Contacts of the strand formed by residues 792 - 805 (chain A) in PDB entry 6S1M
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 LEU 792 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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601A LEU* 3.6 25.4 - - + +
602A ASP* 3.5 36.3 - - - +
603A PHE* 3.9 28.3 - - + +
731A THR* 4.7 11.0 - - + -
779A ALA* 3.8 24.1 - - - +
780A ASP* 4.8 4.2 - - - +
782A VAL* 3.7 34.1 - - + -
783A SER* 2.7 27.0 + - - +
791A ARG* 1.3 76.6 - - - +
793A GLU* 1.3 62.6 + - - +
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Residues in contact with GLU 793 (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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601A LEU* 3.4 2.6 - - - -
602A ASP* 2.9 46.2 + - - +
604A SER* 4.4 21.9 + - - +
779A ALA* 3.8 7.9 - - - -
780A ASP* 5.7 1.1 - - - -
791A ARG* 4.8 10.7 + - + +
792A LEU* 1.3 76.6 - - - +
794A PHE* 1.3 68.3 + - - +
795A GLU* 3.3 26.2 - - - +
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Residues in contact with PHE 794 (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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599A ALA* 4.0 10.8 - - + -
600A THR 3.8 4.0 - - - -
601A LEU* 4.0 9.6 - - + -
772A MET* 3.9 31.4 - - + -
775A GLY* 3.4 36.6 - - - -
776A ARG* 3.6 36.8 - - + +
779A ALA* 3.5 13.3 - - + +
793A GLU* 1.3 83.2 - - - +
795A GLU* 1.3 67.5 - - - +
796A LYS* 3.3 33.7 - - - -
797A VAL* 3.6 15.0 - - + -
814A PHE 5.7 0.2 - - - -
815A SER 5.5 2.2 - - - -
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Residues in contact with GLU 795 (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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600A THR* 3.0 17.5 + - + +
602A ASP* 2.9 39.7 - - - +
604A SER* 6.1 0.5 - - - -
793A GLU* 3.3 25.5 - - - +
794A PHE* 1.3 79.3 - - - +
796A LYS* 1.3 100.5 + - + +
814A PHE 4.8 1.6 - - - +
815A SER* 5.6 2.8 - - - -
101T TTP 5.1 4.9 + - - -
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Residues in contact with LYS 796 (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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600A THR* 3.4 42.6 + - + +
794A PHE* 3.3 21.8 - - - -
795A GLU* 1.3 113.1 + - - +
797A VAL* 1.3 63.1 + - - +
798A TYR* 3.6 34.3 - - + +
813A LEU* 3.7 31.2 - - + -
814A PHE 3.8 8.3 - - - +
825A ASP* 4.6 2.5 - - - -
827A LYS* 6.3 0.9 - - - +
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Residues in contact with VAL 797 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A PRO* 3.8 26.7 - - + -
598A ILE 3.5 4.7 - - - +
599A ALA* 4.2 13.5 - - + -
768A VAL* 4.1 18.4 - - + -
771A ALA* 4.4 12.8 - - + -
772A MET* 4.0 15.7 - - + -
794A PHE* 3.6 19.3 - - + -
796A LYS* 1.3 80.2 - - - +
798A TYR* 1.3 65.7 + - - +
799A PHE* 4.6 4.0 - - + -
812A LEU 3.4 10.4 - - - +
813A LEU* 4.3 0.7 - - - -
814A PHE* 3.4 30.3 + - + +
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Residues in contact with TYR 798 (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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596A VAL 4.6 1.2 - - - +
597A PRO* 3.4 3.8 - - - +
598A ILE* 3.0 37.5 + - + +
600A THR* 3.9 16.4 - - - -
760A MET* 4.5 16.6 - - + -
796A LYS* 3.6 28.0 - - + +
797A VAL* 1.3 72.0 - - - +
799A PHE* 1.3 64.1 + - - +
800A PRO 3.9 9.1 - - - +
801A TYR* 4.2 21.8 - + + -
809A TYR* 4.3 14.2 + + - -
810A ALA 5.1 1.1 - - - -
811A GLY* 3.6 25.1 - - - -
812A LEU 3.3 11.4 - - - -
813A LEU* 4.6 4.0 - - + -
825A ASP* 2.6 46.5 + - + +
827A LYS* 4.4 8.0 + - - -
