Contacts of the strand formed by residues 653 - 656 (chain A) in PDB entry 4BI2
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 PHE 653 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608A ASP* 3.4 8.5 - - - +
609A LEU* 2.9 34.3 + - + -
630A ASN 5.1 0.4 - - - -
631A MET* 3.6 40.2 - - + -
634A ALA* 4.3 11.0 - - + -
635A VAL* 4.3 9.6 - - + -
648A LEU* 4.0 23.1 - - + -
649A LYS 3.7 12.8 - - - -
650A PRO* 2.9 11.6 + - + +
651A ALA 3.7 1.3 - - - +
652A ASN* 1.3 78.2 - - + +
654A LEU* 1.3 61.7 + - - +
660A LEU* 3.8 25.1 - - + -
661A LYS* 3.3 17.0 - - - -
662A LEU* 4.1 21.8 - - + -
663A ILE* 4.4 0.2 - - - -
720A LEU* 4.3 2.2 - - + -
723A ILE* 4.1 16.2 - - + -
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Residues in contact with LEU 654 (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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586A ILE* 4.0 13.2 - - + -
603A GLU 4.7 1.1 - - - +
605A GLY* 3.7 9.9 - - - +
607A ILE 3.5 19.3 - - - +
608A ASP* 4.1 1.6 - - + +
653A PHE* 1.3 77.2 - - - +
655A ILE* 1.3 62.4 + - - +
656A VAL* 3.6 24.6 + - + +
659A MET 3.4 2.3 - - - +
660A LEU* 3.8 3.6 - - - -
661A LYS* 2.8 35.2 + - + +
663A ILE* 3.5 30.5 - - + -
1797A ZO8 3.3 55.0 - - + +
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Residues in contact with ILE 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A GLY* 3.6 1.2 - - - -
606A ASN* 2.9 33.8 + - + +
607A ILE* 2.8 23.7 + - + +
609A LEU* 3.9 23.1 - - + -
612A TRP* 3.5 44.4 - - + -
627A TYR* 3.8 24.2 - - + +
654A LEU* 1.3 70.7 - - - +
656A VAL* 1.3 62.0 + - - +
658A GLY* 4.0 20.6 - - - +
659A MET 3.6 5.2 - - - +
660A LEU* 3.5 14.8 - - + -
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Residues in contact with VAL 656 (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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603A GLU* 3.9 19.7 - - - +
604A CYS 3.6 21.5 - - - +
605A GLY* 3.8 3.6 - - - +
606A ASN* 3.4 4.0 - - - +
654A LEU* 3.7 31.9 - - + +
655A ILE* 1.3 78.7 - - - +
657A ASP* 1.3 90.5 + - - +
659A MET* 2.8 26.8 + - - +
661A LYS* 4.0 23.2 - - + -
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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
------------------------------------------------------------
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