Contacts of the strand formed by residues 428 - 434 (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 THR 428 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377C TYR* 3.0 48.1 + - + +
426C THR 4.4 7.0 - - - +
427C LEU* 1.3 77.9 - - - +
429C GLU* 1.3 65.1 + - - +
430C VAL* 3.3 16.8 - - - +
443C ASN* 4.3 6.6 + - - -
450C MET* 3.7 11.1 - - + +
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Residues in contact with GLU 429 (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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375C ALA 4.0 4.9 - - - +
376C ASN* 4.0 14.0 + - - +
427C LEU* 5.0 5.2 - - + +
428C THR* 1.3 71.6 + - - +
430C VAL* 1.3 57.2 + - - +
443C ASN* 2.7 16.4 + - - +
444C ALA* 2.7 36.1 + - + +
445C ASP* 5.3 4.4 - - + +
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Residues in contact with VAL 430 (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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374C ALA* 3.2 8.7 - - - +
375C ALA 3.0 39.2 + - - +
377C TYR* 4.0 5.6 - - + -
428C THR* 3.3 19.1 - - - +
429C GLU* 1.3 83.0 - - - +
431C ASP* 1.3 58.8 - - - +
432C LEU* 3.8 13.7 - - + -
441C VAL* 3.8 19.3 - - + -
442C LEU 3.6 3.8 - - - +
443C ASN* 3.8 1.8 - - - -
444C ALA* 3.2 13.8 - - - +
450C MET* 3.4 30.3 - - + -
505C PHE* 3.9 11.7 - - + -
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Residues in contact with ASP 431 (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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404B ARG* 3.1 31.1 + - - +
372C ILE* 3.2 19.8 - - + +
373C PHE 3.4 3.1 - - - -
374C ALA* 3.6 16.5 - - - +
430C VAL* 1.3 73.4 - - - +
432C LEU* 1.3 63.8 + - - +
433C PHE 3.4 1.4 + - - -
441C VAL* 3.4 3.6 - - - -
442C LEU* 2.9 45.2 + - + +
444C ALA* 3.4 17.1 - - - +
447C GLN* 3.0 29.2 + - - +
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Residues in contact with LEU 432 (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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372C ILE* 3.2 4.4 - - - -
373C PHE* 2.5 42.8 + - + +
375C ALA* 4.4 16.8 - - + +
430C VAL* 3.8 22.7 - - + -
431C ASP* 1.3 75.8 - - - +
433C PHE* 1.3 59.7 + - - +
434C ILE* 3.3 21.9 - - + +
439C ILE* 4.7 9.9 - - + -
440C LYS 3.7 1.8 - - - +
441C VAL* 3.6 22.7 - - + -
470C LEU* 5.9 3.1 - - + -
505C PHE* 4.1 25.4 - - + -
513C ILE* 4.5 13.9 - - + -
517C ILE* 6.1 3.8 - - + -
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Residues in contact with PHE 433 (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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407B ARG* 3.9 22.2 - - - -
369C ASP 3.6 17.5 - - - -
370C GLY* 3.5 20.6 - - - -
371C ILE 3.7 2.2 - - - -
372C ILE* 3.7 26.5 - - + -
431C ASP 3.4 1.8 + - - -
432C LEU* 1.3 71.8 - - - +
434C ILE* 1.3 60.5 + - - +
435C SER* 3.6 27.6 - - - -
438C ARG* 4.1 13.0 - - + -
439C ILE* 3.2 5.5 - - - -
440C LYS* 2.8 69.0 + - + +
442C LEU* 4.5 9.9 - - + -
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Residues in contact with ILE 434 (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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367C LEU* 3.6 24.7 - - + -
370C GLY* 3.0 23.3 - - - -
371C ILE* 3.0 19.7 + - + +
373C PHE* 3.9 20.0 - - + -
432C LEU* 3.3 35.7 - - + +
433C PHE* 1.3 76.2 - - - +
435C SER* 1.3 70.9 + - - +
438C ARG 4.2 1.8 - - - -
439C ILE* 4.4 12.1 - - + -
513C ILE* 4.3 9.6 - - + +
516C SER* 3.8 14.4 - - - +
517C ILE* 3.8 26.5 - - + +
520C ALA* 4.2 4.0 - - + -
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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