Contacts of the strand formed by residues 846 - 854 (chain A) in PDB entry 6BM0
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 846 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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696A ILE* 3.3 28.5 - - + +
697A THR* 3.8 13.0 - - + -
788A VAL* 4.2 22.2 - - + -
811A PHE* 4.2 12.1 - - + -
812A PRO* 4.7 15.0 - - + -
845A LEU* 1.3 75.8 - - - +
847A LYS* 1.3 63.4 + - - +
848A GLU 4.3 2.7 - - - +
849A VAL* 3.7 31.0 - - + -
866A HIS 3.7 6.7 - - - +
867A VAL* 3.8 22.7 - - + -
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Residues in contact with LYS 847 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648A GLN* 5.3 1.7 - - - +
696A ILE* 5.2 0.3 - - - +
697A THR* 3.8 13.5 + - - -
845A LEU* 3.4 43.2 + - + +
846A VAL* 1.3 78.6 - - - +
848A GLU* 1.3 61.2 + - + +
866A HIS* 2.7 53.9 + - + +
868A ASP* 4.5 15.3 + - - +
869A GLN* 5.2 3.0 - - - +
927A ARG* 5.0 11.4 + - - -
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Residues in contact with GLU 848 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648A GLN* 5.3 6.5 - - - +
697A THR* 4.0 5.6 - - - +
846A VAL* 3.9 0.6 - - - +
847A LYS* 1.3 81.9 - - + +
849A VAL* 1.3 70.6 + - - +
850A LEU* 5.5 1.5 - - + +
864A LEU 4.4 0.2 - - - -
865A VAL* 3.3 3.6 - - - -
866A HIS* 2.8 36.0 + - + +
928A VAL 3.9 3.5 - - - +
929A ALA* 3.3 21.6 - - - +
930A ARG* 2.5 44.0 + - - +
931A PHE* 3.3 27.6 + - + +
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Residues in contact with VAL 849 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697A THR* 3.8 18.0 + - + -
698A LEU 3.2 21.7 - - - +
699A CYS* 3.5 5.5 - - + +
786A LEU* 3.6 32.3 - - + -
788A VAL* 4.1 3.4 - - + -
811A PHE* 4.0 20.9 - - + -
846A VAL* 3.7 24.5 - - + -
848A GLU* 1.3 85.0 - - - +
850A LEU* 1.3 64.5 + - - +
863A LEU* 3.7 14.4 - - + -
864A LEU 3.3 3.6 - - - +
865A VAL* 4.2 6.7 - - + -
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Residues in contact with LEU 850 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699A CYS* 3.7 13.7 - - - -
700A LEU 5.3 0.9 - - - +
848A GLU* 5.5 2.2 - - - +
849A VAL* 1.3 76.4 - - - +
851A LEU* 1.3 68.1 + - - +
852A VAL* 3.8 29.6 - - + -
862A TYR 3.6 2.9 - - - +
863A LEU* 4.4 2.2 - - - -
864A LEU* 2.8 42.5 + - + +
931A PHE* 3.4 47.8 - - + +
933A TYR* 4.4 10.5 - - + +
943A VAL* 4.9 5.6 - - + -
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Residues in contact with LEU 851 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699A CYS* 2.9 22.4 - - - +
700A LEU 3.8 4.5 - - - +
701A TYR* 3.8 34.5 - - + -
708A PHE* 4.8 14.8 - - + -
784A TRP* 5.7 4.9 - - + +
786A LEU* 3.7 37.5 - - + +
796A ILE* 5.3 10.3 - - + -
850A LEU* 1.3 74.4 - - - +
852A VAL* 1.3 65.9 + - - +
861A PRO* 5.2 4.7 - - + -
862A TYR 3.4 17.3 - - - +
863A LEU* 3.7 21.5 - - + -
892A PHE* 4.6 13.7 - - + -
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Residues in contact with VAL 852 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701A TYR* 3.8 10.5 - - - -
850A LEU* 3.8 17.7 - - + -
851A LEU* 1.3 79.9 - - - +
853A ALA* 1.3 58.8 + - - +
854A LEU* 3.7 18.7 - - + +
861A PRO* 3.3 1.3 - - - +
862A TYR 2.8 31.7 + - - +
864A LEU* 4.1 16.2 - - + -
933A TYR* 3.6 41.5 - - + -
943A VAL* 3.7 18.4 - - + -
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Residues in contact with ALA 853 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701A TYR* 3.3 30.7 - - + +
702A ARG 5.2 1.1 - - - +
852A VAL* 1.3 73.0 - - - +
854A LEU* 1.3 66.9 + - - +
858A GLN* 2.9 52.1 + - + +
860A ARG 3.5 7.4 - - - +
933A TYR* 3.5 12.7 + - - -
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Residues in contact with LEU 854 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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852A VAL* 3.7 25.6 - - + +
853A ALA* 1.3 88.5 - - - +
855A GLY* 1.3 60.2 + - - +
858A GLN* 4.5 2.0 - - - -
859A SER 4.4 3.1 - - - -
860A ARG* 2.9 35.6 + - - +
862A TYR* 3.6 25.1 - - + -
933A TYR* 4.7 1.6 - - + -
941A SER* 4.5 4.7 - - - +
942A GLY* 3.7 30.7 - - - +
943A VAL* 4.4 7.9 - - + +
953A LEU* 4.4 15.9 - - + +
954A LEU 4.4 0.7 - - - -
955A VAL* 3.7 39.9 - - + +
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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