Contacts of the strand formed by residues 824 - 828 (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 VAL 824 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778D CYS* 3.4 3.1 - - - -
779D LEU* 2.7 58.4 + - + -
802D ILE* 3.8 30.1 - - + -
819D LEU* 4.4 10.1 - - + -
820D ALA 3.5 16.8 - - - +
821D ALA* 3.3 10.7 + - - +
823D ASN* 1.3 80.5 - - - +
825D LEU* 1.3 58.5 + - - +
832D VAL* 3.8 17.3 - - + -
833D LYS 3.4 11.2 - - - +
834D ILE* 4.3 10.5 - - + -
884D THR* 4.5 1.1 - - + -
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Residues in contact with LEU 825 (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 3.5 46.9 - - + +
756D VAL* 4.0 8.1 - - + -
772D GLN 5.8 0.2 - - - +
774D MET* 3.7 24.0 - - + -
777D GLY 3.6 3.6 - - - +
778D CYS* 3.7 30.3 - - + +
822D ARG 4.8 3.8 - - - +
824D VAL* 1.3 74.5 - - - +
826D VAL* 1.3 62.6 + - - +
827D LYS 4.0 0.4 - - - -
832D VAL* 3.2 8.3 - - - +
833D LYS* 2.6 38.8 + - + +
835D THR* 3.5 37.0 - - + +
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Residues in contact with VAL 826 (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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774D MET* 3.6 12.0 - - - +
775D PRO* 3.9 0.5 - - - +
776D HIS* 3.6 35.9 + - + -
777D GLY 2.8 20.5 + - - +
779D LEU* 3.6 38.4 - - + -
782D TYR* 3.9 21.8 - - + -
825D LEU* 1.3 75.3 - - - +
827D LYS* 1.3 61.2 + - - +
828D SER 3.4 29.8 - - - +
829D PRO* 4.1 5.4 - - + +
831D HIS 4.0 2.2 - - - +
832D VAL* 4.5 4.3 - - + -
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Residues in contact with LYS 827 (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* 4.9 9.8 + - - +
827B LYS* 5.1 14.1 - - - +
833B LYS* 5.3 7.7 - - - +
772D GLN* 4.0 23.3 - - - +
773D LEU 5.9 0.6 + - - -
774D MET* 3.5 31.8 - - + -
775D PRO* 3.9 19.1 - - + +
776D HIS* 3.4 14.5 + - - -
825D LEU 3.9 2.2 + - - -
826D VAL* 1.3 72.0 - - - +
828D SER* 1.3 62.3 + - - +
831D HIS* 2.9 40.4 + - + +
833D LYS* 4.2 14.3 - - + +
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Residues in contact with SER 828 (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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751B ASP* 2.7 27.0 + - - -
752B HIS 4.8 0.9 + - - -
757B ARG* 4.3 13.9 - - - -
776D HIS* 4.0 4.0 - - - -
826D VAL* 3.4 10.0 - - - +
827D LYS* 1.3 80.1 - - - +
829D PRO* 1.4 70.4 - - - +
831D HIS* 2.7 45.4 + - - +
832D VAL* 4.9 0.2 - - - +
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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
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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