Contacts of the strand formed by residues 768 - 772 (chain D) 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 GLN 768 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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690D GLU* 5.0 2.9 - - - +
693D LEU* 5.2 4.5 - - - +
695D ARG* 4.4 9.5 - - - +
725D ILE* 3.4 30.8 - - + +
726D LYS 3.5 3.6 - - - -
727D ILE* 3.5 33.8 - - + +
761D VAL* 3.3 6.4 - - - -
762D CYS* 2.8 55.6 + - + +
764D SER 3.3 22.9 - - - +
765D PRO* 4.1 7.9 - - + +
766D THR 3.5 10.3 - - - +
767D ILE* 1.3 74.6 - - - +
769D LEU* 1.3 64.3 + - - +
770D VAL* 3.7 3.2 + - + +
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Residues in contact with LEU 769 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D FMM 3.3 32.8 - - + +
725D ILE* 3.6 2.9 - - - -
726D LYS* 2.9 49.4 + - + +
728D LEU* 4.7 15.7 - - + -
740D PHE* 4.7 8.1 - - + -
744D ALA* 6.5 0.2 - - + -
747D MET* 5.7 3.4 - - + -
758D LEU* 3.8 19.7 - - + -
760D GLY 4.1 2.9 - - - -
761D VAL* 4.6 10.1 - - + -
767D ILE* 3.8 24.5 - - + -
768D GLN* 1.3 71.5 - - - +
770D VAL* 1.3 60.1 + - - +
839D LEU* 4.0 19.5 - - + -
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Residues in contact with VAL 770 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688D LEU* 3.8 31.6 - - + -
693D LEU* 4.1 22.2 - - + -
712D TRP* 6.0 0.4 - - + -
723D VAL* 3.8 29.2 - - + -
724D ALA 3.6 6.5 - - - +
725D ILE* 4.4 10.8 - - + -
758D LEU* 3.7 2.4 - - - +
759D LEU* 2.9 29.1 + - + +
760D GLY 2.9 23.9 + - - +
762D CYS 4.7 0.7 - - - +
768D GLN* 3.8 10.1 - - + +
769D LEU* 1.3 78.3 - - - +
771D THR* 1.3 66.0 + - - +
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Residues in contact with THR 771 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D FMM 3.1 61.4 + - + +
723D VAL* 3.5 4.9 - - - +
724D ALA* 2.7 33.8 + - - +
756D VAL* 3.7 18.0 - - + +
757D ARG 3.4 18.6 - - - +
758D LEU* 4.0 4.3 - - + -
759D LEU* 4.1 10.1 - - - -
770D VAL* 1.3 77.9 - - - +
772D GLN* 1.3 62.0 + - - +
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Residues in contact with GLN 772 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772B GLN* 4.1 19.8 + - - +
827B LYS* 4.8 9.5 + - - +
91D FMM 4.0 4.5 - - - -
721D ILE* 5.4 8.7 - - + +
722D PRO 4.1 12.1 - - - +
723D VAL* 4.5 1.1 - - - +
756D VAL* 5.4 0.9 - - - +
757D ARG 5.0 1.2 + - - -
759D LEU* 3.6 26.5 - - + +
771D THR* 1.3 81.5 + - - +
773D LEU* 1.3 74.8 + - - +
774D MET* 3.4 22.7 + - + +
825D LEU* 5.8 0.2 - - - +
827D LYS* 4.0 27.1 - - - +
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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