Contacts of the strand formed by residues 824 - 828 (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 VAL 824 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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778B CYS* 3.5 3.5 - - - +
779B LEU* 2.7 47.4 + - + -
802B ILE* 4.1 23.3 - - + -
819B LEU* 4.3 16.6 - - + -
820B ALA 3.3 16.9 + - - +
821B ALA* 3.2 7.0 + - - +
822B ARG 3.3 0.2 - - - -
823B ASN* 1.3 80.8 - - - +
825B LEU* 1.3 58.4 + - - +
832B VAL* 3.7 30.5 - - + -
833B LYS 3.4 13.9 - - - +
834B ILE* 4.4 5.6 - - + +
884B THR* 4.4 4.3 - - + -
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Residues in contact with LEU 825 (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 3.5 44.0 - - + +
756B VAL* 4.3 13.5 - - + -
771B THR* 5.3 1.6 - - + -
774B MET* 3.6 27.8 - - + -
777B GLY 3.6 3.8 - - - +
778B CYS* 3.8 27.8 - - + +
822B ARG 4.2 5.4 - - - +
824B VAL* 1.3 75.5 - - - +
826B VAL* 1.3 64.8 + - - +
827B LYS 4.0 0.7 - - - -
832B VAL* 3.2 8.2 - - - +
833B LYS* 2.8 37.9 + - - +
835B THR* 3.8 29.2 - - + -
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Residues in contact with VAL 826 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774B MET* 3.9 14.9 - - - +
775B PRO 4.7 0.2 - - - -
776B HIS* 3.3 34.0 + - + +
777B GLY 2.8 20.0 + - - +
779B LEU* 3.8 36.8 - - + -
782B TYR* 4.0 26.9 - - + -
798B TRP* 5.8 0.2 - - - +
825B LEU* 1.3 76.3 - - - +
827B LYS* 1.3 60.2 + - - +
828B SER 3.5 27.6 - - - +
829B PRO* 4.3 2.7 - - + +
831B HIS 4.1 1.8 - - - +
832B VAL* 4.3 5.2 - - + -
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Residues in contact with LYS 827 (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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772B GLN* 3.4 29.8 - - - +
773B LEU 5.7 0.9 - - - +
774B MET* 3.6 30.4 - - + +
775B PRO* 5.0 8.3 - - + +
776B HIS* 3.3 13.6 + - - -
825B LEU 3.9 2.4 + - - -
826B VAL* 1.3 72.7 - - - +
828B SER* 1.3 63.4 + - - +
831B HIS* 2.9 41.0 + - + +
833B LYS* 4.4 16.2 - - + +
772D GLN* 4.8 10.7 + - - +
827D LYS* 5.1 10.2 - - - +
833D LYS* 5.6 6.1 - - - +
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Residues in contact with SER 828 (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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776B HIS* 3.8 6.1 - - - -
826B VAL* 3.5 9.8 - - - +
827B LYS* 1.3 81.8 - - - +
829B PRO* 1.3 77.5 - - - +
831B HIS* 2.8 34.9 + - - +
832B VAL* 4.9 0.2 - - - +
751D ASP* 2.4 30.6 + - - -
757D ARG* 5.6 6.1 - - - -
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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