Contacts of the strand formed by residues 797 - 806 (chain A) in PDB entry 2O8F
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 VAL 797 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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662A GLN* 4.6 0.8 - - - +
664A PHE* 3.4 20.0 - - + +
666A ILE* 3.7 33.7 - - + -
771A ALA* 3.9 9.6 - - + -
790A LEU* 4.1 14.4 - - + +
791A ALA* 3.4 37.9 - - + +
794A ILE* 3.6 33.8 - - + +
795A PRO 3.2 7.2 - - - +
796A THR* 1.3 81.8 - - - +
798A ASN* 1.3 62.0 + - - +
799A ASN* 4.3 0.9 - - - +
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Residues in contact with ASN 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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662A GLN* 3.1 40.2 + - - +
664A PHE 2.9 11.0 + - - +
665A HIS* 3.4 17.0 + - - +
666A ILE* 2.8 27.0 + - - +
791A ALA* 4.7 0.4 - - - -
796A THR 4.0 0.2 + - - -
797A VAL* 1.3 73.1 + - - +
799A ASN* 1.3 79.5 + - - +
800A LEU* 3.4 21.7 + - - +
819A LYS* 4.9 11.2 - - - +
820A GLY 5.4 0.6 - - - +
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Residues in contact with ASN 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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666A ILE* 3.5 23.0 - - - +
788A THR* 2.6 42.7 + - - +
791A ALA* 3.5 18.6 - - - +
792A ASN* 5.7 0.6 + - - -
798A ASN* 1.3 86.2 + - - +
800A LEU* 1.3 63.7 + - - +
820A GLY* 2.7 32.2 + - - -
821A VAL* 3.8 18.7 - - + +
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Residues in contact with LEU 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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665A HIS* 3.6 33.2 - - + +
666A ILE 2.7 17.5 + - - +
667A ILE* 3.2 10.1 - - + -
668A THR* 2.9 26.2 + - - -
678A TYR* 4.2 21.5 - - + +
779A MET* 5.7 0.2 - - + -
798A ASN* 3.4 16.6 - - - +
799A ASN* 1.3 81.7 - - - +
801A HIS* 1.3 59.5 + - - +
817A VAL* 3.6 25.4 - - + +
818A LYS 3.6 14.1 - - - +
819A LYS* 3.9 17.0 - - + -
820A GLY 3.3 5.8 - - - -
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Residues in contact with HIS 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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668A THR* 3.3 14.6 - - - +
669A GLY* 5.4 0.2 - - - -
800A LEU* 1.3 74.1 - - - +
802A VAL* 1.3 68.9 + - - +
803A THR* 3.6 29.2 - - + +
817A VAL* 3.4 20.4 - - - +
818A LYS* 3.3 39.8 + - + +
819A LYS 3.7 14.4 + - - -
820A GLY 2.6 29.4 + - - +
821A VAL* 3.7 13.4 + - + -
822A CYS* 4.0 29.5 - - + +
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Residues in contact with VAL 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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667A ILE* 4.5 7.0 - - + -
668A THR 3.2 15.8 + - - +
669A GLY* 4.1 8.6 - - - -
670A PRO* 3.6 17.9 - - + +
673A GLY* 3.3 37.0 - - - +
674A GLY 4.6 3.1 - - - +
675A LYS* 3.8 26.9 - - + +
801A HIS* 1.3 85.5 - - - +
803A THR* 1.3 73.3 + - - +
804A ALA 4.2 0.2 + - - -
815A TYR* 5.3 3.6 - - - +
816A GLN 4.3 6.5 - - - +
817A VAL* 5.1 8.1 - - + -
822A CYS* 5.0 2.6 - - - -
826A PHE* 4.5 5.2 - - - -
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Residues in contact with THR 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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801A HIS* 3.6 27.1 - - + +
802A VAL* 1.3 86.9 - - - +
804A ALA* 1.3 65.7 + - - +
813A MET* 4.2 2.3 - - - +
814A LEU* 3.4 44.6 + - - +
815A TYR 4.4 0.5 + - - -
816A GLN* 3.6 13.9 + - - +
818A LYS* 3.8 30.0 - - + +
822A CYS* 5.6 2.5 - - - -
826A PHE* 5.2 1.8 - - - -
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Residues in contact with ALA 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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670A PRO* 4.5 4.0 - - + -
803A THR* 1.3 78.1 - - - +
805A LEU* 1.3 68.7 + - - +
806A THR 4.3 0.2 + - - -
811A LEU* 4.1 9.2 - - + -
812A THR 3.3 14.6 - - - +
813A MET* 3.9 17.5 - - - -
814A LEU* 4.4 5.1 - - - +
824A GLN* 4.2 4.5 - - - +
826A PHE* 3.4 40.8 - - + -
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Residues in contact with LEU 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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804A ALA* 1.3 78.0 - - - +
806A THR* 1.3 64.2 + - - +
807A THR* 5.2 0.6 + - - -
810A THR* 3.7 1.4 - - - +
811A LEU* 3.4 8.3 - - - +
812A THR* 2.9 41.7 + - + +
814A LEU* 3.8 34.3 - - + -
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Residues in contact with THR 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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804A ALA 4.3 0.2 + - - -
805A LEU* 1.3 78.0 - - - +
807A THR* 1.3 69.0 + - - +
810A THR 3.6 3.4 - - - -
811A LEU* 3.8 10.3 - - + -
824A GLN* 5.1 5.1 + - - +
826A PHE* 3.6 33.4 - - + -
829A HIS* 4.1 22.7 - - + +
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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