Contacts of the strand formed by residues 722 - 728 (chain B) in PDB entry 3BBT
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 PRO 722 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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710B GLY 3.9 7.3 - - - +
711B ILE* 4.1 2.1 - - + -
720B LYS 3.8 0.2 - - - -
721B ILE* 1.3 100.1 - - + +
723B VAL* 1.3 58.2 + - - +
772B GLN* 4.2 4.9 - - - +
773B LEU* 3.2 36.4 + - + +
719D VAL* 3.5 41.5 - - + -
721D ILE* 4.1 18.4 - - + -
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Residues in contact with VAL 723 (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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693B LEU* 4.2 3.1 - - + -
709B LYS 3.9 0.3 - - - -
710B GLY 2.9 41.7 + - - +
712B TRP* 4.1 17.7 - - + -
721B ILE* 2.9 20.4 + - + +
722B PRO* 1.3 71.3 - - - +
724B ALA* 1.3 58.3 + - - +
725B ILE* 4.1 12.3 - - + -
759B LEU* 4.2 9.0 - - + -
770B VAL* 3.3 31.4 - - + -
771B THR 2.7 27.4 - - - +
772B GLN* 3.9 4.7 - - - +
773B LEU* 3.7 10.4 - - - +
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Residues in contact with ALA 724 (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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91B FMM 3.2 49.5 - - + +
699B LEU* 5.0 1.6 - - + -
707B VAL* 4.6 2.9 - - + -
708B TYR 3.4 7.0 - - - +
709B LYS* 4.9 0.2 - - - +
723B VAL* 1.3 73.9 - - - +
725B ILE* 1.3 62.6 + - - +
770B VAL* 3.5 3.8 - - - +
771B THR* 2.5 43.3 + - + +
773B LEU* 4.1 8.9 - - + +
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Residues in contact with ILE 725 (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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91B FMM 3.9 1.8 - - - -
693B LEU* 3.8 37.2 - - + -
694B LYS 4.6 3.8 - - - +
695B ARG* 4.5 16.6 - - + -
706B THR 3.4 2.6 - - - +
707B VAL* 3.4 2.3 - - - -
708B TYR* 2.7 45.9 + - + +
710B GLY* 3.8 26.7 - - - +
711B ILE 4.8 0.2 - - - +
723B VAL* 4.1 6.1 - - + -
724B ALA* 1.3 77.5 - - - +
726B LYS* 1.3 61.0 + - - +
727B ILE* 3.7 15.2 + - + -
768B GLN* 4.0 31.4 - - + +
769B LEU 3.5 4.0 - - - +
770B VAL* 4.7 5.8 - - + -
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Residues in contact with LYS 726 (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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91B FMM 3.4 25.4 - - + +
702B GLY* 5.8 4.9 - - - +
704B PHE* 4.4 10.1 - - - +
705B GLY 4.8 6.5 - - - +
706B THR 3.4 9.0 - - - +
707B VAL* 3.6 25.8 - - + +
725B ILE* 1.3 70.2 - - - +
727B ILE* 1.3 61.2 + - - +
728B LEU* 3.7 20.8 + - + +
767B ILE 3.8 0.3 - - - +
768B GLN* 3.2 3.6 - - - -
769B LEU* 2.7 58.7 + - + +
836B ASP* 3.9 17.9 + - - -
839B LEU* 3.8 31.9 - - - +
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Residues in contact with ILE 727 (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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695B ARG* 3.5 42.4 - - - +
705B GLY* 3.3 2.5 - - - -
706B THR* 2.8 41.0 + - - +
708B TYR* 3.6 20.2 - - + -
725B ILE* 4.0 11.7 - - + -
726B LYS* 1.3 70.4 - - - +
728B LEU* 1.3 64.5 + - - +
729B ASN* 3.7 5.7 + - + +
766B THR* 3.4 25.1 - - - +
767B ILE 3.9 2.9 - - - -
768B GLN* 3.6 26.5 - - + +
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Residues in contact with LEU 728 (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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704B PHE* 3.7 37.2 - - + +
705B GLY 4.2 0.4 - - - +
726B LYS* 4.1 24.2 - - + +
727B ILE* 1.3 73.5 - - - +
729B ASN* 1.3 58.3 + - - +
730B GLU* 4.3 2.7 + - - +
733B GLY 4.9 5.0 + - - -
734B PRO* 4.5 13.7 - - + -
766B THR* 4.1 21.3 + - - +
767B ILE* 3.4 28.1 + - + +
769B LEU* 4.2 9.6 - - + -
839B LEU* 4.9 4.9 - - + -
842B LEU* 3.9 30.1 - - + -
843B LEU* 3.9 20.6 - - + -
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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