Contacts of the strand formed by residues 783 - 789 (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 HIS 783 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652A ALA 5.0 0.4 - - - -
653A ASP* 3.6 38.1 + - + +
654A PRO* 5.2 5.5 - - + +
655A TYR* 3.8 21.4 - + + -
701A TYR 3.6 4.7 - - - +
702A ARG* 3.5 26.5 + - + -
781A PRO* 4.4 13.8 + - + -
782A THR* 1.3 78.2 - - - +
784A TRP* 1.3 68.2 + - - +
798A GLN* 4.1 1.0 - - - -
799A LEU* 3.2 41.2 + - + -
800A PRO* 4.0 12.7 - - + +
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Residues in contact with TRP 784 (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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700A LEU* 3.5 7.3 - - - +
701A TYR* 2.7 44.9 + + + +
703A ASP* 2.9 25.5 + - - -
708A PHE* 3.4 33.9 - + + +
709A THR 5.1 3.4 - - - -
710A THR 4.2 16.6 - - - -
782A THR* 3.2 41.3 + - + +
783A HIS* 1.3 74.8 - - - +
785A CYS* 1.3 59.7 + - - +
786A LEU 4.2 0.2 + - - -
796A ILE* 3.9 18.4 - - + -
797A TYR 3.3 21.5 - - - -
798A GLN* 3.6 30.3 - - + -
799A LEU* 4.2 4.3 - - - +
805A VAL* 3.8 20.9 - - + -
851A LEU* 5.7 4.0 - - + +
888A LEU* 3.8 23.8 - - + -
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Residues in contact with CYS 785 (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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657A VAL* 5.0 6.1 - - - -
698A LEU* 4.5 12.6 - - - -
699A CYS 4.1 2.5 - - - -
700A LEU* 3.7 17.0 - - + -
784A TRP* 1.3 74.1 - - - +
786A LEU* 1.3 69.8 + - - +
787A LEU* 5.0 0.4 - - - -
795A GLU 3.9 0.5 - - - +
796A ILE* 3.4 3.7 - - - +
797A TYR* 2.5 50.4 + - + +
799A LEU* 3.7 15.1 - - + +
802A TRP* 3.1 39.0 - - + -
851A LEU* 6.1 0.2 - - - -
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Residues in contact with LEU 786 (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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698A LEU* 3.3 12.6 - - - +
699A CYS* 3.0 40.7 + - + +
784A TRP 4.2 0.6 + - - -
785A CYS* 1.3 72.7 - - - +
787A LEU* 1.3 69.7 + - - +
788A VAL* 5.0 2.9 - - + -
794A MET* 3.6 32.5 - - + -
795A GLU 3.9 2.2 - - - +
796A ILE* 3.6 20.6 - - + -
849A VAL* 3.6 30.1 - - + -
851A LEU* 3.7 35.9 - - + -
863A LEU* 3.8 8.5 - - + -
892A PHE* 6.2 0.2 - - + -
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Residues in contact with LEU 787 (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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665A VAL* 4.8 4.9 - - + -
689A LEU* 4.0 18.2 - - + -
695A VAL* 3.8 26.0 - - + -
697A THR 3.9 0.4 - - - -
698A LEU* 3.8 17.9 - - + -
785A CYS* 5.0 0.7 - - - -
786A LEU* 1.3 78.5 - - - +
788A VAL* 1.3 64.0 + - - +
789A ARG* 3.7 26.8 + - + +
793A THR 4.3 0.2 - - - +
795A GLU* 2.9 61.8 + - - +
797A TYR* 3.7 25.1 - - + +
802A TRP* 4.7 5.2 - - + -
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Residues in contact with VAL 788 (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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695A VAL* 3.6 2.5 - - - -
696A ILE* 2.7 35.6 + - + -
697A THR* 3.3 21.2 + - + +
786A LEU* 5.0 1.3 - - + -
787A LEU* 1.3 78.7 - - - +
789A ARG* 1.3 63.9 - - - +
792A GLY* 5.9 0.7 - - - -
793A THR 3.6 12.8 - - - +
794A MET* 4.7 7.2 - - + -
811A PHE* 3.6 38.1 - - + -
812A PRO* 6.5 0.2 - - + -
846A VAL* 4.2 20.0 - - + -
849A VAL* 4.1 19.1 - - + -
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Residues in contact with ARG 789 (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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689A LEU* 4.8 3.8 - - - +
690A HIS 3.3 23.0 + - - +
691A HIS* 4.3 10.7 - - - +
692A GLN* 2.4 37.4 + - - +
693A SER* 3.3 31.4 + - - +
694A LYS 3.3 5.8 - - - +
695A VAL* 4.4 7.4 - - + +
696A ILE* 4.1 3.1 - - - +
787A LEU* 3.7 19.8 + - + +
788A VAL* 1.3 85.2 - - - +
790A GLU* 1.3 65.2 + - - +
791A ASN* 3.3 14.1 + - - +
792A GLY* 3.6 9.4 + - - -
793A THR* 3.3 14.1 + - - +
795A GLU* 3.2 39.3 + - - +
797A TYR* 3.4 10.3 + - - -
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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