Contacts of the helix formed by residues 431 - 441 (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 SER 431 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424A GLN* 3.5 24.8 + - - -
425A ILE* 4.2 6.9 + - - +
428A GLY* 4.0 13.1 + - - -
429A TYR 3.8 0.8 - - - -
430A GLN* 1.3 81.2 + - - +
432A GLY* 1.4 65.0 + - - +
433A HIS 3.4 2.6 + - - -
434A ASN* 3.5 10.1 + - - +
435A VAL* 3.4 26.2 + - - +
469A ARG* 3.9 19.6 + - - +
248C MET* 4.8 0.7 - - - -
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Residues in contact with GLY 432 (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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430A GLN* 3.7 1.4 - - - +
431A SER* 1.4 78.3 - - - +
433A HIS* 1.3 60.9 + - - +
435A VAL* 3.2 8.9 + - - +
436A LEU* 3.2 31.2 + - - +
593A GLN* 4.7 2.3 + - - -
248C MET* 3.6 39.3 - - - +
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Residues in contact with HIS 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A SER 3.4 0.4 - - - -
432A GLY* 1.3 74.5 - - - +
434A ASN* 1.4 64.0 + - - +
436A LEU* 3.3 17.6 + - + +
437A LYS* 3.1 50.2 + - + +
1C MET 3.2 29.6 + - - -
2C GLY* 4.3 8.2 - - - -
3C GLY 5.1 3.6 - - - -
132C ASN* 4.5 7.2 - - - -
248C MET* 5.1 1.6 - - - +
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Residues in contact with ASN 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A SER* 3.5 14.7 + - - +
433A HIS* 1.4 80.1 - - - +
435A VAL* 1.3 54.8 + - - +
437A LYS* 3.3 4.8 + - - +
438A PHE* 2.8 34.4 + - - +
465A PHE* 3.3 38.4 - - - -
469A ARG* 3.4 36.5 - - - +
479A ARG* 3.6 12.7 - - - +
484A ILE* 6.1 2.8 - - - +
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Residues in contact with VAL 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A SER* 3.4 20.4 + - - +
432A GLY* 3.2 10.6 + - - +
434A ASN* 1.3 78.9 - - + +
436A LEU* 1.3 63.0 + - - +
438A PHE* 3.6 7.7 - - + +
439A LEU* 3.1 30.4 + - + +
589A GLN* 6.2 2.5 - - + -
590A LEU* 3.5 33.4 - - + -
593A GLN* 3.8 25.6 - - + +
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Residues in contact with LEU 436 (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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432A GLY 3.2 19.6 + - - +
433A HIS* 3.6 17.7 - - + +
435A VAL* 1.3 78.9 - - - +
437A LYS* 1.3 65.3 + - + +
439A LEU* 3.4 5.8 + - + +
440A THR* 3.1 26.8 + - + +
593A GLN* 3.6 38.4 - - + +
597A ARG* 4.1 18.8 - - + +
248C MET* 4.5 19.7 - - + +
251C SER* 5.9 4.3 - - - -
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Residues in contact with LYS 437 (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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433A HIS* 3.1 46.7 + - + +
434A ASN* 4.0 2.9 - - - +
436A LEU* 1.3 77.6 - - + +
438A PHE* 1.4 61.0 + - - +
440A THR* 2.8 39.8 + - - +
441A LYS* 3.5 18.2 + - - -
465A PHE* 4.1 15.9 - - + -
1C MET 5.3 1.3 - - - +
132C ASN* 3.8 27.5 + - - +
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Residues in contact with PHE 438 (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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434A ASN* 2.8 24.8 + - - +
435A VAL* 3.6 9.2 - - + +
437A LYS* 1.4 71.9 - - - +
439A LEU* 1.4 57.3 + - + +
441A LYS* 2.8 26.2 - - - +
446A LEU* 4.9 12.7 - - + +
458A TYR* 4.0 31.4 - + - -
461A LEU* 3.6 23.5 - - + +
462A LEU* 4.6 8.3 - - + -
465A PHE* 3.7 25.4 - + + -
484A ILE* 3.9 32.3 - - + -
560A LEU* 4.4 14.4 - - + -
590A LEU* 4.3 26.0 - - + -
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Residues in contact with LEU 439 (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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435A VAL* 3.1 36.0 + - + +
436A LEU* 3.7 6.3 - - + +
438A PHE* 1.4 63.9 - - + +
440A THR* 1.4 67.9 + - - +
441A LYS 3.4 5.2 - - - +
442A ASN 4.3 0.3 - - - -
443A MET* 3.8 10.9 - - - -
446A LEU* 4.4 21.5 - - + +
590A LEU* 3.9 24.0 - - + -
593A GLN* 4.0 7.0 - - + +
594A TYR* 3.6 46.9 - - + +
597A ARG* 3.3 27.4 + - - +
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Residues in contact with THR 440 (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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436A LEU* 3.1 17.5 + - + +
437A LYS* 2.8 43.4 + - - +
439A LEU* 1.4 77.9 - - - +
441A LYS* 1.3 64.3 + - - +
442A ASN 3.4 2.8 + - - -
443A MET* 3.6 12.5 + - - +
597A ARG* 3.6 33.8 + - - +
601A GLU* 5.7 2.7 - - - +
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Residues in contact with LYS 441 (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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437A LYS* 3.5 20.5 + - - +
438A PHE 2.8 19.4 - - - +
439A LEU 3.3 1.8 - - - +
440A THR* 1.3 78.3 + - - +
442A ASN* 1.3 70.2 + - - +
446A LEU* 4.8 1.2 - - - +
461A LEU* 3.4 37.4 - - + +
464A ASN* 4.6 11.7 - - - +
465A PHE* 3.3 36.6 - - - -
468A GLU* 4.5 7.1 + - - -
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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