Contacts of the strand formed by residues 786 - 792 (chain A) in PDB entry 3M8S
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 GLU 786 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MG 4.1 3.5 - - - -
595A ARG* 4.8 2.1 + - - -
608A ALA* 4.1 3.1 - - - +
609A LEU 3.1 15.5 - - - +
610A ASP* 3.8 11.6 - - - +
761A MET* 3.3 4.4 - - - +
782A GLN* 3.4 10.4 - - - +
783A VAL* 2.9 45.1 + - + +
785A ASP* 1.3 81.3 - - - +
787A LEU* 1.3 70.4 + - - +
788A VAL* 3.8 5.1 - - + +
827A TRP* 3.0 35.9 + - - -
831A LYS* 3.2 36.4 + - - +
112B DOC 4.9 3.5 + - - +
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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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607A VAL 3.5 1.9 - - - +
608A ALA* 3.4 3.6 - - - -
609A LEU* 2.8 42.6 + - + +
761A MET* 3.8 17.4 - - + +
764A ALA 5.5 0.4 - - - +
765A MET* 3.9 31.2 - - + +
768A LEU* 3.9 29.2 - - + -
779A MET* 4.3 13.5 - - + -
781A LEU 3.4 15.5 - - - +
782A GLN* 3.8 18.6 - - + -
786A GLU* 1.3 78.5 - - - +
788A VAL* 1.3 64.1 + - - +
789A LEU* 4.1 10.1 - - + -
807A MET* 4.3 12.8 - - + -
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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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449A VAL* 6.2 1.6 - - + -
606A LEU* 4.5 24.0 - - + -
607A VAL 3.5 6.5 - - - +
608A ALA* 4.8 3.4 - - + -
780A LEU* 2.9 32.1 + - + +
781A LEU* 3.0 33.3 + - + +
783A VAL* 5.1 0.9 - - + -
786A GLU* 3.8 9.0 - - + +
787A LEU* 1.3 76.8 - - - +
789A LEU* 1.3 71.8 + - - +
827A TRP* 3.6 44.9 - - + +
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Residues in contact with LEU 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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606A LEU* 3.4 13.0 - - - +
607A VAL* 2.8 41.7 + - + +
609A LEU* 3.7 21.8 - - + -
768A LEU* 4.5 1.1 - - + -
772A LEU* 3.8 29.8 - - + -
777A ALA* 5.8 0.7 - - + -
778A ARG 3.2 9.6 - - - +
779A MET* 3.8 27.4 - - + -
780A LEU* 4.2 2.5 - - - +
787A LEU* 4.3 16.4 - - + -
788A VAL* 1.3 81.5 - - - +
790A GLU* 1.3 65.7 + - - +
799A VAL* 4.0 13.0 - - + -
803A ALA* 4.0 17.0 - - + -
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Residues in contact with GLU 790 (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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559A ARG* 2.9 31.9 + - - -
599A ILE 4.6 1.6 - - - +
600A ALA* 3.8 3.2 - - + -
601A GLU* 2.9 29.7 + - - +
604A TRP* 3.4 23.3 - - + -
605A LEU 3.4 9.2 - - - +
606A LEU* 4.1 7.2 - - + -
777A ALA* 3.6 1.0 - - - -
778A ARG* 2.9 61.7 + - + -
780A LEU* 3.6 19.3 - - + +
789A LEU* 1.3 76.6 - - - +
791A ALA* 1.3 60.4 + - - +
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Residues in contact with ALA 791 (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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604A TRP* 3.3 6.9 - - - -
605A LEU* 2.8 30.2 + - - +
607A VAL* 4.5 4.9 - - + +
777A ALA* 4.3 1.6 - - + -
789A LEU 4.3 0.2 - - - -
790A GLU* 1.3 74.6 - - - +
792A PRO* 1.3 74.8 - - + +
793A LYS* 4.2 0.2 - - - -
796A ALA* 3.7 28.0 - - + -
799A VAL* 4.0 26.9 - - + -
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Residues in contact with PRO 792 (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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603A GLY 3.9 7.6 - - - +
604A TRP* 3.4 23.5 - - + -
775A MET 4.9 0.2 - - - +
776A GLY 3.5 28.3 - - - +
777A ALA* 4.4 1.1 - - + -
791A ALA* 1.3 85.0 - - + +
793A LYS* 1.3 67.1 + - - +
794A GLU* 4.5 6.3 - - + +
795A ARG* 2.9 49.5 + - + +
796A ALA 2.9 11.3 + - - -
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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