Contacts of the strand formed by residues 778 - 788 (chain B) in PDB entry 3PT6
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 778 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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720B LYS 4.5 3.6 + - - -
721B LEU* 3.4 46.1 - - + -
723B GLN* 5.1 3.3 - - - +
724B GLY* 4.0 25.5 + - - -
726B LYS* 5.1 6.1 - - + -
767B SER* 3.4 3.6 - - - -
768B VAL* 3.1 40.9 + - + +
770B PRO* 4.1 20.4 - - + +
775B LYS* 3.6 40.3 + - - +
776B PRO 3.6 13.0 - - - -
777B LEU* 1.3 74.8 - - - +
779B LEU* 1.3 65.1 + - - +
799B TRP* 3.2 30.3 - + + -
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Residues in contact with LEU 779 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721B LEU* 4.8 1.6 - - - +
766B VAL 3.8 4.3 - - - +
767B SER* 4.2 3.4 - - - +
777B LEU* 3.7 27.6 - - + +
778B TYR* 1.3 78.5 - - - +
780B ALA* 1.3 63.1 + - - +
799B TRP* 3.4 6.8 - - - -
800B PHE* 2.7 39.2 + - + +
817B LEU* 4.1 23.8 - - + -
835B VAL* 3.9 28.9 - - + -
837B VAL* 6.0 0.4 - - + -
867B TYR* 3.4 46.4 - - + +
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Residues in contact with ALA 780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765B CYS* 3.4 11.1 - - - +
766B VAL* 3.1 30.4 + - + +
768B VAL* 6.1 1.8 - - + -
779B LEU* 1.3 76.1 - - - +
781B ARG* 1.3 61.5 + - - +
782B VAL* 5.9 0.2 - - - -
795B PHE* 5.5 3.4 - - + -
797B ALA* 4.0 17.7 - - + -
798B HIS 3.5 17.9 - - - +
799B TRP* 3.7 19.7 - - + -
800B PHE* 3.7 10.3 - - - -
835B VAL* 5.0 0.3 - - - +
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Residues in contact with ARG 781 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763B GLY* 3.3 23.3 + - - +
764B ASP 3.7 9.0 - - - +
765B CYS* 3.8 20.0 - - - -
780B ALA* 1.3 76.9 - - - +
782B VAL* 1.3 76.7 + - - +
783B THR* 3.7 6.6 + - + +
795B PHE* 4.8 0.4 - - - -
797B ALA* 3.5 8.3 - - - +
798B HIS* 3.1 46.7 + - + +
800B PHE* 4.0 19.0 - - + -
819B LEU* 4.9 5.3 - - - +
837B VAL 4.0 15.4 + - - -
869B PHE* 4.2 24.4 - - - -
898B LEU* 5.9 7.7 - - - +
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Residues in contact with VAL 782 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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760B LEU* 5.5 10.1 - - + -
761B GLU 4.7 3.6 - - - +
762B VAL* 3.8 7.6 - - - +
763B GLY* 2.6 35.1 + - - +
764B ASP* 3.0 20.0 + - + +
766B VAL* 4.8 15.9 - - + -
781B ARG* 1.3 74.7 - - - +
783B THR* 1.3 61.8 + - - +
784B ALA 3.7 13.7 - - - +
785B LEU* 3.5 34.1 - - + -
795B PHE* 3.8 23.3 - - + -
796B HIS 3.8 2.7 - - - -
831B ILE* 5.3 5.2 - - + -
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Residues in contact with THR 783 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762B VAL* 3.7 11.9 - - - +
781B ARG* 4.0 8.7 - - + +
782B VAL* 1.3 76.1 - - - +
784B ALA* 1.3 62.4 + - - +
796B HIS* 3.1 35.4 + - + +
798B HIS* 3.6 31.9 - - + +
894B HIS 3.0 16.1 - - - +
895B LYS* 3.5 11.3 + - - -
896B PHE 3.2 23.4 + - - +
897B CYS* 3.9 12.2 - - + +
898B LEU* 6.5 0.7 - - + -
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Residues in contact with ALA 784 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749B TYR* 4.2 8.5 - - + -
762B VAL* 4.1 3.8 - - - +
782B VAL* 3.4 4.0 - - - +
783B THR* 1.3 88.3 + - - +
785B LEU* 1.3 64.1 - - - +
786B TRP* 4.1 20.4 - - + -
795B PHE* 3.1 10.6 - - - +
796B HIS* 3.1 24.9 + - + -
894B HIS 3.3 15.9 - - - +
895B LYS* 3.9 11.7 - - + +
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Residues in contact with LEU 785 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736B TRP* 3.7 14.1 - - + -
749B TYR* 3.2 9.9 - - - -
750B TYR 2.8 32.6 + - - +
751B GLN 4.0 6.5 - - - +
752B LYS 3.9 28.0 - - - +
753B VAL* 4.1 11.2 - - + -
760B LEU* 3.9 24.9 - - + +
761B GLU* 4.6 0.2 - - - -
762B VAL* 4.0 17.4 - - + +
782B VAL* 3.5 24.5 - - + -
784B ALA* 1.3 75.9 - - - +
786B TRP* 1.3 62.3 + - - +
794B MET 3.7 1.6 - - - -
795B PHE* 3.7 12.3 - - + -
828B LEU* 4.1 13.0 - - + -
894B HIS 4.7 0.2 + - - -
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Residues in contact with TRP 786 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736B TRP* 3.1 13.5 - - - -
747B ARG* 3.6 33.1 - - + +
748B THR 3.2 14.4 - - - +
749B TYR* 3.5 36.1 - + + -
750B TYR 4.4 0.2 - - - +
784B ALA* 4.1 9.9 - - + -
785B LEU* 1.3 76.3 - - - +
787B GLU* 1.3 69.8 + - - +
788B ASP* 3.1 22.9 + - - -
794B MET* 2.7 66.6 + - + +
795B PHE 3.7 10.8 - - - -
796B HIS* 3.5 28.0 - - + -
825B ASN* 3.3 31.6 - - + -
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Residues in contact with GLU 787 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736B TRP* 2.8 37.5 + - + +
747B ARG* 3.2 4.7 - - - -
748B THR* 3.0 47.5 + - + +
750B TYR* 4.6 0.6 + - + -
786B TRP* 1.3 73.7 - - - +
788B ASP* 1.3 71.2 + - - +
791B GLY* 3.3 27.4 - - - +
792B GLN 3.8 2.7 - - - +
793B MET* 3.6 18.3 - - - +
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Residues in contact with ASP 788 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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746B ASN* 3.1 14.6 - - - +
747B ARG* 3.6 19.7 + - - -
786B TRP* 3.1 27.2 + - - +
787B GLU* 1.3 78.9 - - - +
789B LYS* 1.3 69.3 + - - +
790B ASN* 2.7 42.4 + - - +
791B GLY* 2.8 18.2 + - - -
792B GLN 3.0 11.3 + - - +
794B MET* 4.4 6.9 - - + +
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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