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Residues in contact with PHE 799 (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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595A ASP* 3.5 29.6 - - - -
597A PRO* 3.6 35.0 - - + -
766A SER* 4.1 17.0 - - - -
768A VAL* 4.0 15.0 - - + -
797A VAL* 4.6 3.6 - - + -
798A TYR* 1.3 75.6 - - - +
800A PRO* 1.3 70.1 + - + +
812A LEU* 3.4 16.2 + - - +
814A PHE* 3.7 37.5 - + + -
817A ARG* 5.7 2.7 - - - -
855A ARG* 4.0 20.9 + - - -
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Residues in contact with PRO 800 (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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593A TYR* 4.3 12.8 - - + +
594A TYR 3.3 14.6 - - - +
595A ASP* 3.5 22.0 - - - +
596A VAL 5.6 0.9 - - - +
798A TYR 3.9 0.7 - - - -
799A PHE* 1.3 94.4 + - + +
801A TYR* 1.3 62.8 + - - +
811A GLY* 3.7 4.0 - - - -
812A LEU* 3.6 33.7 + - + -
852A LEU* 3.8 32.9 - - + +
855A ARG* 4.3 16.2 - - + +
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Residues in contact with TYR 801 (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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593A TYR* 3.6 6.5 - - - -
594A TYR* 2.9 45.0 + + + +
598A ILE* 3.6 39.0 - - + -
752A VAL* 4.4 17.0 - - + -
753A TYR* 4.2 6.4 - - - -
760A MET* 2.8 33.8 - - - -
798A TYR* 4.2 24.5 - + + +
800A PRO* 1.3 75.2 - - - +
802A LEU* 1.3 64.1 + - - +
803A LEU* 4.3 16.2 - - + +
809A TYR* 3.2 41.4 - + + +
810A ALA 3.1 18.2 - - - -
811A GLY* 5.2 0.2 - - - -
852A LEU* 5.6 1.3 - - - -
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Residues in contact with LEU 802 (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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592A GLY 3.4 16.8 - - - +
593A TYR* 4.1 24.9 - - + -
801A TYR* 1.3 77.8 - - - +
803A LEU* 1.3 59.0 + - - +
804A ILE* 3.7 24.7 + - + +
809A TYR* 3.2 6.0 - - - +
810A ALA* 2.9 52.2 + - + +
829A LEU* 5.6 3.1 - - + -
848A LEU* 5.0 11.2 - - + -
851A LEU* 5.6 6.5 - - + -
852A LEU* 5.1 12.8 - - + -
969A ILE* 4.8 22.4 - - + +
972A PRO* 4.9 8.1 - - + -
973A ILE* 5.1 5.6 - - + -
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Residues in contact with LEU 803 (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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589A PRO* 3.7 28.3 - - + -
590A LEU 3.9 15.7 - - - +
591A LYS* 3.3 8.4 + - - +
592A GLY* 2.9 36.4 + - - +
594A TYR* 5.4 4.4 - - + -
752A VAL* 4.2 13.9 - - + +
753A TYR* 4.4 22.4 - - + -
801A TYR* 4.3 22.8 - - + +
802A LEU* 1.3 72.3 - - - +
804A ILE* 1.3 62.5 + - - +
805A SER 3.7 22.0 - - - +
809A TYR* 3.8 19.3 - - + -
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Residues in contact with ILE 804 (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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591A LYS* 3.2 35.0 - - - +
802A LEU* 3.7 36.1 - - + +
803A LEU* 1.3 81.6 - - - +
805A SER* 1.3 70.1 + - - +
808A ARG* 3.1 21.0 + - + +
809A TYR* 4.9 0.9 - - - -
829A LEU* 4.4 18.8 - - + -
968A ARG* 4.5 33.9 - - + +
969A ILE* 5.2 6.7 - - + -
972A PRO* 4.5 15.9 - - + -
6T T 5.9 1.6 - - - +
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Residues in contact with SER 805 (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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589A PRO* 4.8 12.4 - - - +
591A LYS* 5.5 0.7 - - - -
753A TYR* 4.6 1.7 + - - -
803A LEU* 3.7 15.6 - - - +
804A ILE* 1.3 83.2 - - - +
806A LYS* 1.3 66.8 + - - +
807A LYS 3.7 1.2 + - - -
808A ARG* 3.3 37.1 + - - +
5T T 4.3 12.4 - - - -
6T T 4.5 10.6 + - - -
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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