Contacts of the helix formed by residues 448 - 453 (chain C) in PDB entry 5M8N
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 THR 448 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C THR* 5.4 2.2 - - + +
436C ARG 3.7 11.7 - - - -
437C GLN* 3.5 29.8 + - - +
438C TYR 3.3 8.1 - - - -
439C ASN* 3.4 20.0 - - - +
440C MET* 3.8 5.1 - - - +
446C PRO 5.8 0.2 - - - -
447C VAL* 1.3 78.1 - - - +
449C ASN* 1.3 65.7 + - - +
450C THR* 3.1 16.5 + - - -
451C GLU* 3.0 40.0 + - - +
452C MET 3.9 1.2 + - - -
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Residues in contact with ASN 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C ALA* 3.1 20.7 - - - +
222C THR* 2.4 46.3 + - - +
425C PHE* 3.7 18.8 - - + -
433C GLY 3.6 18.2 + - - -
434C HIS 4.0 1.6 - - - -
435C ASN 3.0 26.7 + - - -
436C ARG* 3.4 7.4 - - + +
438C TYR 3.4 9.1 + - - -
440C MET* 3.4 17.8 - - - +
448C THR* 1.3 72.5 - - - +
450C THR* 1.3 64.4 + - - +
452C MET 3.0 11.8 + - - -
453C PHE* 3.4 2.6 + - - +
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Residues in contact with THR 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C ILE* 4.2 17.5 - - + -
436C ARG* 3.1 20.1 + - - +
437C GLN* 2.7 28.1 + - - +
448C THR* 3.0 10.1 + - - -
449C ASN* 1.3 76.9 - - - +
451C GLU* 1.3 58.3 + - + +
453C PHE* 2.9 30.9 + - - +
454C VAL* 4.2 4.0 - - - +
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Residues in contact with GLU 451 (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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64A ARG* 6.2 1.6 - - - -
114C ARG* 4.0 21.3 + - - -
446C PRO 4.2 4.3 - - - +
447C VAL* 3.5 24.3 - - + +
448C THR* 3.0 39.5 + - - +
450C THR* 1.3 77.2 - - + +
452C MET* 1.3 71.5 + - + +
453C PHE 3.5 0.4 - - - -
454C VAL* 3.9 17.7 - - - +
460C LEU* 4.2 2.6 - - - +
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Residues in contact with MET 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C PRO* 5.4 4.0 - - + -
222C THR* 3.7 35.7 - - + +
225C ARG* 2.9 58.1 + - + +
226C TYR* 3.8 36.1 - - + -
229C LEU* 4.8 9.6 - - + -
411C PHE* 3.9 4.5 - - - -
440C MET* 4.1 11.7 - - + -
447C VAL* 4.0 11.0 - - + -
448C THR 4.4 0.7 - - - +
449C ASN 3.0 3.2 + - - -
451C GLU* 1.3 98.1 - - + +
453C PHE* 1.3 57.5 + - - +
454C VAL* 3.0 8.2 + - - -
460C LEU* 4.2 17.7 - - + -
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Residues in contact with PHE 453 (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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222C THR* 4.4 2.0 - - + -
342C PHE* 3.6 38.6 - + - -
411C PHE* 4.0 17.0 - + - -
414C TRP* 3.9 11.4 - + - -
415C LEU* 3.6 16.8 - - + -
420C ALA* 3.3 34.4 - - - +
421C ASP 3.8 11.0 - - - -
422C ILE* 3.6 40.2 - - + +
425C PHE* 4.0 19.1 - + + -
449C ASN 3.4 8.1 + - - +
450C THR 2.9 12.8 + - - +
451C GLU 3.5 0.2 - - - -
452C MET* 1.3 74.4 - - - +
454C VAL* 1.3 65.2 + - - +
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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