Contacts of the helix formed by residues 811 - 822 (chain A) in PDB entry 5ID6
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 LYS 811 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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810A PHE* 1.3 74.0 - - - +
812A ILE* 1.3 67.8 + - - +
813A ASN* 4.9 11.3 - - - +
814A THR* 3.2 24.6 + - - +
815A GLU* 3.0 24.8 + - - +
1207A ASP* 3.4 23.8 + - - -
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Residues in contact with ILE 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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7A PHE* 4.2 8.7 - - + -
10A CYS* 4.6 7.0 - - + -
11A TYR* 3.9 31.2 - - + -
810A PHE* 3.5 28.5 + - + +
811A LYS* 1.3 72.1 - - - +
813A ASN* 1.3 59.5 + - - +
815A GLU* 3.5 1.2 + - - +
816A VAL* 2.9 29.6 + - - +
975A GLN 3.4 22.9 - - - +
976A ILE 4.2 11.2 - - - -
977A THR 4.2 5.4 - - - +
978A ASN* 3.7 22.6 + - - +
991A GLY* 3.6 24.0 - - - +
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Residues in contact with ASN 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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811A LYS* 3.3 14.9 - - - +
812A ILE* 1.3 75.0 - - - +
814A THR* 1.3 63.2 + - - +
816A VAL 3.4 0.7 + - - -
817A ARG* 3.1 31.5 + - - +
978A ASN* 3.2 18.6 + - - +
989A GLN* 3.0 47.8 + - - +
990A ASN* 4.3 0.4 - - - +
991A GLY* 2.6 30.6 + - - -
1207A ASP* 5.9 1.6 - - - +
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Residues in contact with THR 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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811A LYS* 3.2 27.8 + - - +
813A ASN* 1.3 78.8 - - - +
815A GLU* 1.3 59.0 + - + +
817A ARG* 3.1 11.4 + - - +
818A VAL* 3.0 38.3 + - + +
1203A ASP 5.4 3.1 - - - +
1206A LEU* 5.3 3.1 - - + -
1207A ASP* 3.8 36.2 + - + +
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Residues in contact with GLU 815 (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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6A LYS* 5.1 7.0 - - + +
7A PHE* 4.0 8.7 - - + -
810A PHE* 3.5 44.3 - - + -
811A LYS 3.0 14.3 + - - +
812A ILE 3.9 2.7 - - - +
814A THR* 1.3 74.3 - - - +
816A VAL* 1.3 64.7 + - - +
818A VAL* 3.9 18.6 - - - +
819A LEU* 3.1 44.9 + - - +
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Residues in contact with VAL 816 (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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7A PHE* 3.8 15.3 - - + -
812A ILE* 2.9 23.6 + - + +
814A THR 3.3 0.2 - - - -
815A GLU* 1.3 75.3 - - - +
817A ARG* 1.3 63.8 + - - +
819A LEU* 3.4 4.2 + - - +
820A LEU* 3.0 43.7 + - + +
921A VAL* 4.2 10.5 - - + -
989A GLN* 3.7 13.5 - - - +
991A GLY* 3.6 34.5 - - - +
992A PHE* 3.7 19.7 - - + -
994A PHE* 4.1 2.5 - - + -
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Residues in contact with ARG 817 (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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813A ASN* 3.1 16.0 + - - +
814A THR* 3.1 9.7 + - - +
816A VAL* 1.3 76.2 - - - +
818A VAL* 1.3 56.3 + - - +
820A LEU* 3.2 2.1 + - - +
821A LYS* 2.8 30.7 + - - +
988A THR* 4.4 8.5 - - - +
989A GLN* 2.7 37.6 + - - +
994A PHE* 5.1 0.2 - - - -
1198A PHE* 3.8 37.9 - - + -
1206A LEU* 3.0 46.3 + - + +
1207A ASP* 3.7 15.0 + - - +
1209A VAL 3.2 20.8 + - - -
1211A ILE* 3.5 21.4 - - - +
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Residues in contact with VAL 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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814A THR* 3.0 32.2 + - + +
815A GLU* 3.9 20.9 - - - +
816A VAL 3.3 0.2 - - - -
817A ARG* 1.3 76.0 - - - +
819A LEU* 1.3 65.2 + - + +
821A LYS* 3.2 2.3 + - - +
822A HIS* 3.1 39.2 + - + -
1203A ASP* 4.5 17.7 - - + +
1206A LEU* 3.9 21.3 - - + -
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Residues in contact with LEU 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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3A LYS* 4.0 30.8 - - + +
6A LYS* 3.4 41.1 - - + +
7A PHE* 3.4 34.3 - - + -
815A GLU* 3.1 29.9 + - - +
816A VAL* 3.9 3.8 - - - +
818A VAL* 1.3 81.3 - - + +
820A LEU* 1.3 57.3 + - - +
822A HIS* 3.3 4.8 + - - +
823A ASP* 2.9 29.6 + - - +
992A PHE* 5.9 0.2 - - + -
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Residues in contact with LEU 820 (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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3A LYS* 4.1 18.8 - - + -
816A VAL* 3.0 40.6 + - + +
817A ARG 3.7 3.6 - - - +
819A LEU* 1.3 72.6 - - - +
821A LYS* 1.3 68.0 + - - +
823A ASP* 3.2 13.6 + - - +
826A PRO* 4.0 24.0 - - + +
827A TYR 5.8 0.2 - - - +
921A VAL* 4.0 19.3 - - + -
994A PHE* 3.7 20.4 - - + -
1195A ILE* 4.0 30.2 - - + +
1198A PHE* 4.2 11.4 - - + -
1199A LYS* 3.5 15.3 + - - -
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Residues in contact with LYS 821 (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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817A ARG 2.8 14.6 + - - +
818A VAL 3.4 9.0 - - - +
820A LEU* 1.3 76.7 - - - +
822A HIS* 1.3 74.7 + - - +
1198A PHE* 3.6 23.7 - - + +
1199A LYS* 3.1 43.2 + - - +
1201A ALA 2.4 33.8 + - - +
1202A GLU* 3.7 5.9 + - - +
1203A ASP* 3.5 32.9 + - - +
1206A LEU* 3.9 12.3 - - + -
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Residues in contact with HIS 822 (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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818A VAL* 3.1 35.9 + - + +
819A LEU* 3.3 5.4 + - - +
820A LEU 3.2 0.2 - - - -
821A LYS* 1.3 97.9 + - + +
823A ASP* 1.3 61.4 + - - +
824A ASP* 3.7 2.9 + - - +
1199A LYS* 4.7 0.2 - - - -
1203A ASP* 3.1 28.6 + - - -
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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