Contacts of the strand formed by residues 475 - 479 (chain C) in PDB entry 2BT4
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 GLY 475 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409C ILE* 4.2 5.6 - - - -
410C MET* 3.0 24.9 + - - +
473C HIS* 3.3 5.5 + - - +
474C CYS* 1.3 83.6 - - - +
476C ILE* 1.3 66.5 + - - +
500C LEU* 3.8 8.7 - - - +
501C PRO* 3.4 15.9 - - - -
545C ILE* 4.3 7.9 - - - -
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Residues in contact with ILE 476 (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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410C MET* 3.3 9.6 - - + +
412C LEU* 4.4 12.3 - - + -
466C ILE* 4.3 8.3 - - + -
469C ALA* 3.9 24.9 - - + -
475C GLY* 1.3 79.7 - - - +
477C VAL* 1.3 78.1 + - - +
478C ILE* 3.9 17.0 - - + -
494C LEU* 3.9 23.3 - - + -
497C CYS* 4.3 9.2 - - - -
500C LEU* 3.8 19.7 - - + -
501C PRO 3.0 10.2 + - - +
502C VAL* 3.3 12.2 - - + +
503C VAL 2.9 25.6 + - - +
545C ILE* 3.9 4.5 - - - +
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Residues in contact with VAL 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C ILE* 4.1 3.6 - - + -
410C MET 2.9 6.7 + - - +
411C ILE* 3.2 35.4 - - + +
412C LEU 2.8 25.8 + - - +
476C ILE* 1.3 78.2 - - - +
478C ILE* 1.3 59.6 + - - +
503C VAL* 3.3 6.1 - - + +
505C VAL* 3.6 30.7 - - + -
538C TYR* 4.5 13.0 - - + +
541C GLY* 3.7 34.3 - - - +
542C VAL 4.0 2.7 - - - +
545C ILE* 4.0 9.9 - - + -
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Residues in contact with ILE 478 (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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412C LEU* 3.4 30.1 - - + +
462C LEU* 5.7 4.9 - - + -
466C ILE* 4.4 7.2 - - + -
476C ILE* 3.9 8.3 - - + -
477C VAL* 1.3 74.6 - - - +
479C ASN* 1.3 61.3 + - - +
480C PRO* 3.6 24.1 - - + +
490C ILE* 4.2 27.8 - - + -
494C LEU* 4.8 6.5 - - + -
502C VAL* 4.4 14.1 - - + -
503C VAL 2.9 15.0 + - - +
504C GLU* 3.3 8.5 - - - -
505C VAL* 2.8 26.9 + - - -
522C VAL* 4.2 17.0 - - + -
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Residues in contact with ASN 479 (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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412C LEU 2.9 7.9 + - - -
413C ASN* 3.4 6.1 - - - +
414C GLY 2.9 24.4 + - - -
417C LEU* 3.7 14.4 - - + +
478C ILE* 1.3 74.0 - - - +
480C PRO* 1.3 60.5 - - - +
481C ALA* 2.9 7.3 + - - -
505C VAL* 3.1 18.7 + - + +
507C ILE* 4.1 9.9 - - - +
538C TYR* 3.1 37.8 + - + +
560C CA2 2.8 41.3 + - - -
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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