Contacts of the helix formed by residues 546 - 553 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544D GLY 4.6 0.7 - - - +
545D GLY* 1.3 76.5 - - - -
547D LEU* 1.3 62.8 + - - +
548D PHE* 3.4 5.9 + - - +
549D SER* 2.9 31.5 + - - -
550D LEU* 3.4 14.6 + - - +
554D GLN* 5.0 0.3 - - - +
591D SER 3.7 5.4 - - - -
592D HIS* 3.7 26.8 + - - -
594D ILE 3.3 6.1 - - - -
595D LEU* 3.9 7.8 - - - +
596D LEU* 3.9 5.5 - - - +
801D 4CW 5.1 1.8 - - - -
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Residues in contact with LEU 547 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545D GLY 3.8 0.8 + - - -
546D SER* 1.3 71.6 - - - +
548D PHE* 1.3 60.9 + - - +
550D LEU* 3.2 3.9 + - + +
551D LEU* 3.2 48.5 + - + +
566D ILE* 4.1 31.0 - - + -
591D SER* 3.5 19.1 - - - +
594D ILE* 2.8 48.8 + - + +
596D LEU* 3.8 15.5 - - + +
654D CYS* 5.1 3.1 - - + +
657D GLU* 5.6 0.7 - - - -
658D ILE* 3.7 28.7 - - + -
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Residues in contact with PHE 548 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630C TRP* 4.2 11.9 - + - -
546D SER* 3.1 8.5 - - - +
547D LEU* 1.3 72.4 - - - +
549D SER* 1.3 65.8 + - - +
552D HIS* 3.1 47.9 + + + +
553D GLU* 3.8 24.4 + - + -
591D SER* 3.1 40.9 + - - +
592D HIS* 3.4 40.6 - + - +
663D ILE* 4.2 22.7 - - + -
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Residues in contact with SER 549 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545D GLY* 5.6 1.8 - - - -
546D SER* 2.9 25.6 + - - -
547D LEU 3.4 0.2 - - - -
548D PHE* 1.3 75.0 - - - +
550D LEU* 1.3 63.5 + - - +
553D GLU* 2.5 37.0 + - - -
554D GLN* 2.9 42.2 + - - -
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Residues in contact with LEU 550 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544D GLY 5.3 4.9 - - - +
546D SER 3.4 9.8 + - - +
547D LEU* 3.2 11.2 + - + +
549D SER* 1.3 78.7 - - - +
551D LEU* 1.3 68.4 + - + +
554D GLN* 3.5 19.0 + - - +
555D LYS* 2.9 27.7 + - - -
556D ARG* 3.2 45.4 + - + +
558D LEU* 3.7 37.0 - - + -
566D ILE* 5.6 1.8 - - + -
596D LEU* 3.8 24.5 - - + -
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Residues in contact with LEU 551 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547D LEU* 3.2 36.7 + - + +
550D LEU* 1.3 93.3 - - + +
552D HIS* 1.3 74.1 + - + +
553D GLU 3.8 0.2 - - - -
555D LYS* 3.5 22.7 - - - +
556D ARG 5.3 4.3 - - - +
558D LEU* 4.0 15.5 - - + -
563D LYS* 5.7 1.6 - - - -
657D GLU* 3.4 35.4 - - + +
658D ILE* 3.9 23.6 - - + +
661D GLY* 3.7 21.8 - - - +
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Residues in contact with HIS 552 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548D PHE* 3.1 56.0 + + + +
551D LEU* 1.3 87.4 - - + +
553D GLU* 1.3 63.3 + - - +
555D LYS* 3.5 22.0 - - - +
591D SER* 4.3 0.2 + - - -
657D GLU* 2.7 28.0 + - + +
661D GLY 3.5 16.0 + - - -
662D GLU* 3.3 32.5 - - - -
663D ILE* 3.4 26.6 + - + +
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Residues in contact with GLU 553 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548D PHE* 3.8 23.0 - - + -
549D SER* 2.5 43.8 + - - +
552D HIS* 1.3 80.8 - - - +
554D GLN* 1.3 65.9 + - + +
555D LYS* 3.2 8.3 + - - +
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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