Contacts of the strand formed by residues 449 - 453 (chain C) in PDB entry 3SRF
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 ILE 449 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427C LEU* 3.2 10.5 - - + +
429C VAL* 3.7 32.1 - - + -
437C ALA* 4.5 13.2 - - + +
440C VAL* 3.8 19.3 - - + -
441C ALA* 3.7 40.6 - - + +
445C PRO* 3.8 17.0 - - + -
447C ALA 4.2 0.9 - - - +
448C PRO* 1.3 73.9 - - - +
450C ILE* 1.3 59.0 + - - +
451C ALA 3.0 6.9 + - - +
466C ARG 4.2 1.8 - - - +
467C GLY* 2.7 24.6 + - - +
468C ILE* 3.5 5.5 - - + +
469C PHE* 2.9 23.7 + - - -
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Residues in contact with ILE 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C ALA* 4.1 10.5 - - + -
427C LEU 2.6 12.7 + - - +
428C ILE* 3.5 11.0 - - + -
429C VAL 3.0 21.2 + - - -
448C PRO* 4.9 2.7 - - + +
449C ILE* 1.3 67.7 - - - +
451C ALA* 1.3 60.1 + - - +
452C VAL* 3.3 4.7 + - - +
469C PHE* 3.4 16.2 - - + +
471C VAL* 4.0 22.4 - - + -
492C ALA* 3.7 32.8 - - + +
495C VAL* 4.8 3.6 - - + -
496C GLY* 4.4 3.4 - - - +
501C PHE* 4.0 26.5 - - + -
502C PHE* 3.7 31.2 - - + -
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Residues in contact with ALA 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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429C VAL* 3.3 8.7 - - - +
431C THR* 3.9 11.0 - - + -
437C ALA* 3.8 20.9 - - + -
449C ILE 3.0 7.2 + - - +
450C ILE* 1.3 68.8 - - - +
452C VAL* 1.3 63.0 + - - +
453C THR* 3.8 3.6 + - + +
462C ALA* 5.5 1.8 - - + -
468C ILE* 3.7 26.9 - - + -
469C PHE 3.3 3.4 + - - -
470C PRO* 3.4 6.2 - - + +
471C VAL* 3.0 26.0 + - - +
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Residues in contact with VAL 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C ILE* 4.3 0.4 - - + -
429C VAL 2.8 8.1 + - - -
430C LEU* 3.6 18.8 - - + +
431C THR* 3.1 24.7 + - - +
450C ILE 3.9 5.8 - - - +
451C ALA* 1.3 72.5 - - - +
453C THR* 1.3 60.8 + - - +
471C VAL* 3.7 14.6 - - + -
473C CYS* 4.4 5.6 - - + -
488C ARG* 3.5 45.6 + - + +
491C PHE* 4.3 13.7 - - + -
492C ALA* 3.3 34.3 - - + +
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Residues in contact with THR 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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431C THR* 3.2 25.2 + - + -
432C GLU* 4.0 1.9 + - - -
451C ALA* 4.6 5.8 - - + +
452C VAL* 1.3 73.9 - - - +
454C ARG* 1.3 64.2 + - - +
455C ASN* 3.2 24.5 + - - +
458C THR* 3.9 12.0 - - + -
459C ALA* 3.7 36.3 - - + +
470C PRO* 5.2 1.6 - - + -
471C VAL 3.1 13.5 + - - +
472C LEU* 3.4 4.1 - - + +
473C CYS* 3.1 25.0 + - - -
488C ARG* 6.1 1.8 - - - +
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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