Contacts of the strand formed by residues 802 - 809 (chain A) in PDB entry 5J68
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 802 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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781A PRO* 4.8 5.8 - - - +
782A LEU* 3.4 27.4 - - - +
783A PRO* 3.8 16.8 - - + -
800A TYR* 3.6 33.6 + - + +
801A PRO* 1.3 74.8 - - - +
803A VAL* 1.3 68.3 + - - +
868A HIS* 3.6 1.2 - - - +
869A PHE* 2.9 41.9 + - + +
871A SER 4.6 0.2 - - - +
872A LYS* 3.6 52.9 - - + +
875A GLN* 4.1 17.9 - - - +
1023A PRO 5.9 0.2 - - - +
1026A GLU* 5.0 3.4 - - - +
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Residues in contact with VAL 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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780A GLU 4.4 0.7 - - - +
781A PRO* 3.5 1.8 - - - +
782A LEU* 2.8 45.0 + - + +
783A PRO 3.9 3.6 - - - +
784A ASP* 3.5 35.7 - - + +
785A LEU 5.2 0.4 - - - +
802A MET* 1.3 79.8 - - - +
804A GLN* 1.3 62.4 + - - +
866A ILE* 4.1 9.4 - - + -
867A ILE 3.3 5.8 - - - +
868A HIS* 3.4 32.8 - - + +
869A PHE* 4.8 2.0 - - - -
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Residues in contact with GLN 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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778A LEU* 3.5 30.3 - - + +
779A SER 2.8 31.7 + - - +
780A GLU* 4.7 2.0 - - - -
781A PRO* 3.6 15.1 - - + +
803A VAL* 1.3 76.7 - - - +
805A GLN* 1.3 61.2 + - - +
866A ILE* 3.6 3.4 - - - -
867A ILE* 2.8 37.2 + - + +
869A PHE* 3.7 12.8 - - + -
875A GLN* 2.6 33.1 + - - +
879A TRP* 5.2 3.8 - - - -
900A PHE* 3.4 19.0 - - - -
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Residues in contact with GLN 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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777A VAL* 3.8 2.5 + - - +
778A LEU* 3.5 6.9 - - - +
779A SER* 2.9 52.0 + - - +
804A GLN* 1.3 74.8 - - - +
806A TRP* 1.3 63.1 + - - +
807A ARG* 4.0 24.9 - - - +
864A THR* 3.9 23.3 - - + +
865A CYS 3.4 11.2 - - - +
866A ILE* 4.5 13.5 - - + +
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Residues in contact with TRP 806 (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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776A GLY* 4.0 17.0 - - - -
777A VAL 3.7 27.8 - - - -
778A LEU* 3.8 27.1 - - + -
804A GLN 4.0 0.4 + - - -
805A GLN* 1.3 74.3 - - - +
807A ARG* 1.3 60.8 + - - +
808A VAL* 3.4 29.8 - - + +
863A LEU* 3.6 6.6 - - + +
864A THR* 3.5 1.7 - - - -
865A CYS* 2.7 51.3 + - + +
867A ILE* 5.1 2.5 - - + -
899A PRO* 4.2 21.1 - - + -
900A PHE* 5.6 2.9 - - + -
901A ILE* 3.6 50.7 - - + +
938A LEU* 4.1 30.3 + - + -
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Residues in contact with ARG 807 (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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775A ARG* 4.0 5.8 - - - +
776A GLY* 3.2 2.6 - - - -
777A VAL* 2.9 57.5 + - + +
805A GLN* 4.0 22.0 - - - +
806A TRP* 1.3 74.9 - - - +
808A VAL* 1.3 66.3 + - - +
809A ARG* 3.4 51.5 - - - +
862A GLU* 3.9 15.0 - - - +
863A LEU 3.2 4.7 - - - +
864A THR* 3.7 22.9 - - + +
955A GLU* 5.4 1.0 + - - -
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Residues in contact with VAL 808 (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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775A ARG 3.7 12.1 - - - +
776A GLY* 3.9 4.0 - - - -
806A TRP* 3.4 43.7 - - + +
807A ARG* 1.3 76.9 - - - +
809A ARG* 1.3 70.7 + - - +
810A SER* 4.6 1.2 + - - -
861A SER 3.8 1.2 - - - +
862A GLU* 3.2 4.0 - - - -
863A LEU* 2.8 39.1 + - + +
936A CYS* 4.3 8.3 - - - -
938A LEU* 3.7 28.9 - - + +
939A CYS* 4.0 22.1 - - + +
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Residues in contact with ARG 809 (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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772A GLU 3.9 3.6 - - - +
774A CYS* 2.8 25.3 + - - -
775A ARG 3.4 11.5 + - - +
807A ARG* 3.4 44.2 - - - +
808A VAL* 1.3 75.8 - - - +
810A SER* 1.3 60.8 + - - +
812A LEU* 3.9 31.2 - - + +
858A LEU* 3.4 24.7 - - - +
861A SER 3.4 4.0 - - - +
862A GLU* 2.8 39.1 + - + +
954A LEU* 4.3 7.1 - - - +
955A GLU* 3.6 32.9 + - - +
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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