Contacts of the helix formed by residues 442 - 448 (chain A) in PDB entry 5FLZ
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 ASN 442 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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439A LEU 4.3 0.7 - - - -
440A THR 3.4 1.0 + - - -
441A LYS* 1.3 75.3 - - - +
443A MET* 1.4 64.9 + - - +
444A GLY 3.4 2.2 - - - -
445A GLU* 3.0 41.7 + - + +
446A LEU* 3.2 30.4 + - + +
457A ASN* 3.4 32.9 - - - +
458A TYR* 3.4 8.7 + - - +
461A LEU* 3.4 22.2 - - + +
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Residues in contact with MET 443 (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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439A LEU 3.8 8.1 - - - +
440A THR 3.6 13.8 + - - +
441A LYS 3.5 1.4 - - - -
442A ASN* 1.4 75.2 - - - +
444A GLY* 1.3 64.6 + - - +
446A LEU* 3.5 5.7 + - - +
447A THR* 2.9 31.3 + - - +
597A ARG* 3.5 26.7 - - - +
598A LEU* 4.6 22.9 - - + -
704A TYR* 3.6 25.4 - - - +
711A LYS* 5.2 6.7 - - - +
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Residues in contact with GLY 444 (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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442A ASN 3.4 0.8 - - - -
443A MET* 1.3 88.2 - - - +
445A GLU* 1.4 58.4 + - - +
447A THR* 3.5 17.1 + - - -
448A LYS* 3.6 23.8 + - - +
704A TYR* 5.7 0.7 - - - -
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Residues in contact with GLU 445 (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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442A ASN* 3.0 42.7 + - + +
444A GLY* 1.4 58.8 - - - +
446A LEU* 1.3 62.8 + - + +
447A THR 3.4 0.2 - - - -
448A LYS* 3.2 20.0 + - - +
453A ASP* 5.0 2.0 - - - +
454A ASN* 3.2 58.8 - - + +
457A ASN* 3.1 30.3 - - - +
486A PHE* 5.4 0.9 - - - -
556A ALA* 4.3 2.8 - - - +
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Residues in contact with LEU 446 (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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438A PHE* 4.9 13.5 - - + +
439A LEU* 4.4 33.4 - - + +
441A LYS 4.8 1.3 - - - +
442A ASN* 3.2 26.5 + - + +
443A MET* 3.8 5.2 - - - +
444A GLY 3.4 0.2 - - - -
445A GLU* 1.3 81.0 - - + +
447A THR* 1.3 59.4 + - - +
448A LYS 2.9 12.6 - - - +
458A TYR* 4.8 14.1 - - + -
461A LEU* 6.3 0.2 - - + -
486A PHE* 5.5 4.0 - - + -
556A ALA* 3.1 34.3 + - + +
557A ILE* 4.1 14.5 - - + +
560A LEU* 4.2 18.4 - - + -
594A TYR* 6.6 0.2 - - + -
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Residues in contact with THR 447 (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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443A MET* 2.9 27.9 + - - +
444A GLY* 3.5 11.2 - - - -
445A GLU 3.4 0.6 - - - -
446A LEU* 1.3 76.6 - - - +
448A LYS* 1.4 60.9 + - + +
554A LYS 5.0 0.5 - - - +
555A SER* 4.0 13.2 - - - -
557A ILE* 5.6 5.6 - - - +
594A TYR* 5.7 6.8 - - + -
598A LEU* 6.0 1.4 - - - +
700A PHE* 6.5 1.1 - - + -
704A TYR* 3.9 33.6 + - + -
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Residues in contact with LYS 448 (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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444A GLY 3.6 19.0 + - - +
445A GLU* 3.2 16.1 - - - +
446A LEU 2.9 15.5 - - - +
447A THR* 1.4 77.7 - - + +
449A HIS* 1.3 71.6 + - + +
451A ARG* 3.9 35.8 - - - +
454A ASN* 4.5 3.8 - - - +
554A LYS 4.5 0.7 - - - -
555A SER* 4.0 1.6 - - - -
556A ALA* 3.0 9.9 + - - +
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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