Contacts of the strand formed by residues 775 - 784 (chain A) in PDB entry 6P0D
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 TYR 775 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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764A ALA* 3.6 25.1 - - + -
765A TYR 3.4 13.2 - - - +
766A LEU* 4.3 8.3 - - + -
767A GLY* 4.2 0.7 - - - -
771A ARG* 4.4 0.4 - - - +
774A ARG* 1.3 81.3 - - - +
776A GLY* 1.3 60.6 + - - +
777A GLY 4.3 1.1 - - - +
778A PHE* 3.7 33.9 - + + -
805A LEU* 3.4 29.9 - - + +
809A HIS* 3.9 47.1 + + + +
812A LEU* 4.4 14.4 - - + -
813A LYS* 4.8 4.9 - - - +
816A VAL* 3.8 16.8 - - - +
834A HIS* 3.0 38.2 + + + +
836A LEU* 4.7 2.1 - - + +
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Residues in contact with GLY 776 (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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765A TYR 2.9 7.7 + - - -
766A LEU 4.6 0.9 - - - -
767A GLY* 3.5 20.7 - - - +
771A ARG* 3.9 18.4 + - - +
775A TYR* 1.3 75.1 - - - +
777A GLY* 1.3 56.7 + - - +
778A PHE* 4.9 2.9 - - - -
797A GLY* 3.8 19.8 - - - +
800A PHE* 4.4 5.8 - - - -
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Residues in contact with GLY 777 (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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764A ALA* 3.5 0.7 - - - +
765A TYR* 2.9 40.3 + - - +
775A TYR* 3.6 0.8 - - - +
776A GLY* 1.3 79.0 - - - +
778A PHE* 1.3 76.2 + - - -
795A LYS* 6.2 0.4 - - - -
796A LEU 3.1 12.6 - - - -
797A GLY* 4.4 1.1 - - - -
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Residues in contact with PHE 778 (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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761A VAL* 4.2 7.9 - - + -
763A GLY 3.4 7.2 - - - +
764A ALA* 3.9 10.8 - - + -
765A TYR* 3.7 7.9 - - - -
775A TYR* 3.7 34.1 - + + -
777A GLY* 1.3 81.7 - - - -
779A LEU* 1.3 61.1 + - - +
780A LEU* 4.5 6.5 - - + -
795A LYS* 3.1 7.2 - - - +
796A LEU* 2.8 42.2 + - + +
800A PHE* 3.8 16.6 - + - -
805A LEU* 3.7 26.5 - - + -
808A HIS* 4.1 8.7 - + + -
812A LEU* 3.4 28.9 - - + -
842A TRP* 3.7 32.1 - + + -
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Residues in contact with LEU 779 (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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761A VAL* 3.6 4.3 - - - +
762A ILE* 2.9 54.8 + - + -
763A GLY* 2.9 16.3 + - - +
765A TYR* 3.6 28.3 - - + +
778A PHE* 1.3 72.7 - - - +
780A LEU* 1.3 61.5 + - - +
792A ALA* 4.1 14.4 - - + -
794A CYS 3.6 14.8 - - - +
795A LYS* 4.0 9.9 - - + -
826A ILE* 3.8 20.0 - - + -
829A ALA* 4.4 4.3 - - + -
830A VAL 4.4 2.7 - - - +
832A PRO* 4.1 18.6 - - + -
835A TRP* 5.0 0.2 - - + -
855A TYR* 4.1 10.1 - - + -
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Residues in contact with LEU 780 (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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759A LEU* 4.0 21.3 - - + +
760A VAL 3.2 7.0 - - - +
761A VAL* 4.0 25.6 - - + -
762A ILE* 4.3 1.6 - - - -
778A PHE* 4.5 8.5 - - + -
779A LEU* 1.3 80.4 - - - +
781A ALA* 1.3 60.3 + - - +
792A ALA* 3.3 7.3 - - - +
793A ILE* 2.8 28.9 + - + +
794A CYS* 2.9 25.9 + - - +
796A LEU* 3.8 24.5 - - + -
842A TRP* 4.3 11.7 - - + -
844A VAL* 3.6 31.0 - - + -
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Residues in contact with ALA 781 (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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759A LEU* 3.6 10.0 - - - -
760A VAL* 2.8 34.0 + - + +
762A ILE* 3.8 27.8 - - + -
780A LEU* 1.3 76.9 - - - +
782A SER* 1.3 58.1 + - - +
790A LEU* 4.0 9.2 - - + -
791A GLN 3.0 31.2 - - - +
792A ALA 3.9 1.8 - - - +
793A ILE* 3.9 1.1 - - - -
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Residues in contact with SER 782 (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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757A LEU* 6.1 0.7 - - - -
758A ASP 5.6 0.9 - - - -
759A LEU* 4.1 17.0 - - - +
760A VAL* 5.6 0.4 - - - -
781A ALA* 1.3 74.3 - - - +
783A TYR* 1.3 63.0 + - - +
784A ASP 3.8 0.5 + - - -
790A LEU* 3.4 6.1 - - - -
791A GLN* 2.8 34.5 + - - +
793A ILE* 4.1 11.1 - - - +
857A ALA* 3.6 24.9 - - - +
858A ALA* 5.0 1.0 + - - +
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Residues in contact with TYR 783 (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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760A VAL* 5.7 3.3 - - + +
782A SER* 1.3 76.0 - - - +
784A ASP* 1.3 63.3 + - - +
785A GLU* 3.4 32.7 + - + +
788A GLU* 3.5 51.5 + - - +
789A GLU 3.6 7.6 - - - -
790A LEU* 3.9 20.2 - - + -
823A TYR* 6.5 0.4 - + - -
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Residues in contact with ASP 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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782A SER 3.8 1.2 + - - -
783A TYR* 1.3 71.1 - - - +
785A GLU* 1.3 55.5 + - - +
786A ASP* 3.3 11.0 + - - +
787A SER* 2.5 35.8 + - - +
788A GLU* 2.7 37.4 + - - -
789A GLU 2.8 17.5 + - - +
791A GLN* 3.6 33.9 + - + +
858A ALA* 5.4 1.2 - - - -
861A LEU* 4.9 14.2 - - - +
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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