Contacts of the strand formed by residues 758 - 762 (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 LEU 758 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B FMM 3.9 24.5 - - + -
685B LEU* 3.8 23.7 - - + +
744B ALA* 3.9 15.7 - - + +
747B MET* 4.0 33.5 + - + +
748B ALA* 4.2 16.4 - - - +
756B VAL 3.9 2.4 + - - -
757B ARG* 1.3 76.6 + - - +
759B LEU* 1.3 66.4 + - - +
760B GLY 3.7 14.8 - - - +
761B VAL* 4.0 9.2 - - + -
769B LEU* 3.9 27.1 - - + -
770B VAL 3.4 17.9 - - - +
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Residues in contact with LEU 759 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684B GLN 5.2 1.7 - - - +
685B LEU* 5.0 1.4 - - - -
686B ARG* 3.4 31.7 + - - +
688B LEU* 6.4 0.4 - - + -
712B TRP* 5.2 16.2 - - + -
721B ILE* 5.6 4.7 - - + -
723B VAL* 4.2 9.9 - - + -
757B ARG* 3.2 19.8 + - + +
758B LEU* 1.3 73.8 - - - +
760B GLY* 1.3 59.1 + - - +
770B VAL* 3.1 14.3 + - + +
771B THR 4.0 2.9 - - - -
772B GLN* 3.5 43.5 - - + +
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Residues in contact with GLY 760 (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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685B LEU* 4.8 3.4 - - - -
686B ARG* 3.1 20.0 - - - -
688B LEU* 4.6 5.3 - - - +
758B LEU* 3.5 4.7 - - - +
759B LEU* 1.3 80.0 - - - +
761B VAL* 1.3 68.5 + - - +
770B VAL* 2.9 37.3 + - - +
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Residues in contact with VAL 761 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685B LEU* 4.0 17.9 - - + -
686B ARG 2.8 8.4 + - - +
687B ILE* 3.4 12.1 - - + +
688B LEU* 2.9 26.2 + - - +
740B PHE* 4.0 16.4 - - + -
741B MET* 4.7 1.6 - - + -
744B ALA* 4.5 6.3 - - + -
758B LEU* 4.0 22.4 - - + -
760B GLY* 1.3 78.2 - - - +
762B CYS* 1.3 73.7 + - - +
763B LEU* 3.8 19.5 - - + -
768B GLN 3.3 10.3 - - - +
769B LEU* 4.1 13.9 - - + -
770B VAL* 4.6 0.9 - - - -
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Residues in contact with CYS 762 (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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688B LEU 3.4 21.5 - - - +
689B LYS 4.0 1.8 - - - -
690B GLU* 3.8 27.8 - - - -
693B LEU* 3.8 15.3 - - + -
761B VAL* 1.3 77.1 - - - +
763B LEU* 1.3 71.9 + - - +
764B SER* 3.9 11.0 - - - -
765B PRO* 4.3 6.3 - - - -
766B THR 3.4 0.8 - - - +
767B ILE* 3.4 2.8 - - - -
768B GLN* 2.8 56.4 + - + +
770B VAL* 4.6 1.4 - - - +
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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