Contacts of the helix formed by residues 546 - 554 (chain A) in PDB entry 6Q6Q
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 ALA 546 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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545A LEU* 1.3 77.7 - - - +
547A ASP* 1.3 65.4 + - - +
548A LYS* 4.3 15.3 - - - +
549A TYR* 3.0 51.2 + - + +
550A GLU* 3.8 5.7 + - - +
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Residues in contact with ASP 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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545A LEU 3.5 3.9 + - - +
546A ALA* 1.3 73.0 - - - +
548A LYS* 1.3 59.4 + - - +
549A TYR 3.2 0.9 + - - -
550A GLU* 4.0 19.2 + - - +
999A GLU 4.4 4.2 - - - +
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Residues in contact with LYS 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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546A ALA* 4.3 12.1 - - + +
547A ASP* 1.3 77.8 - - - +
549A TYR* 1.3 88.3 + - + +
550A GLU 3.7 0.7 - - - -
551A SER* 4.4 2.2 + - - -
999A GLU 3.6 20.9 - - - +
1000A ASN* 4.1 2.4 - - - -
1001A TYR* 3.1 51.0 + - + +
1002A TRP 4.4 1.2 + - - -
1293A GLU* 5.7 2.5 - - - +
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Residues in contact with TYR 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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487A GLU* 5.2 12.2 + - - -
524A PHE* 3.9 19.5 - + - -
528A LEU* 4.0 19.5 - - + +
545A LEU* 5.5 5.7 - - + +
546A ALA* 3.0 28.8 + - + +
548A LYS* 1.3 118.8 + - + +
550A GLU* 1.3 64.5 + - - +
551A SER* 3.2 4.1 + - - -
552A ALA* 3.3 18.8 + - - +
553A LEU* 4.5 2.4 + - - +
1001A TYR* 4.1 13.4 - + - -
1002A TRP* 3.4 40.8 - + + -
1318A LYS* 5.4 5.7 + - - -
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Residues in contact with GLU 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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532A GLN* 4.8 18.1 + - - +
545A LEU* 6.2 3.6 - - + -
546A ALA 3.8 5.7 + - - +
547A ASP* 4.0 17.8 + - - +
548A LYS 3.7 1.2 - - - -
549A TYR* 1.3 79.2 - - - +
551A SER* 1.3 63.2 + - - +
553A LEU* 3.2 24.5 + - + +
554A GLU* 4.0 2.9 + - - +
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Residues in contact with SER 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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548A LYS 4.4 3.0 + - - -
549A TYR 4.6 0.2 - - - -
550A GLU* 1.3 78.3 - - - +
552A ALA* 1.3 64.1 + - - +
553A LEU 3.1 1.2 + - - -
554A GLU* 3.1 19.3 + - - +
996A PHE* 4.8 4.0 - - - -
1000A ASN* 3.1 41.5 + - - +
1001A TYR 4.3 0.5 + - - -
1002A TRP 4.2 4.0 + - - -
1003A LYS* 3.3 41.0 + - - +
1172A GLU* 5.8 0.2 - - - -
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Residues in contact with ALA 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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525A LYS* 2.7 30.0 + - + +
528A LEU* 4.0 16.6 - - + -
549A TYR 3.3 12.7 + - - +
550A GLU 3.2 1.0 - - - -
551A SER* 1.3 80.7 + - - +
553A LEU* 1.3 61.3 + - + +
554A GLU 3.5 2.2 - - - +
555A ASP* 5.3 0.5 - - - +
1002A TRP* 3.7 25.3 - - + +
1003A LYS* 4.0 10.8 + - - +
1176A LEU* 3.9 15.9 - - + -
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Residues in contact with LEU 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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525A LYS* 4.4 4.0 - - + +
528A LEU* 3.5 49.4 - - + +
529A GLU* 3.9 29.9 - - + +
532A GLN* 3.2 39.5 - - + +
545A LEU* 4.8 5.6 - - + -
549A TYR 4.8 3.1 - - - +
550A GLU* 3.2 15.0 + - + +
551A SER 3.1 1.0 - - - -
552A ALA* 1.3 83.2 - - + +
554A GLU* 1.3 63.7 + - - +
555A ASP* 3.5 11.5 + - - +
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Residues in contact with GLU 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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525A LYS* 5.3 0.5 + - - -
550A GLU 4.0 2.1 + - - +
551A SER* 3.1 16.9 + - - +
552A ALA 4.0 1.4 - - - +
553A LEU* 1.3 79.8 - - - +
555A ASP* 1.3 76.4 + - - +
556A LEU* 5.5 3.4 - - + -
1003A LYS* 3.1 28.2 + - + -
1172A GLU* 5.6 2.9 - - - +
1174A ASP* 4.9 0.3 - - - +
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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