Contacts of the strand formed by residues 458 - 464 (chain C) in PDB entry 3SV1
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 458 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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439C ILE* 4.3 17.5 - - + -
453C HIS* 3.1 33.4 - - + +
454C ALA 3.0 21.1 - - - +
455C LEU* 3.6 19.6 - - - +
456C ARG 2.8 14.6 + - - +
457C THR* 1.3 78.2 - - - +
459C SER* 1.3 62.7 + - - +
460C TYR 3.6 22.9 - - - +
461C ILE* 5.0 2.9 - - + -
470C LEU* 4.4 18.6 - - + -
471C MET 3.8 9.0 - - - +
472C ALA* 4.2 2.9 - - + +
521C PHE* 3.8 17.9 - - + -
757F TYR* 3.0 13.4 - - - +
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Residues in contact with SER 459 (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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394C ARG* 2.9 33.2 + - - -
456C ARG 5.4 0.2 - - - -
457C THR 3.7 2.7 + - - -
458C ILE* 1.3 75.6 - - - +
460C TYR* 1.3 65.2 + - - +
471C MET* 3.2 5.1 + - - +
473C ARG* 5.7 2.0 - - - -
500C MET* 3.0 31.8 - - - +
757F TYR* 3.2 20.6 + - - -
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Residues in contact with TYR 460 (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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391C LYS* 5.5 5.6 - - + -
394C ARG* 3.6 43.3 - - + +
395C MET* 4.0 23.2 - - - +
398C ALA* 4.4 13.5 - - + -
458C ILE* 3.6 6.3 - - - +
459C SER* 1.3 82.2 + - - +
461C ILE* 1.3 100.5 + - - +
462C ALA* 3.6 17.1 - - + +
464C ILE* 5.8 1.4 - - - +
469C VAL* 4.2 6.3 - - + -
470C LEU* 3.1 27.9 - - - +
471C MET* 3.3 31.3 + - + -
756F GLY* 4.2 17.7 - - - -
757F TYR* 3.9 2.0 - - - +
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Residues in contact with ILE 461 (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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458C ILE* 5.0 2.7 - - + -
460C TYR* 1.3 100.8 + - - +
462C ALA* 1.3 62.0 + - - +
463C ASP* 5.8 1.1 - - - +
468C VAL* 5.9 0.9 - - + -
469C VAL 3.4 4.5 - - - +
470C LEU* 4.4 8.5 - - + -
514C ALA* 4.5 22.0 - - + +
517C ILE* 3.5 44.4 - - + -
518C GLY* 4.9 4.9 - - - +
521C PHE* 4.3 7.9 - - + -
756F GLY 3.1 34.1 - - - +
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Residues in contact with ALA 462 (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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398C ALA* 4.6 2.9 - - + -
460C TYR* 3.6 20.4 - - + +
461C ILE* 1.3 77.6 - - - +
463C ASP* 1.3 58.3 + - - +
464C ILE* 3.1 27.8 - - + -
467C ILE 3.1 17.3 - - - +
468C VAL* 3.4 15.4 - - - +
469C VAL* 3.0 22.8 + - + +
514C ALA* 4.4 3.7 - - - +
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Residues in contact with ASP 463 (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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461C ILE* 5.8 1.1 - - - +
462C ALA* 1.3 70.5 - - - +
464C ILE* 1.3 62.4 + - - +
465C GLY 3.3 12.6 + - - +
467C ILE 4.2 2.0 - - - -
510C ALA* 4.3 6.3 - - - -
511C GLN* 2.5 59.5 + - - +
514C ALA* 3.6 24.3 - - + +
515C GLN* 4.6 3.3 - - - +
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Residues in contact with ILE 464 (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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395C MET* 6.2 4.9 - - + -
398C ALA* 4.8 6.5 - - + -
399C GLN* 4.6 25.8 - - + +
402C VAL* 5.0 4.7 - - + -
460C TYR* 5.8 1.3 - - - +
462C ALA* 3.1 25.6 + - + -
463C ASP* 1.3 77.8 - - - +
465C GLY* 1.3 61.7 + - - +
467C ILE* 3.3 33.5 + - + +
469C VAL* 4.6 10.8 - - + -
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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