Contacts of the helix formed by residues 437 - 443 (chain C) in PDB entry 1FSX
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 PRO 437 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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433C PHE 3.4 12.5 - - - +
434C LEU 3.7 13.0 - - - +
435C SER 3.4 9.4 - - - +
436C PHE* 1.3 85.1 - - - +
438C THR* 1.3 63.7 + - - +
439C THR 3.1 0.2 - - - -
440C LYS* 3.0 37.3 + - + +
441C THR* 4.2 1.6 + - - -
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Residues in contact with THR 438 (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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297B HIS* 3.7 32.9 + - + +
298B VAL 5.7 0.4 - - - -
299B ASP* 5.4 11.9 - - + +
345B TYR* 3.4 25.9 + - + +
436C PHE* 3.0 4.1 + - - -
437C PRO* 1.3 78.4 - - - +
439C THR* 1.3 58.1 + - - +
441C THR* 2.8 35.0 - - + -
442C TYR* 4.5 5.2 - - + -
497C ASN* 5.1 7.9 - - - +
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Residues in contact with THR 439 (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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432C MET* 3.4 41.3 + - + -
433C PHE* 3.5 13.1 - - - -
436C PHE* 2.7 21.2 + - + +
438C THR* 1.3 73.5 - - - +
440C LYS* 1.3 62.0 + - - +
441C THR 3.0 6.2 + - - -
442C TYR* 3.1 24.2 + - - +
443C PHE* 3.8 7.3 - - - -
497C ASN* 3.1 28.7 - - + +
500C LEU* 4.1 17.5 - - + -
543C HEM 4.2 4.5 - - + -
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Residues in contact with LYS 440 (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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433C PHE* 3.5 50.2 + - + +
434C LEU* 5.3 7.1 - - - +
437C PRO* 3.0 28.9 + - + +
439C THR* 1.3 77.4 + - - +
441C THR* 1.3 55.5 + - - +
443C PHE* 2.9 29.4 + - - +
444C PRO* 3.8 2.3 - - - +
448C LEU* 4.2 26.6 - - + +
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Residues in contact with THR 441 (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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240B ARG* 3.7 35.6 + - - +
296B LEU 5.3 2.7 - - - +
297B HIS* 3.6 39.3 - - + +
437C PRO 4.8 0.7 + - - -
438C THR* 2.8 22.0 + - + +
440C LYS* 1.3 78.3 - - - +
442C TYR* 1.3 60.3 + - + +
443C PHE 3.3 0.2 - - - -
444C PRO* 3.4 17.4 - - - +
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Residues in contact with TYR 442 (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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240B ARG* 3.6 44.4 + - - +
241B PHE* 5.7 1.2 - - - -
438C THR* 4.5 6.5 - - + -
439C THR* 3.1 19.3 + - - +
440C LYS 2.9 1.0 + - - -
441C THR* 1.3 80.0 - - + +
443C PHE* 1.3 72.3 + - + +
444C PRO* 3.2 9.8 - - - +
445C HIS* 4.0 5.2 - - - -
491C LEU* 4.3 6.1 - - + -
492C ARG 4.0 2.1 + - - -
493C VAL* 3.7 32.7 - - + -
494C ASP* 3.1 27.0 + - - +
497C ASN* 3.5 26.1 + - - -
543C HEM 3.3 39.6 - - + +
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Residues in contact with PHE 443 (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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429C LEU* 5.2 2.7 - - + -
432C MET* 5.0 1.8 - - + -
433C PHE* 3.7 33.4 - + - -
439C THR 3.8 6.3 - - - -
440C LYS 2.9 10.2 + - - +
442C TYR* 1.3 92.1 - - + +
444C PRO* 1.3 61.0 - - - +
445C HIS* 3.1 11.4 - + - -
446C PHE* 3.0 51.2 + + + +
448C LEU* 3.8 16.4 - - + +
458C HIS* 3.9 20.4 - + - -
542C CMO 4.1 10.3 - - - -
543C HEM 3.6 57.9 - + + -
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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