Contacts of the helix formed by residues 448 - 454 (chain U) in PDB entry 1FM6
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 ASP 448 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270U GLN* 3.7 28.7 - - - +
273U ASP* 3.2 44.2 - - + +
447U ILE* 1.3 80.2 - - - +
449U THR* 1.3 63.8 + - - +
450U PHE 3.2 1.0 + - - +
451U LEU* 3.3 3.4 + - - +
452U MET* 2.8 24.9 + - - +
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Residues in contact with THR 449 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277U PHE* 6.2 0.3 - - - -
447U ILE 4.5 0.9 - - - +
448U ASP* 1.3 73.5 - - - +
450U PHE* 1.3 58.6 + - - +
452U MET* 3.8 6.7 - - - +
453U GLU* 2.9 27.4 + - - +
632V ILE* 3.7 18.1 - - - +
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Residues in contact with PHE 450 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273U ASP* 2.9 18.0 + - - +
276U LEU* 3.5 44.7 - - + +
277U PHE* 3.5 37.2 - + + -
280U VAL* 4.4 11.7 - - + -
448U ASP 3.2 0.8 - - - -
449U THR* 1.3 77.9 + - - +
451U LEU* 1.3 66.5 + - - +
453U GLU* 3.1 24.1 + - - -
454U MET* 3.2 25.4 + - + +
632V ILE* 3.7 28.3 - - + -
633V LEU* 4.1 19.3 - - + -
636V LEU* 4.0 8.5 - - + -
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Residues in contact with LEU 451 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269U CYS* 3.8 46.2 - - + +
272U ALA* 4.6 9.2 - - + -
273U ASP* 2.8 23.6 + - + +
276U LEU* 3.6 12.5 - - + +
305U TRP* 3.6 34.8 - - + -
436U LEU* 4.2 12.8 - - + -
447U ILE* 3.8 21.1 - - + -
448U ASP 3.3 6.9 + - - +
450U PHE* 1.3 72.0 - - - +
452U MET* 1.3 66.3 + - - +
454U MET* 3.2 13.0 + - - +
455U LEU* 3.4 19.4 + - + +
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Residues in contact with MET 452 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440U LYS* 3.4 48.9 + - + +
446U PRO* 6.0 2.5 - - - -
447U ILE* 3.9 26.0 - - + +
448U ASP 2.8 19.3 + - - +
449U THR* 3.8 7.6 - - - +
451U LEU* 1.3 78.7 - - - +
453U GLU* 1.3 62.9 + - - +
455U LEU* 3.0 35.7 + - + +
456U GLU* 4.1 1.6 + - - +
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Residues in contact with GLU 453 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302U ARG* 3.5 14.6 + - - -
449U THR 2.9 20.2 + - - +
450U PHE* 3.1 12.5 + - - +
452U MET* 1.3 78.1 - - - +
454U MET* 1.3 60.8 + - + +
455U LEU 3.0 4.3 + - - -
456U GLU* 3.6 6.8 + - - +
629V ARG 5.3 0.9 - - - +
630V HIS* 3.4 32.8 - - + +
631V LYS* 3.1 10.2 + - - +
632V ILE* 3.0 33.5 + - + +
633V LEU* 3.2 26.3 + - - +
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Residues in contact with MET 454 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276U LEU* 4.4 10.3 - - + -
279U LEU* 6.1 0.9 - - + -
301U LEU* 3.7 17.0 - - + +
302U ARG* 3.7 25.1 - - + +
305U TRP* 3.6 47.8 - - + -
450U PHE* 3.2 26.6 + - + +
451U LEU 3.2 9.3 + - - +
453U GLU* 1.3 80.0 - - - +
455U LEU* 1.3 59.2 + - - +
456U GLU 3.5 1.1 - - - -
457U ALA* 2.9 22.5 - - + +
630V HIS* 6.3 0.2 - - + -
633V LEU* 3.2 42.8 - - + -
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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