Contacts of the strand formed by residues 828 - 835 (chain B) in PDB entry 3I8E
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 828 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727B GLN* 2.9 18.9 - - - +
818B SER* 3.2 18.7 - - - -
819B CYS 2.8 19.1 + - - +
821B LEU* 5.0 9.6 - - + -
824B ASP* 3.0 42.4 + - + -
826B ASN* 3.7 23.0 + - + -
827B THR* 1.3 70.8 - - - +
829B PHE* 1.3 60.3 + - - +
830B ILE* 4.1 8.3 - - + -
850B VAL* 3.7 24.9 - - + -
851B PHE 3.2 17.3 - - - +
852B GLN* 3.6 21.3 + - + +
861B VAL* 3.5 29.0 - - + +
893B TRP* 4.0 15.0 - + - -
897B LYS* 3.6 15.8 - - - +
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Residues in contact with PHE 829 (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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725B CYS* 4.6 2.9 - - + -
727B GLN* 3.0 57.4 - - + -
732B CYS* 4.0 12.3 - - - -
734B GLY* 4.1 15.9 - - - -
791B LEU* 4.3 12.1 - - + -
793B ILE* 3.6 40.6 - - + -
816B LEU* 4.6 9.9 - - + -
817B VAL 3.5 4.9 - - - +
818B SER* 3.6 12.6 - - - -
828B TYR* 1.3 73.5 - - - +
830B ILE* 1.3 60.4 + - - +
831B VAL* 4.8 0.9 - - - -
849B VAL 3.7 0.5 - - - +
850B VAL 3.5 0.5 - - - -
851B PHE* 2.7 54.2 + - + +
852B GLN* 4.8 0.4 - - - +
853B TYR* 4.5 12.3 - - + -
858B LEU* 5.0 3.8 - - + -
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Residues in contact with ILE 830 (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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815B SER 4.2 0.3 - - - -
816B LEU* 3.3 7.3 + - - -
817B VAL* 3.0 38.0 + - + +
819B CYS* 3.3 35.0 - - - +
821B LEU* 3.6 21.1 - - + -
828B TYR* 4.3 10.3 - - + -
829B PHE* 1.3 76.6 - - - +
831B VAL* 1.3 65.5 + - - +
832B GLY 4.1 0.6 + - - -
848B ILE* 3.7 24.2 - - + -
849B VAL 3.3 11.0 - - - +
850B VAL* 3.9 21.3 - - + -
873B MET* 4.0 6.7 - - - +
880B LEU* 3.8 21.5 - - + -
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Residues in contact with VAL 831 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736B LEU* 4.0 9.4 - - + -
791B LEU* 4.3 5.4 - - + -
807B PHE* 3.4 30.3 - - + -
813B ALA* 3.6 22.2 - - + -
815B SER 3.4 10.3 - - - +
816B LEU* 3.8 20.0 - - + -
830B ILE* 1.3 79.6 - - - +
832B GLY* 1.3 61.2 + - - +
833B THR* 4.0 4.0 - - + +
847B ARG 3.6 2.9 - - - +
848B ILE* 4.6 0.7 - - - -
849B VAL* 3.1 30.0 + - - +
851B PHE* 4.0 25.4 - - + -
873B MET* 4.6 1.1 - - - -
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Residues in contact with GLY 832 (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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813B ALA* 3.7 0.5 - - - -
814B LEU* 2.8 30.7 + - - -
815B SER* 3.3 25.8 + - - -
831B VAL* 1.3 73.9 - - - +
833B THR* 1.3 55.6 + - - +
847B ARG 3.9 3.6 - - - -
848B ILE* 4.4 1.8 - - - -
870B VAL* 3.7 20.9 - - - -
873B MET* 3.9 11.6 - - - -
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Residues in contact with THR 833 (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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807B PHE* 4.3 9.6 - - + -
811B GLU* 2.9 28.6 + - + +
812B TYR 3.4 11.4 - - - -
813B ALA* 3.9 18.8 - - + +
814B LEU* 4.0 3.4 - - - +
831B VAL* 4.0 11.9 - - + +
832B GLY* 1.3 77.4 - - - +
834B ALA* 1.3 68.0 + - - +
846B GLY* 4.0 3.1 - - - -
847B ARG 2.7 40.8 + - - +
849B VAL* 4.9 2.9 - - + -
869B ALA* 4.0 0.5 - - - -
870B VAL* 3.0 27.0 + - - +
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Residues in contact with ALA 834 (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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811B GLU* 3.4 2.9 - - - -
812B TYR* 2.9 29.0 + - - +
814B LEU* 3.6 18.6 - - + -
833B THR* 1.3 82.6 + - - +
835B MET* 1.3 65.2 + - - +
836B VAL* 4.1 0.8 + - - +
843B PRO* 4.3 3.1 - - + -
845B GLN 3.8 10.8 - - - +
846B GLY* 3.8 2.9 - - - -
869B ALA* 3.7 22.9 - - + -
155D LEU* 4.2 10.3 - - + -
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Residues in contact with MET 835 (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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771B PHE* 4.3 32.3 - - + -
808B LEU* 4.8 10.3 - - + -
809B GLN 3.9 17.0 - - - +
810B ASN 3.4 3.6 - - - +
811B GLU* 3.6 33.2 - - + +
834B ALA* 1.3 74.0 - - - +
836B VAL* 1.3 60.4 + - - +
837B TYR* 3.6 38.2 + - + +
840B GLU* 4.8 2.4 - - - +
843B PRO* 3.4 21.0 - - - +
845B GLN* 3.8 31.0 + - + +
846B GLY* 4.1 7.9 - - - +
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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