Contacts of the helix formed by residues 808 - 821 (chain A) in PDB entry 5WRZ
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 SER 808 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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804A VAL* 3.6 9.1 - - - +
805A ASP* 2.7 33.9 + - - +
807A ASP* 1.3 81.9 - - - +
809A GLU* 1.3 64.3 + - - +
810A GLU* 3.7 14.3 - - - +
811A ALA* 3.3 14.7 + - - +
812A GLU* 3.3 22.2 + - - +
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Residues in contact with GLU 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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808A SER* 1.3 74.4 - - - +
810A GLU* 1.3 64.0 + - - +
812A GLU* 3.2 20.1 + - + +
813A ILE* 3.1 42.0 + - + +
963A SER 5.5 0.9 - - - +
964A LEU* 5.8 2.3 - - + +
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Residues in contact with GLU 810 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804A VAL* 3.6 29.4 - - + +
808A SER* 3.7 10.7 + - - +
809A GLU* 1.3 79.7 - - - +
811A ALA* 1.3 57.6 + - - +
813A ILE* 3.4 2.2 + - - +
814A ILE* 3.0 36.0 + - - +
838A LYS* 4.3 7.1 - - - +
964A LEU* 4.2 23.8 - - + +
965A ASP* 5.7 1.6 - - - +
1001A TYR* 2.9 39.9 + - + +
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Residues in contact with ALA 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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804A VAL* 4.3 6.1 - - + -
805A ASP 3.2 28.3 - - - +
806A ARG* 3.5 17.3 - - - +
808A SER* 3.3 9.8 + - - +
809A GLU 3.3 0.2 - - - -
810A GLU* 1.3 78.4 - - - +
812A GLU* 1.4 56.9 + - - +
814A ILE* 3.5 2.8 + - - +
815A ARG* 3.0 43.3 + - - +
836A ILE* 4.1 14.5 - - + +
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Residues in contact with GLU 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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807A ASP* 4.6 6.9 - - - +
808A SER 3.3 12.4 + - - +
809A GLU* 3.2 29.6 + - + +
811A ALA* 1.4 76.8 - - - +
813A ILE* 1.3 59.8 + - + +
815A ARG* 3.5 23.5 + - - +
816A LYS* 3.0 28.5 + - - +
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Residues in contact with ILE 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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809A GLU* 3.1 34.8 + - + +
810A GLU* 3.8 4.7 - - - +
812A GLU* 1.3 76.0 - - + +
814A ILE* 1.3 66.8 + - + +
816A LYS* 3.2 8.9 + - - +
817A TYR* 3.0 21.0 + - - +
859A LEU* 5.8 0.7 - - + -
962A ILE* 4.5 12.6 - - + -
963A SER 4.1 15.3 - - - +
964A LEU* 4.1 35.4 - - + -
969A VAL* 4.3 18.4 - - + -
971A LEU* 3.8 15.1 - - + +
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Residues in contact with ILE 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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810A GLU* 3.0 28.4 + - + +
811A ALA 3.8 4.3 - - - +
812A GLU 3.4 0.2 - - - -
813A ILE* 1.3 77.1 - - + +
815A ARG* 1.3 64.4 + - + +
817A TYR* 3.1 9.3 + - - +
818A VAL* 3.1 22.0 + - + +
836A ILE* 3.9 25.4 - - + -
859A LEU* 5.5 2.2 - - + -
921A LEU* 4.0 17.5 - - + -
964A LEU* 5.0 6.7 - - + -
1001A TYR* 3.8 43.5 - - + -
1003A LEU* 3.8 34.3 - - + -
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Residues in contact with ARG 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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806A ARG* 2.8 42.6 + - - +
807A ASP* 5.3 1.2 + - - +
811A ALA* 3.0 31.5 + - - +
812A GLU* 4.0 25.8 - - - +
814A ILE* 1.3 76.2 - - - +
816A LYS* 1.3 57.8 + - - +
818A VAL* 3.6 8.9 + - - +
819A LYS* 2.8 30.2 + - - +
833A VAL* 4.4 20.6 - - + -
836A ILE* 4.3 15.3 - - + +
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Residues in contact with LYS 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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812A GLU 3.0 18.6 + - - +
813A ILE* 3.2 7.2 + - - +
815A ARG* 1.3 74.1 - - - +
817A TYR* 1.3 60.4 + - - +
819A LYS* 3.6 11.8 - - + +
820A ASN* 2.9 56.4 + - - +
962A ILE* 5.6 7.0 - - + +
971A LEU* 4.0 21.6 - - + +
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Residues in contact with TYR 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 ILE 3.0 12.4 + - - +
814A ILE* 3.1 11.6 + - - +
816A LYS* 1.3 75.8 - - - +
818A VAL* 1.3 62.4 - - - +
821A THR* 2.8 35.2 + - + +
859A LEU* 2.8 32.5 + - + -
860A LEU* 3.8 8.0 - - - -
861A TRP* 3.4 30.7 - + + -
899A ASP* 3.5 24.5 - - - -
921A LEU* 3.5 25.6 - - + -
969A VAL* 3.7 19.3 - - + -
970A PRO* 3.4 30.3 - - + +
971A LEU* 3.8 21.7 - - + +
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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 ILE 3.1 10.1 + - - +
815A ARG 3.7 7.2 - - - +
817A TYR* 1.3 83.0 - - - +
819A LYS* 1.3 63.3 + - - +
820A ASN 3.4 0.2 + - - -
821A THR 3.7 2.1 + - - -
822A HIS* 4.2 5.7 + - - +
831A LEU* 4.5 31.6 - - + +
833A VAL* 3.9 20.6 - - + +
861A TRP* 3.5 26.9 - - + -
901A VAL* 3.7 24.3 - - + +
1003A LEU* 3.8 17.5 - - + -
1005A LEU* 5.2 2.7 - - + -
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Residues in contact with LYS 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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815A ARG 2.8 22.5 + - - +
816A LYS* 3.2 13.8 + - + +
818A VAL* 1.3 76.2 - - - +
820A ASN* 1.3 70.8 + - - +
821A THR 3.7 0.3 + - - -
822A HIS* 4.5 6.4 + - - +
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Residues in contact with ASN 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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816A LYS* 2.9 46.2 + - - +
818A VAL 3.3 0.2 - - - -
819A LYS* 1.3 90.0 + - - +
821A THR* 1.3 59.2 + - + +
822A HIS 3.5 3.3 + - - +
900A MET* 5.3 0.5 - - - +
960A ALA* 6.1 0.2 - - - +
971A LEU* 2.8 33.7 + - - +
972A GLY* 4.2 2.1 - - - -
973A THR* 3.5 44.9 - - + +
974A GLY 4.3 2.8 + - - -
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Residues in contact with THR 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 TYR* 2.8 35.1 + - + +
818A VAL 3.7 0.4 + - - -
819A LYS 3.5 0.6 - - - -
820A ASN* 1.3 81.1 - - - +
822A HIS* 1.3 61.9 + - - +
823A ALA 3.6 1.0 + - - -
861A TRP* 3.8 4.7 + - - -
899A ASP 3.7 20.9 - - - +
900A MET* 3.5 25.8 - - - +
901A VAL* 3.0 38.5 + - - +
902A SER 3.8 1.0 + - - -
956A PRO* 4.8 0.4 - - + -
970A PRO 4.1 5.2 - - - +
971A LEU* 4.2 4.3 - - - -
972A GLY 3.7 17.7 - - - +
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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