Contacts of the strand formed by residues 458 - 462 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439A ILE* 3.3 46.7 - - + -
453A HIS* 4.0 19.5 - - + +
454A ALA 3.8 5.4 - - - +
455A LEU* 2.8 22.5 + - - +
457A THR* 1.3 80.4 - - - +
459A SER* 1.3 61.0 + - - +
460A TYR 4.3 1.1 - - - +
461A ILE* 4.3 10.1 - - + -
470A LEU* 4.2 20.6 - - + -
471A MET 4.0 7.9 - - - +
472A ALA* 3.7 6.5 - - + -
521A PHE* 3.9 18.6 - - + -
759D ASN* 3.1 26.7 + - - +
762D TYR* 3.5 3.8 - - - +
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Residues in contact with SER 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A ARG* 4.4 4.4 - - - -
457A THR 3.8 0.2 + - - -
458A ILE* 1.3 72.4 - - - +
460A TYR* 1.3 64.8 + - - +
471A MET* 3.0 20.9 + - - +
500A MET* 3.9 16.3 - - - -
521A PHE* 3.9 2.2 - - - -
758D GLU* 3.1 7.8 - - - +
759D ASN 2.8 25.8 + - - -
762D TYR* 3.3 42.1 - - - -
763D LYS* 4.0 11.1 + - - +
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Residues in contact with TYR 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A LYS* 3.7 15.4 + - - -
394A ARG* 3.5 51.8 - - + -
395A MET* 3.4 24.1 + - - +
398A ALA* 4.3 6.5 - - + -
458A ILE* 3.9 0.8 - - - +
459A SER* 1.3 83.7 + - - +
461A ILE* 1.3 71.5 + - - +
462A ALA* 4.2 11.3 - - + +
469A VAL 5.4 0.2 - - - -
470A LEU* 3.3 2.1 - - - +
471A MET* 3.0 52.2 + - + +
521A PHE* 4.0 2.5 - - - -
756D GLY* 3.2 39.4 + - - -
757D TYR 3.0 24.5 - - - -
758D GLU* 3.8 5.6 - - + -
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Residues in contact with ILE 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A ILE* 4.3 9.0 - - + -
460A TYR* 1.3 83.8 - - - +
462A ALA* 1.3 63.2 + - - +
468A VAL* 5.4 2.5 - - + -
469A VAL 3.1 11.7 - - - +
470A LEU* 3.4 19.5 - - + -
514A ALA* 4.1 11.0 - - + +
517A ILE* 3.4 51.8 - - + -
518A GLY 4.4 1.8 - - - +
521A PHE* 4.0 5.6 - - + -
756D GLY* 3.0 22.3 - - - -
757D TYR* 3.0 49.4 + - + +
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Residues in contact with ALA 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A MET* 5.9 2.2 - - + -
398A ALA* 5.1 9.0 - - + -
460A TYR* 4.2 13.5 - - + +
461A ILE* 1.3 78.1 - - - +
463A ASP* 1.3 61.9 + - - +
464A ILE* 3.8 16.1 - - + +
467A ILE 3.7 1.1 - - - +
468A VAL* 3.3 9.4 - - - +
469A VAL* 2.9 33.1 + - + +
514A ALA* 4.3 2.5 - - - -
755D ASN 3.0 16.4 - - - +
756D GLY* 3.9 5.6 - - - -
757D TYR* 5.2 0.2 - - - -
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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