Contacts of the strand formed by residues 428 - 434 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376B ASN* 3.5 4.5 - - - -
377B TYR* 2.7 53.6 + - + +
426B THR 4.8 4.0 - - - +
427B LEU* 1.3 80.3 - - - +
429B GLU* 1.3 63.1 + - - +
430B VAL* 3.6 15.9 - - - +
443B ASN* 4.4 7.2 + - - -
450B MET* 4.4 6.9 - - + +
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Residues in contact with GLU 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375B ALA 3.7 5.6 - - - +
376B ASN* 3.9 14.8 - - - +
428B THR* 1.3 68.1 + - - +
430B VAL* 1.3 70.8 + - - +
443B ASN* 3.2 8.6 + - - +
444B ALA* 2.9 32.5 + - + -
445B ASP* 3.7 18.9 - - + +
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Residues in contact with VAL 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B ALA* 3.3 7.8 - - - +
375B ALA 2.9 45.5 + - - +
377B TYR* 3.9 7.4 - - + +
428B THR* 3.6 10.3 - - - +
429B GLU* 1.3 86.3 - - - +
431B ASP* 1.3 66.9 + - - +
432B LEU* 4.0 6.1 - - + -
441B VAL* 4.3 2.5 - - + -
442B LEU 3.3 11.7 - - - +
443B ASN* 4.2 0.7 - - - -
444B ALA* 3.6 4.6 - - - +
450B MET* 3.3 35.2 - - + -
505B PHE* 3.7 34.3 - - + -
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Residues in contact with ASP 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A ARG* 2.6 36.0 + - - -
372B ILE* 3.6 18.8 - - + +
373B PHE 3.8 4.7 - - - -
374B ALA* 5.0 5.4 - - - +
430B VAL* 1.3 76.3 - - - +
432B LEU* 1.3 70.7 + - - +
433B PHE* 3.9 1.6 - - + +
441B VAL* 3.3 3.8 - - - +
442B LEU* 2.9 38.2 + - + +
444B ALA* 3.9 8.1 - - - +
447B GLN* 2.5 32.7 + - - +
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Residues in contact with LEU 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371B ILE 3.4 0.2 - - - +
372B ILE* 3.2 21.4 - - - +
373B PHE* 3.0 23.1 + - + +
375B ALA* 3.8 25.1 - - + -
430B VAL* 4.0 7.2 - - + +
431B ASP* 1.3 85.0 - - - +
433B PHE* 1.3 60.7 + - - +
434B ILE* 3.1 15.6 + - + +
439B ILE* 5.8 4.0 - - + -
440B LYS 3.7 2.7 - - - +
441B VAL* 3.3 24.5 - - + -
468B VAL* 5.2 3.4 - - + -
505B PHE* 3.6 26.9 - - + -
513B ILE* 3.7 31.0 - - + -
517B ILE* 6.5 1.3 - - + -
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Residues in contact with PHE 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A ARG* 3.5 24.7 - - - -
369B ASP 3.3 15.7 - - - -
370B GLY* 3.3 24.7 - - - -
371B ILE 3.4 13.0 - - - -
372B ILE* 4.1 10.5 - - + +
431B ASP* 3.9 1.9 - - + +
432B LEU* 1.3 68.2 - - - +
434B ILE* 1.3 60.8 + - - +
435B SER* 3.7 20.1 + - - -
437B GLN* 4.9 6.3 - - - -
438B ARG* 4.0 30.5 - - + -
439B ILE* 3.0 27.2 - - - -
440B LYS* 3.0 33.2 + - + +
442B LEU* 5.8 5.6 - - + +
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Residues in contact with ILE 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B LEU* 3.9 6.1 - - + +
370B GLY* 3.4 2.1 - - - -
371B ILE* 3.3 33.0 + - + +
373B PHE* 3.8 19.1 - - + -
432B LEU* 3.1 16.8 + - + +
433B PHE* 1.3 71.4 - - - +
435B SER* 1.3 69.5 + - - +
439B ILE* 4.4 7.9 - - + -
513B ILE* 3.5 30.1 - - + +
516B SER* 3.4 38.4 - - - +
517B ILE* 3.5 27.1 - - + -
520B ALA* 3.9 7.9 - - + -
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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