Contacts of the strand formed by residues 793 - 802 (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 MET 793 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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734B ILE* 3.5 49.6 - - + +
736B TRP* 3.4 39.9 - - + -
786B TRP 3.8 2.9 - - - -
787B GLU* 3.6 19.7 - - - +
791B GLY 4.3 0.9 + - - +
792B GLN* 1.3 73.7 - - - +
794B MET* 1.3 60.5 + - - +
827B GLN* 3.4 13.2 - - + +
828B LEU* 2.9 36.3 + - + -
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Residues in contact with MET 794 (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* 4.0 0.9 - - - -
785B LEU* 3.7 1.2 - - - -
786B TRP* 2.7 76.5 + - + +
788B ASP* 4.4 7.4 - - + +
790B ASN* 4.4 10.3 - - - +
792B GLN* 3.4 39.3 - - - +
793B MET* 1.3 75.7 - - - +
795B PHE* 1.3 62.9 + - - +
825B ASN* 5.2 4.5 - - + -
826B MET* 3.1 33.0 - - - +
827B GLN* 3.6 8.7 - - - +
828B LEU* 3.7 7.5 - - - +
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Residues in contact with PHE 795 (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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766B VAL* 5.7 3.1 - - + -
768B VAL* 5.2 6.1 - - + -
780B ALA* 5.5 2.5 - - + -
781B ARG 4.8 0.9 - - - -
782B VAL* 3.8 23.8 - - + -
784B ALA 3.1 15.0 - - - +
785B LEU* 3.7 8.1 - - + -
786B TRP* 3.7 7.7 - - - -
794B MET* 1.3 73.8 - - - +
796B HIS* 1.3 67.3 - - - +
797B ALA* 3.5 30.0 + - + -
825B ASN* 3.6 2.9 - - - -
826B MET* 3.0 67.5 + - + -
827B GLN 4.1 5.4 - - - -
828B LEU* 3.4 24.7 - - + -
831B ILE* 3.7 30.5 - - + -
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Residues in contact with HIS 796 (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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1B ZN 2.0 37.1 - - - -
781B ARG 3.6 2.1 - - - +
783B THR* 3.1 52.3 + - + +
784B ALA* 3.1 12.8 + - + -
786B TRP* 3.5 18.3 - - + -
795B PHE* 1.3 76.2 - - - +
797B ALA* 1.3 61.2 + - - +
823B CYS* 3.4 15.6 - - - +
824B GLU* 3.3 19.4 + - - -
825B ASN* 3.2 21.8 + - - +
895B LYS 5.5 0.9 - - - -
897B CYS* 3.6 7.8 - - + -
900B CYS* 3.5 7.4 - - - -
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Residues in contact with ALA 797 (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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780B ALA* 4.0 16.2 - - + -
781B ARG 3.5 4.7 - - - -
795B PHE* 3.5 26.4 + - + -
796B HIS* 1.3 72.9 - - - +
798B HIS* 1.3 59.9 + - - +
799B TRP* 3.7 18.2 + - + -
823B CYS* 2.9 27.1 - - - +
824B GLU 2.8 21.6 + - - +
826B MET* 4.9 4.0 - - + -
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Residues in contact with HIS 798 (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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780B ALA* 3.5 1.3 - - - -
781B ARG* 3.1 42.1 + - + +
783B THR* 3.6 23.1 - - + -
796B HIS 3.9 1.4 + - - -
797B ALA* 1.3 70.3 - - - +
799B TRP* 1.3 68.6 + - - +
800B PHE* 4.3 3.3 - + - -
819B LEU* 4.2 19.4 - - + +
820B VAL 3.0 30.1 + - - -
822B GLU 3.6 1.0 + - - -
823B CYS* 3.6 3.8 - - - -
872B TRP* 4.1 16.8 - + - -
897B CYS* 3.9 9.6 - - - -
898B LEU* 4.2 17.1 - - + +
899B SER* 3.1 32.5 - - - -
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Residues in contact with TRP 799 (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* 3.5 43.0 + - + +
726B LYS* 5.8 0.4 - - + -
768B VAL* 4.1 24.0 - - + -
778B TYR* 3.2 38.6 - + + -
779B LEU 3.4 22.2 - - - -
780B ALA* 3.7 13.2 - - + -
797B ALA* 4.1 8.6 + - + -
798B HIS* 1.3 79.5 + - - +
800B PHE* 1.3 59.5 + - - +
819B LEU* 4.8 0.9 - - - -
820B VAL* 3.5 25.4 + - + +
822B GLU* 2.8 41.1 + - + +
823B CYS* 3.8 8.1 - - - -
824B GLU* 3.5 30.4 - - + +
826B MET* 3.9 23.3 - - + -
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Residues in contact with PHE 800 (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* 3.7 22.3 - - - +
765B CYS* 3.9 13.9 - - - -
779B LEU* 2.7 26.4 + - + +
780B ALA* 3.7 31.6 - - - -
781B ARG* 4.0 21.1 - - + -
798B HIS* 4.7 1.6 - + - -
799B TRP* 1.3 76.8 - - - +
801B CYS* 1.3 59.0 + - - +
817B LEU* 3.6 34.5 - - + -
818B PHE 3.9 7.4 - - - -
819B LEU* 3.7 31.2 - - + -
820B VAL* 4.3 1.6 - - - -
837B VAL* 3.9 19.7 - - + -
869B PHE* 3.9 21.3 - + + -
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Residues in contact with CYS 801 (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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720B LYS* 5.2 10.3 - - + -
721B LEU* 5.3 3.1 - - + -
800B PHE* 1.3 75.7 - - - +
802B ALA* 1.3 74.1 + - - +
805B ASP* 4.1 14.4 - - - -
806B THR* 3.8 19.3 - - - -
817B LEU* 3.2 8.3 - - - -
818B PHE* 2.7 49.8 + - + +
820B VAL* 4.1 19.5 - - + -
873B TYR* 4.1 11.9 - - + -
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Residues in contact with ALA 802 (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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776B PRO* 6.2 4.5 - - + -
779B LEU* 5.9 3.6 - - + -
801B CYS* 1.3 84.1 - - - +
803B GLY* 1.3 67.0 + - - +
804B THR* 4.2 6.7 - - - +
805B ASP* 3.0 38.0 + - - +
806B THR* 3.6 3.1 - - - +
817B LEU* 4.1 15.9 - - + +
818B PHE* 4.4 1.3 - - - -
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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