Contacts of the helix formed by residues 409 - 417 (chain A) in PDB entry 4FLZ
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 409 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406A PHE* 2.9 26.2 + - + +
408A SER* 1.3 78.5 - - - +
410A TYR* 1.3 70.9 + - + +
411A PRO 3.6 0.2 - - - -
412A SER* 3.4 10.7 + - - -
413A ILE* 3.4 31.7 + - + +
518A GLY* 4.0 24.2 - - - +
521A TYR* 3.8 24.7 - - + -
522A ILE* 4.4 13.2 - - + -
571A LEU* 5.8 4.3 - - + -
575A LEU* 3.6 38.0 - - + +
576A GLU 4.3 8.7 + - - +
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Residues in contact with TYR 410 (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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406A PHE* 4.0 13.5 - - + -
407A ARG* 3.6 22.0 - - + +
409A LEU* 1.3 77.3 - - + +
411A PRO* 1.4 69.8 - - + +
413A ILE* 3.0 18.6 + - + +
414A ILE* 3.0 18.1 + - - +
492A ASN* 6.5 0.4 - - - -
495A TYR* 3.4 54.0 + + + -
514A VAL* 3.2 33.4 - - + -
515A THR* 4.9 1.7 - - - -
518A GLY* 4.4 9.9 - - - -
522A ILE* 3.7 15.4 - - + +
541A THR* 2.6 42.8 + - - +
542A ASP* 5.4 0.7 - - - -
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Residues in contact with PRO 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ARG 3.6 14.4 - - - +
408A SER 4.0 6.5 - - - +
409A LEU 3.7 2.2 - - - -
410A TYR* 1.4 88.7 - - + +
412A SER* 1.3 62.0 + - - +
414A ILE* 3.2 6.8 + - + +
415A ILE* 3.0 30.6 + - - +
454A LEU* 4.0 30.2 - - + +
458A LEU* 4.1 17.3 - - + -
491A ALA* 3.6 20.6 - - + +
492A ASN* 3.5 20.6 - - - +
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Residues in contact with SER 412 (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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408A SER 4.7 1.0 + - - -
409A LEU 3.4 4.4 + - - -
410A TYR 3.2 0.4 - - - -
411A PRO* 1.3 79.7 - - - +
413A ILE* 1.3 56.7 + - - +
415A ILE* 3.4 8.2 + - - +
416A THR* 3.0 38.5 + - - +
458A LEU* 4.1 7.2 - - - +
574A LEU* 3.5 34.2 + - - +
575A LEU* 3.4 29.4 - - - -
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Residues in contact with ILE 413 (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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409A LEU* 3.4 36.2 + - + +
410A TYR* 3.0 12.7 + - + +
412A SER* 1.3 73.4 - - - +
414A ILE* 1.3 64.9 + - - +
416A THR* 3.4 6.4 + - - +
417A HIS* 3.1 32.8 + - + +
419A VAL* 4.2 0.2 - - - +
514A VAL* 4.1 25.8 - - + +
517A TRP* 3.7 28.3 - - + -
518A GLY* 3.6 28.9 - - - +
521A TYR* 4.2 12.1 - - + -
575A LEU* 4.5 7.0 - - + -
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Residues in contact with ILE 414 (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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410A TYR 3.0 23.5 + - - +
411A PRO* 3.5 6.5 - - + +
413A ILE* 1.3 75.7 - - - +
415A ILE* 1.4 55.7 + - - +
418A ASN* 3.0 7.8 + - - -
419A VAL* 2.9 52.4 + - + +
450A ILE* 4.2 3.8 - - + -
451A PRO* 3.7 10.0 - - + +
454A LEU* 3.7 28.7 - - + -
494A TYR* 4.3 2.9 - - + -
495A TYR* 4.2 27.6 - - + +
498A TYR* 4.1 19.7 - - + +
514A VAL* 3.6 22.9 - - + -
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Residues in contact with ILE 415 (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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411A PRO 3.0 22.2 + - - +
412A SER* 4.0 4.5 - - - +
414A ILE* 1.4 74.4 - - - +
416A THR* 1.3 68.3 + - + +
418A ASN* 3.1 16.3 + - - +
451A PRO* 3.5 30.1 - - + +
454A LEU* 3.7 13.0 - - + -
455A GLY* 3.5 26.0 - - - +
458A LEU* 3.6 27.6 - - + -
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Residues in contact with THR 416 (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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412A SER* 3.0 23.7 + - - +
413A ILE* 3.4 6.9 + - - +
415A ILE* 1.3 79.6 - - + +
417A HIS* 1.3 78.6 + - - +
418A ASN* 5.1 0.7 - - - +
433A ASP* 3.9 6.6 - - - +
444A LYS* 5.1 6.4 + - - -
575A LEU* 6.3 0.9 - - + -
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Residues in contact with HIS 417 (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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413A ILE* 3.1 25.1 + - + +
416A THR* 1.3 99.9 + - - +
418A ASN* 1.4 69.9 + - - +
419A VAL* 3.3 4.7 + - + +
433A ASP* 2.7 34.4 + - - +
442A PHE* 3.7 15.9 - - - +
444A LYS* 6.0 0.7 - - - +
517A TRP* 3.4 68.8 + + + +
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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