Contacts of the strand formed by residues 860 - 867 (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 ARG 860 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ARG* 3.3 16.5 - - - +
67A GLU* 2.6 32.9 + - - +
68A LEU* 2.7 27.4 + - - +
69A ALA* 4.4 9.5 + - - +
707A MET* 4.6 9.0 - - + -
853A ALA* 4.3 1.1 - - - -
854A LEU 2.9 36.4 + - - +
855A GLY* 5.4 0.2 - - - -
859A SER* 1.3 82.9 + - - +
861A PRO* 1.3 69.5 - - + +
862A TYR* 3.5 28.4 + - + -
875A GLU* 5.8 4.2 + - - -
876A ALA 5.3 4.0 - - - +
955A VAL* 4.9 1.3 - - - -
959A GLY* 3.1 29.4 + - - -
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Residues in contact with PRO 861 (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 30.3 - - + +
706A GLY* 6.3 0.2 - - - -
707A MET* 3.7 22.4 - - + +
708A PHE* 4.2 20.0 - - + -
851A LEU* 5.2 4.9 - - + -
852A VAL 3.3 7.0 - - - +
853A ALA* 4.0 1.8 - - - -
859A SER 3.4 8.7 - - - +
860A ARG* 1.3 88.2 - - + +
862A TYR* 1.3 69.7 + - - +
876A ALA* 3.6 36.7 + - + +
892A PHE* 6.3 0.2 - - + -
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Residues in contact with TYR 862 (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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850A LEU 3.6 1.6 - - - +
851A LEU* 3.4 9.5 - - - +
852A VAL 2.8 31.1 + - - +
854A LEU* 3.6 29.4 - - + -
860A ARG* 3.5 37.1 + - + -
861A PRO* 1.3 77.9 - - - +
863A LEU* 1.3 59.7 + - - +
864A LEU* 4.0 18.4 - - + +
873A ILE* 5.1 9.2 - - + -
874A TYR 3.4 15.3 - - - +
875A GLU* 3.6 31.2 + - + +
895A VAL* 6.0 0.2 - - + -
953A LEU* 5.7 3.1 - - + -
955A VAL* 3.7 30.4 - - + +
959A GLY 4.2 6.8 + - - -
961A LEU* 4.1 23.9 - - + +
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Residues in contact with LEU 863 (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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786A LEU* 3.8 8.5 - - + -
794A MET* 4.0 6.3 - - - -
811A PHE* 4.0 21.1 - - + -
849A VAL* 3.7 29.6 - - + -
850A LEU 3.8 2.0 - - - +
851A LEU* 3.7 22.9 - - + -
862A TYR* 1.3 72.9 - - - +
864A LEU* 1.3 61.9 + - - +
865A VAL* 3.9 8.6 + - + +
872A LEU 4.3 0.5 - - - +
873A ILE* 3.2 5.9 - - - +
874A TYR* 2.8 70.9 + - + +
875A GLU 5.1 0.6 + - - +
892A PHE* 3.9 21.1 - - + -
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Residues in contact with LEU 864 (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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849A VAL* 3.3 2.8 - - - +
850A LEU* 2.8 47.8 + - + +
852A VAL* 4.1 16.4 - - + -
862A TYR* 4.0 21.3 - - + +
863A LEU* 1.3 76.3 - - - +
865A VAL* 1.3 59.8 + - - +
873A ILE* 3.7 21.1 - - + -
931A PHE* 3.3 24.4 - - + -
943A VAL* 3.8 28.3 - - + -
945A ILE* 4.0 16.8 - - + -
953A LEU* 3.8 20.6 - - + -
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Residues in contact with VAL 865 (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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811A PHE* 3.5 31.4 - - + +
848A GLU 3.3 7.6 - - - -
849A VAL* 4.2 10.5 - - + -
863A LEU* 3.9 18.8 - - + -
864A LEU* 1.3 76.2 - - - +
866A HIS* 1.3 61.4 + - - +
867A VAL* 3.9 17.9 - - + +
871A LEU* 3.3 14.1 - - - +
872A LEU* 3.3 48.1 + - + +
874A TYR* 5.4 1.6 - - + -
931A PHE* 3.2 15.1 - - - -
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Residues in contact with HIS 866 (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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846A VAL* 3.6 2.0 - - - +
847A LYS* 2.7 61.2 + - + +
848A GLU* 2.8 24.9 + - + +
849A VAL* 5.0 0.4 - - - +
865A VAL* 1.3 76.2 - - - +
867A VAL* 1.3 61.6 + - - +
869A GLN* 4.2 18.4 + - - +
870A GLU 4.4 2.2 - - - -
901A PHE* 3.4 35.2 - + - +
930A ARG* 3.4 42.1 - - - -
931A PHE* 4.2 9.0 - + + -
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Residues in contact with VAL 867 (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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811A PHE* 5.3 2.9 - - + +
812A PRO* 4.6 22.9 - - + +
813A VAL* 4.8 4.5 - - - +
844A PRO 3.7 30.1 - - - +
845A LEU 4.3 2.5 - - - -
846A VAL* 3.8 22.9 - - + -
865A VAL* 3.9 22.2 - - + -
866A HIS* 1.3 78.3 - - - +
868A ASP* 1.3 71.9 + - + +
869A GLN 3.5 1.3 - - - -
870A GLU* 3.2 28.2 + - - +
872A LEU* 4.9 8.5 - - + +
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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