Contacts of the strand formed by residues 810 - 819 (chain A) in PDB entry 5C58
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 810 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A GLU* 4.6 10.2 + - - +
766A ARG* 4.7 14.4 + - - +
787A ARG* 3.5 30.6 - - + +
788A PHE* 3.3 3.0 + - - +
789A ALA* 3.1 52.1 + - + +
808A PRO 4.2 9.6 - - - -
809A LYS* 1.3 85.8 - - - +
811A THR* 1.3 66.3 + - - +
812A LEU* 3.7 24.7 - - + -
837A ARG* 5.3 7.2 - - - +
838A ALA 5.4 0.4 - - - +
839A TYR* 3.6 35.9 - + + -
840A VAL 4.3 17.7 - - - -
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Residues in contact with THR 811 (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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786A VAL* 4.5 7.6 - - + -
787A ARG 3.8 2.0 - - - -
788A PHE* 4.1 14.0 - - + +
809A LYS* 5.2 6.9 + - - -
810A TYR* 1.3 78.5 + - - +
812A LEU* 1.3 66.8 + - - +
813A PHE* 4.1 25.9 - - + -
835A THR* 4.0 7.4 + - - -
837A ARG* 4.3 17.5 + - - +
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Residues in contact with LEU 812 (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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786A VAL* 3.3 13.9 - - - +
787A ARG* 2.9 73.0 + - + +
810A TYR* 3.7 18.2 - - + -
811A THR* 1.3 80.9 - - - +
813A PHE* 1.3 68.3 + - - +
814A ASP* 4.6 0.4 - - - +
832A GLU 5.3 0.2 - - - +
833A ASN* 3.5 22.4 - - - +
835A THR* 4.2 1.8 - - - +
837A ARG* 4.2 16.8 - - + -
839A TYR* 3.5 42.2 - - + +
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Residues in contact with PHE 813 (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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784A VAL* 4.4 12.6 - - + -
785A THR 3.9 2.2 - - - -
786A VAL* 3.6 30.7 - - + -
811A THR* 4.1 24.7 - - + -
812A LEU* 1.3 80.6 - - - +
814A ASP* 1.3 66.6 + - - +
815A LEU* 5.9 0.2 - - + -
833A ASN* 3.5 0.7 + - - -
834A LEU* 2.8 52.3 + - + +
835A THR* 3.5 31.9 + - + -
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Residues in contact with ASP 814 (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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134A ARG* 3.4 19.3 - - + +
784A VAL* 3.3 6.8 - - - +
785A THR* 2.8 52.0 + - - +
787A ARG* 2.9 38.6 + - - -
813A PHE* 1.3 80.5 + - - +
815A LEU* 1.3 63.3 + - - +
816A TYR* 4.6 2.1 - - + -
831A VAL 3.2 9.0 - - - +
832A GLU* 2.7 33.3 - - - +
833A ASN* 3.9 0.9 - - - -
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Residues in contact with LEU 815 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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783A GLY 3.8 4.9 - - - +
784A VAL* 3.7 31.4 - - + -
813A PHE* 5.4 0.7 - - + -
814A ASP* 1.3 76.5 - - - +
816A TYR* 1.3 64.7 + - - +
830A SER* 3.2 6.0 - - - -
831A VAL* 2.9 45.9 + - + +
834A LEU* 3.7 40.2 - - + -
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Residues in contact with TYR 816 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A ASN* 3.1 58.6 + - + +
134A ARG* 6.1 0.9 - - + -
700A TYR* 2.7 38.6 + - - -
770A THR* 4.6 6.2 - - - -
772A GLY* 4.2 1.6 + - - -
781A ASP* 4.5 4.3 - - - -
782A ALA* 3.4 5.8 - - - +
783A GLY* 3.2 66.6 + - - +
784A VAL* 3.8 1.5 + - - -
785A THR* 3.7 23.1 - - - -
814A ASP* 4.6 2.9 - - + -
815A LEU* 1.3 80.0 - - - +
817A ALA* 1.3 67.6 + - - +
829A GLY 3.4 11.4 - - - +
830A SER* 4.2 2.0 - - - +
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Residues in contact with ALA 817 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A ASN* 5.8 0.2 - - - -
780A LEU* 5.5 5.4 - - + -
781A ASP 3.1 11.0 - - - +
782A ALA* 3.9 11.0 - - + -
816A TYR* 1.3 82.4 - - - +
818A SER* 1.3 61.7 + - - +
828A ARG* 3.1 25.5 - - - +
829A GLY 3.1 14.4 + - - +
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Residues in contact with SER 818 (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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133A ASN* 4.3 9.3 + - - -
779A LYS* 3.8 14.2 + - - +
780A LEU* 3.8 3.6 - - - +
781A ASP* 2.7 51.4 + - - +
816A TYR* 5.9 0.2 - - - -
817A ALA* 1.3 77.6 - - - +
819A TYR* 1.3 60.7 + - - +
826A THR* 4.6 6.5 - - - -
827A LEU 3.4 6.1 - - - -
828A ARG* 3.7 25.4 - - - -
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Residues in contact with TYR 819 (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 PHE* 5.0 17.7 - + + +
779A LYS* 3.3 21.5 - - + -
780A LEU* 4.3 20.0 - - + -
818A SER* 1.3 74.6 - - - +
820A LYS* 1.3 77.4 + - - +
821A LEU* 3.5 36.0 + - + -
826A THR* 3.4 2.5 - - - -
827A LEU* 3.1 40.0 + - + +
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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