Contacts of the helix formed by residues 544 - 552 (chain H) in PDB entry 6X34
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 LEU 544 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540H PHE* 5.0 8.1 - - + +
541H SER* 5.4 4.0 - - - +
542H ASN 4.1 1.4 + - - -
543H ASN* 1.3 78.1 - - - +
545H ASP* 1.3 66.5 + - - +
546H TRP 3.3 2.2 - - - -
547H LEU* 3.2 42.5 + - + +
548H VAL* 3.4 12.5 + - + +
564H LEU* 5.2 5.2 - - + -
567H VAL* 5.5 2.0 - - + -
568H LEU* 6.0 0.4 - - + -
574H VAL* 3.8 33.7 - - + +
577H ILE* 4.1 22.4 - - + -
578H ILE* 4.6 4.0 - - + -
582H HIS* 3.5 36.3 - - + +
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Residues in contact with ASP 545 (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 LEU* 1.3 74.1 - - - +
546H TRP* 1.3 61.6 + - - +
548H VAL* 3.2 12.7 - - + +
549H SER* 2.9 29.2 + - - -
581H ASN* 5.5 4.9 - - - +
582H HIS* 4.6 9.0 - - + -
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Residues in contact with TRP 546 (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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488H LEU* 5.1 7.0 - - + -
491H ILE* 3.5 39.7 - - + -
492H ASP* 4.7 19.3 - - + +
495H ASN* 5.8 6.0 + - + +
523H TYR* 5.9 4.5 - + - -
526H LEU* 5.4 2.5 - - + -
540H PHE* 3.9 28.3 - + - -
543H ASN* 5.3 15.8 - - + +
544H LEU* 3.3 1.4 - - - +
545H ASP* 1.3 78.3 - - - +
547H LEU* 1.3 74.5 + - + +
549H SER* 3.5 8.5 - - - -
550H LYS* 2.9 42.1 + - + +
560H ILE* 6.3 2.2 - - + -
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Residues in contact with LEU 547 (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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540H PHE* 4.0 22.0 - - + -
543H ASN 5.2 0.2 - - - +
544H LEU* 3.2 32.5 + - + +
545H ASP 3.2 0.6 - - - -
546H TRP* 1.3 99.3 - - + +
548H VAL* 1.3 59.4 + - + +
550H LYS* 3.3 2.8 + - + +
551H LEU* 2.9 27.7 + - + +
560H ILE* 3.9 21.2 - - + +
563H VAL* 4.3 18.4 - - + -
564H LEU* 3.8 34.5 - - + -
567H VAL* 4.4 8.7 - - + -
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Residues in contact with VAL 548 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544H LEU* 3.5 13.9 - - + +
545H ASP* 3.2 20.6 - - + +
547H LEU* 1.3 77.3 - - + +
549H SER* 1.3 60.3 + - - +
551H LEU* 3.4 18.2 - - + +
552H ASP* 2.9 27.9 + - - +
564H LEU* 5.0 11.2 - - + -
581H ASN* 5.7 2.2 - - - +
582H HIS* 4.1 33.4 - - + +
585H SER* 3.8 28.0 + - - +
586H ILE* 5.5 1.3 - - + -
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Residues in contact with SER 549 (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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545H ASP 2.9 19.3 + - - -
546H TRP* 3.5 11.7 - - - -
547H LEU 3.2 0.2 - - - -
548H VAL* 1.3 78.2 - - - +
550H LYS* 1.3 62.0 + - - +
552H ASP* 3.3 19.0 + - - +
553H ARG* 3.8 4.7 + - - +
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Residues in contact with LYS 550 (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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495H ASN* 4.7 21.2 + - - +
523H TYR* 5.0 4.1 + - + +
546H TRP* 2.9 37.7 + - + +
547H LEU* 3.9 4.0 - - + +
549H SER* 1.3 74.3 - - - +
551H LEU* 1.3 64.8 + - - +
553H ARG* 3.3 24.0 + - - +
555H GLU 5.2 1.4 - - - +
556H ALA 5.5 0.2 - - - +
560H ILE* 4.3 21.9 - - + +
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Residues in contact with LEU 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 LEU* 2.9 18.5 + - + +
548H VAL* 3.4 11.0 - - + +
549H SER 3.2 0.2 - - - -
550H LYS* 1.3 77.0 - - - +
552H ASP* 1.3 61.3 + - - +
553H ARG 3.1 9.4 + - - +
557H SER* 4.3 12.1 - - - +
560H ILE* 3.6 29.1 - - + +
561H LEU* 4.4 8.3 - - + +
564H LEU* 4.1 15.3 - - + -
585H SER* 4.4 13.2 - - - +
586H ILE* 3.9 27.8 - - + -
589H LEU* 3.6 42.6 - - + +
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Residues in contact with ASP 552 (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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548H VAL 2.9 12.9 + - - +
549H SER* 3.5 12.8 - - - +
550H LYS 3.3 0.6 - - - -
551H LEU* 1.3 76.2 - - - +
553H ARG* 1.3 60.6 + - - +
554H LEU* 3.6 1.6 + - - +
585H SER* 5.2 6.7 + - - +
588H SER* 6.2 0.2 - - - +
589H LEU* 5.4 3.4 - - - -
593H HIS* 4.5 8.7 - - - -
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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