Contacts of the helix formed by residues 960 - 973 (chain A) in PDB entry 3POZ
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 960 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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829A GLU* 5.4 6.5 - - - +
894A GLN* 3.3 38.6 - - - +
956A ASP* 4.1 17.9 + - - +
958A ARG 4.1 7.0 - - - -
959A PRO* 1.3 74.5 - - - +
961A PHE* 1.3 67.1 + - - +
962A ARG* 3.8 45.1 - - + +
963A GLU* 2.9 32.2 + - - +
964A LEU* 3.0 14.1 + - - +
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Residues in contact with PHE 961 (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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822A ALA* 3.8 20.5 - - - +
825A MET* 3.5 46.7 - - + -
826A ASN* 3.9 11.4 - - - +
829A GLU* 3.7 21.8 + - + +
893A HIS* 3.6 22.9 - - + -
894A GLN* 5.2 0.2 + - - -
896A ASP* 3.6 14.4 - - + -
897A VAL* 3.6 28.4 - - + +
900A TYR* 3.6 27.1 - + + -
959A PRO 4.2 0.4 + - - -
960A LYS* 1.3 71.6 - - - +
962A ARG* 1.3 63.3 + - - +
964A LEU* 3.1 15.8 + - + +
965A ILE* 2.9 29.0 + - - +
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Residues in contact with ARG 962 (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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826A ASN* 3.9 20.3 + - - +
829A GLU* 5.1 11.9 + - - -
960A LYS* 3.8 31.8 - - + +
961A PHE* 1.3 74.2 - - - +
963A GLU* 1.3 82.0 + - - +
965A ILE* 3.5 11.7 + - + +
966A ILE* 3.3 32.1 + - + +
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Residues in contact with GLU 963 (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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958A ARG 4.7 0.3 - - - +
959A PRO* 3.5 13.4 - - + +
960A LYS* 2.9 39.0 + - - +
962A ARG* 1.3 89.9 + - - +
964A LEU* 1.3 61.3 + - - +
966A ILE* 3.3 11.3 + - + +
967A GLU* 2.9 30.9 + - - +
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Residues in contact with LEU 964 (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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822A ALA* 4.2 12.3 - - + +
897A VAL* 4.2 11.9 - - + -
900A TYR* 3.8 32.5 - - + +
946A ILE* 3.5 31.2 - - + -
950A CYS* 4.5 1.6 - - - -
959A PRO* 3.8 24.7 - - + -
960A LYS 3.0 18.9 + - - +
961A PHE* 3.1 23.1 + - + +
963A GLU* 1.3 75.3 - - - +
965A ILE* 1.3 64.0 + - - +
967A GLU* 4.5 6.3 - - - +
968A PHE* 3.0 32.9 + - + +
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Residues in contact with ILE 965 (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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819A VAL* 4.4 5.5 - - + +
822A ALA* 3.7 18.6 - - + -
823A LYS* 3.7 51.6 - - + +
826A ASN* 3.7 29.8 - - + +
961A PHE 2.9 16.6 + - - +
962A ARG* 3.6 10.3 - - - +
964A LEU* 1.3 76.1 - - - +
966A ILE* 1.3 59.5 + - + +
968A PHE* 4.4 0.5 - - - +
969A SER* 2.8 43.3 + - - +
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Residues in contact with ILE 966 (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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962A ARG* 3.3 22.5 + - + +
963A GLU* 3.3 12.5 + - + +
965A ILE* 1.3 79.1 - - + +
967A GLU* 1.3 62.9 + - - +
969A SER* 3.7 5.1 - - - -
970A LYS* 3.0 24.9 + - + +
973A ARG* 5.0 1.8 + - - +
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Residues in contact with GLU 967 (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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942A ASP 5.1 0.9 - - - +
946A ILE* 3.4 40.6 - - + +
949A LYS* 5.4 6.9 + - - +
963A GLU 2.9 20.9 + - - +
964A LEU* 4.2 7.1 - - + +
966A ILE* 1.3 75.0 - - - +
968A PHE* 1.3 58.8 + - - +
970A LYS* 3.3 26.2 + - - +
971A MET* 3.0 39.6 + - + +
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Residues in contact with PHE 968 (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 LEU* 3.8 25.9 - - + +
818A CYS* 3.6 25.1 - - + -
819A VAL* 3.6 22.5 - - + +
900A TYR* 3.4 31.4 - + - -
904A VAL* 4.2 17.5 - - + -
908A MET* 4.6 0.7 - - + -
943A VAL* 4.5 12.8 - - + -
946A ILE* 3.7 43.5 - - + -
964A LEU* 3.0 27.3 + - + +
967A GLU* 1.3 79.1 - - + +
969A SER* 1.3 51.7 + - - +
971A MET* 3.2 9.5 + - - +
972A ALA* 2.8 35.7 + - - +
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Residues in contact with SER 969 (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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819A VAL* 3.6 23.9 - - - +
823A LYS* 5.0 2.4 + - - -
965A ILE* 2.8 31.7 + - - +
966A ILE* 3.7 5.8 - - - -
968A PHE* 1.3 71.7 - - - +
970A LYS* 1.3 64.9 + - - +
972A ALA* 3.3 12.2 + - - +
973A ARG* 3.4 34.0 + - - +
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Residues in contact with LYS 970 (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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966A ILE* 3.0 16.2 + - + +
967A GLU* 3.3 35.6 + - - +
969A SER* 1.3 76.5 - - - +
971A MET* 1.3 68.0 + - - +
973A ARG* 3.2 39.2 + - - +
974A ASP* 3.9 3.1 + - - +
978A TYR* 4.4 21.4 + - - +
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Residues in contact with MET 971 (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 LEU* 4.0 13.7 - - + -
942A ASP* 3.9 22.2 - - + +
943A VAL* 3.7 20.0 - - + -
946A ILE* 3.5 33.4 - - + -
967A GLU* 3.0 28.8 + - + +
968A PHE* 3.2 15.7 + - - +
970A LYS* 1.3 81.0 - - - +
972A ALA* 1.3 57.8 + - - +
974A ASP 3.0 29.8 + - - +
975A PRO* 3.3 5.4 - - - +
978A TYR* 3.7 44.1 - - + -
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Residues in contact with ALA 972 (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 GLN* 2.9 30.3 + - - +
815A LEU* 4.1 19.2 - - + +
816A ASN* 3.5 23.8 - - - +
819A VAL* 4.6 3.6 - - + -
968A PHE 2.8 20.0 + - - +
969A SER* 3.7 10.5 - - - +
970A LYS 3.3 0.2 - - - -
971A MET* 1.3 72.6 - - - +
973A ARG* 1.3 61.2 + - + +
974A ASP 3.3 0.2 - - - -
975A PRO* 3.5 3.4 - - - +
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Residues in contact with ARG 973 (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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966A ILE* 5.0 1.6 + - - +
969A SER* 3.4 30.4 + - - +
970A LYS* 3.2 36.1 + - - +
971A MET 3.1 1.2 - - - -
972A ALA* 1.3 78.9 - - + +
974A ASP* 1.3 58.2 + - + +
975A PRO* 3.7 3.2 - - - +
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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