Contacts of the helix formed by residues 544 - 552 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540F PHE* 5.0 8.5 - - + +
541F SER* 5.4 4.3 - - - +
542F ASN 4.1 1.6 + - - -
543F ASN* 1.3 78.3 - - - +
545F ASP* 1.3 66.5 + - - +
546F TRP 3.3 2.0 - - - -
547F LEU* 3.2 41.7 + - + +
548F VAL* 3.4 12.5 + - + +
564F LEU* 5.2 5.8 - - + -
567F VAL* 5.5 1.8 - - + -
568F LEU* 6.0 0.4 - - + -
574F VAL* 3.8 33.9 - - + +
577F ILE* 4.1 21.9 - - + +
578F ILE* 4.6 3.4 - - + -
582F HIS* 3.5 36.6 - - + +
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Residues in contact with ASP 545 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543F ASN* 5.3 0.2 - - - +
544F LEU* 1.3 75.0 - - - +
546F TRP* 1.3 60.7 + - - +
548F VAL* 3.2 12.8 - - + +
549F SER* 2.9 29.2 + - - -
581F ASN* 5.5 4.9 - - - +
582F HIS* 4.6 8.6 - - + -
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Residues in contact with TRP 546 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488F LEU* 5.1 8.3 - - + -
491F ILE* 3.5 39.9 - - + -
492F ASP* 4.7 19.7 - - + +
495F ASN* 5.8 5.6 + - + +
523F TYR* 5.9 4.7 - + - -
526F LEU* 5.4 2.0 - - + -
540F PHE* 3.9 28.5 - + - -
543F ASN* 5.3 14.7 - - + +
544F LEU 3.3 1.4 - - - +
545F ASP* 1.3 77.9 - - - +
547F LEU* 1.3 75.5 + - + +
549F SER* 3.5 8.6 - - - -
550F LYS* 2.9 43.1 + - + +
560F ILE* 6.3 2.0 - - + -
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Residues in contact with LEU 547 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540F PHE* 4.0 22.9 - - + -
543F ASN 5.2 0.4 + - - +
544F LEU* 3.2 32.7 + - + +
545F ASP 3.2 0.4 - - - -
546F TRP* 1.3 99.8 - - + +
548F VAL* 1.3 60.9 + - + +
550F LYS* 3.3 3.1 + - + +
551F LEU* 2.9 26.8 + - + +
560F ILE* 3.9 22.0 - - + +
563F VAL* 4.3 17.7 - - + -
564F LEU* 3.8 34.1 - - + -
567F VAL* 4.4 8.7 - - + -
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Residues in contact with VAL 548 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544F LEU* 3.5 12.8 - - + +
545F ASP* 3.2 21.3 - - + +
547F LEU* 1.3 77.9 - - + +
549F SER* 1.3 60.8 + - - +
551F LEU* 3.4 17.0 - - + +
552F ASP* 2.9 28.1 + - - +
564F LEU* 5.0 11.7 - - + -
581F ASN* 5.7 2.5 - - - +
582F HIS* 4.1 33.4 - - + +
585F SER* 3.8 28.2 + - - +
586F ILE* 5.5 1.3 - - + -
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Residues in contact with SER 549 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545F ASP 2.9 19.9 + - - -
546F TRP* 3.5 11.9 - - - -
548F VAL* 1.3 78.9 - - - +
550F LYS* 1.3 60.4 - - - +
552F ASP* 3.3 19.4 + - - +
553F ARG* 3.8 4.2 + - - +
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Residues in contact with LYS 550 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495F ASN* 4.7 21.4 + - - +
523F TYR* 5.0 4.1 + - + +
546F TRP* 2.9 38.8 + - + +
547F LEU* 3.9 4.5 - - + +
549F SER* 1.3 73.1 - - - +
551F LEU* 1.3 64.3 + - - +
553F ARG* 3.3 22.2 + - - +
555F GLU 5.2 1.2 - - - +
556F ALA 5.5 0.2 - - - +
560F ILE* 4.3 22.4 - - + +
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Residues in contact with LEU 551 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547F LEU* 2.9 18.6 + - + +
548F VAL* 3.4 12.3 - - + +
549F SER 3.2 0.4 - - - -
550F LYS* 1.3 76.8 - - - +
552F ASP* 1.3 63.3 + - - +
553F ARG 3.1 9.5 + - - +
557F SER* 4.3 12.1 - - - +
560F ILE* 3.6 28.7 - - + +
561F LEU* 4.4 7.6 - - + +
564F LEU* 4.1 15.3 - - + -
585F SER* 4.4 13.2 - - - +
586F ILE* 3.9 27.8 - - + -
589F LEU* 3.6 42.8 - - + +
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Residues in contact with ASP 552 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548F VAL 2.9 12.5 + - - +
549F SER* 3.5 13.2 - - - +
550F LYS 3.3 0.4 - - - -
551F LEU* 1.3 77.1 - - - +
553F ARG* 1.3 60.7 + - - +
554F LEU* 3.6 1.9 + - - +
585F SER* 5.2 6.5 + - - +
588F SER* 6.2 0.2 - - - +
589F LEU* 5.4 3.1 - - - -
593F HIS* 4.5 9.4 - - - -
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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