Contacts of the helix formed by residues 546 - 553 (chain C) in PDB entry 4YFI
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 SER 546 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544C GLY 4.6 0.7 - - - +
545C GLY* 1.3 75.8 - - - -
547C LEU* 1.3 63.6 + - - +
548C PHE* 3.6 5.9 + - - +
549C SER* 3.0 32.1 + - - -
550C LEU* 3.2 19.1 + - - +
591C SER 3.8 4.5 - - - -
592C HIS* 3.7 27.3 - - - -
594C ILE 3.3 7.0 - - - -
595C LEU* 4.2 5.8 - - - -
596C LEU* 4.4 2.5 - - - +
801C 4CW 4.5 6.7 - - - -
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Residues in contact with LEU 547 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545C GLY 4.0 0.2 + - - -
546C SER* 1.3 68.9 - - - +
548C PHE* 1.3 67.8 + - - +
550C LEU* 3.0 16.1 + - + +
551C LEU* 3.1 44.1 + - + +
558C LEU* 5.4 0.9 - - + -
566C ILE* 4.4 16.8 - - + -
591C SER* 3.6 20.2 - - - +
594C ILE* 2.8 41.2 + - + +
596C LEU* 4.1 22.7 - - + +
654C CYS* 5.1 3.4 - - + +
657C GLU* 5.5 0.9 - - - -
658C ILE* 3.6 32.5 - - + -
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Residues in contact with PHE 548 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546C SER* 3.2 4.7 - - - +
547C LEU* 1.3 76.5 - - - +
549C SER* 1.3 64.4 + - - +
552C HIS* 3.0 52.8 + + + +
553C GLU* 3.6 26.9 - - + -
591C SER* 2.9 44.2 + - - +
592C HIS* 3.1 43.7 - + + -
657C GLU* 4.3 0.7 - - - -
663C ILE* 4.2 19.7 - - + -
630D TRP* 4.5 6.1 - + - -
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Residues in contact with SER 549 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545C GLY* 5.3 2.2 - - - -
546C SER* 3.0 28.9 + - - -
547C LEU 3.2 0.4 - - - -
548C PHE* 1.3 73.6 - - - +
550C LEU* 1.3 66.8 + - - +
553C GLU* 2.9 35.4 + - - -
554C GLN* 2.9 41.1 + - - +
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Residues in contact with LEU 550 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544C GLY 5.5 5.4 - - - +
546C SER 3.2 9.0 + - - +
547C LEU* 3.0 10.3 + - + +
549C SER* 1.3 78.5 - - - +
551C LEU* 1.3 80.6 + - + +
554C GLN* 3.6 18.1 - - - +
555C LYS 3.0 7.8 + - - -
556C ARG* 3.0 64.1 + - + +
558C LEU* 3.8 29.2 - - + -
566C ILE* 5.5 0.7 - - + -
596C LEU* 3.5 26.2 - - + -
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Residues in contact with LEU 551 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547C LEU* 3.1 42.3 + - + +
550C LEU* 1.3 97.6 - - + +
552C HIS* 1.3 77.9 + - + +
555C LYS* 3.5 16.1 - - - +
556C ARG 4.7 8.5 - - - +
558C LEU* 4.6 9.0 - - + -
563C LYS* 5.8 1.6 - - - -
657C GLU* 3.8 33.0 - - + +
658C ILE* 4.1 18.4 - - - +
661C GLY* 3.6 22.7 - - - +
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Residues in contact with HIS 552 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548C PHE* 3.0 45.9 + + + +
551C LEU* 1.3 90.9 - - + +
553C GLU* 1.3 63.2 + - - +
555C LYS* 3.6 23.0 - - - -
657C GLU* 2.6 28.2 + - + -
661C GLY 3.0 29.9 + - - -
662C GLU 3.6 18.8 - - - -
663C ILE* 3.5 31.0 + - + +
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Residues in contact with GLU 553 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548C PHE* 3.6 23.2 - - + -
549C SER* 2.9 37.3 + - - +
552C HIS* 1.3 81.0 - - - +
554C GLN* 1.3 67.4 + - + +
555C LYS* 3.3 10.1 - - - +
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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