 1.3 69.6 + - - +
550A MET* 4.1 4.0 - - + +
551A LEU* 2.9 44.3 + - + +
573A TRP* 4.3 28.9 - - + -
578A LEU* 4.4 23.3 - - + -
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Residues in contact with MET 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 TYR* 3.0 57.6 + - + +
545A GLU* 2.8 26.4 + - + +
547A VAL* 1.3 78.7 - - - +
549A ASN* 1.3 66.2 + - - +
551A LEU* 3.2 2.2 + - - -
552A PHE 3.1 10.6 + - - -
47K ARG* 5.1 7.9 - - - +
51K ALA* 4.5 18.8 - - + -
56K VAL* 6.3 0.4 - - - -
57K THR 4.8 0.4 - - - +
58K PHE* 3.4 32.7 - - + -
59K VAL* 3.3 38.8 - - + +
60K ALA* 3.9 3.5 - - + +
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Residues in contact with ASN 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 GLU 3.6 5.5 + - - -
546A GLN* 3.3 10.3 + - - +
547A VAL 3.2 0.4 - - - -
548A MET* 1.3 77.4 - - - +
550A MET* 1.3 53.1 + - - +
551A LEU 2.5 1.4 + - - -
552A PHE* 2.2 36.7 + - - +
553A TRP* 3.2 9.3 + - + +
656A TYR* 2.9 34.9 + - + +
47K ARG* 3.8 29.9 + - - +
60K ALA* 3.0 24.3 - - - +
61K TYR* 3.4 26.5 + - - +
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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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535A MET* 4.1 10.1 - - - -
542A ILE* 4.4 4.5 - - + -
546A GLN* 3.0 25.0 + - - +
547A VAL* 3.2 4.7 + - - +
549A ASN* 1.3 76.5 - - - +
551A LEU* 1.3 65.0 + - - +
553A TRP* 4.4 9.2 + - - +
554A VAL* 4.6 3.1 + - - +
578A LEU* 3.5 32.4 - - + +
653A VAL* 4.2 31.5 - - + +
656A TYR* 3.1 29.8 - - + -
657A TRP* 3.3 52.9 - - + +
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Residues in contact with LEU 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 VAL* 2.9 29.0 + - + +
548A MET* 3.6 4.9 - - - +
549A ASN 2.5 5.1 + - - -
550A MET* 1.3 81.9 - - - +
552A PHE* 1.3 61.9 + - - +
554A VAL* 4.2 5.0 + - + +
557A TRP* 3.0 54.9 - - + +
561A VAL* 4.3 9.9 - - + -
562A PRO* 3.6 29.6 - - + -
578A LEU* 4.4 10.8 - - + -
581A ILE* 4.0 34.5 - - + -
58K PHE* 4.9 2.0 - - + -
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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