Contacts of the helix formed by residues 965 - 980 (chain A) in PDB entry 6PUO
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 TRP 965 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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962A ARG* 3.8 15.8 - - + +
963A VAL 3.7 0.4 - - - +
964A ASP* 1.3 78.5 - - - +
966A LEU* 1.3 63.8 + - + +
968A ARG* 4.3 0.2 - - - +
969A GLY* 2.9 24.8 + - - -
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Residues in contact with LEU 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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953A GLN* 4.6 18.8 - - - +
960A GLU* 5.2 11.9 - - + +
962A ARG* 3.7 19.3 - - + +
965A TRP* 1.3 77.3 - - - +
967A PHE* 1.3 61.5 + - - +
969A GLY* 4.4 1.3 - - - +
970A ALA* 2.9 30.7 + - - +
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Residues in contact with PHE 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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953A GLN* 5.9 2.2 - - - +
962A ARG 4.4 6.4 + - - +
963A VAL 3.4 21.8 - - - +
965A TRP 3.4 0.6 - - - +
966A LEU* 1.3 79.4 - - - +
968A ARG* 1.3 57.4 + - - +
970A ALA* 3.4 6.2 + - - +
971A VAL* 2.9 27.6 + - - +
818B MET* 6.5 0.9 - - + -
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Residues in contact with ARG 968 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964A ASP* 3.2 28.2 + - + +
965A TRP 3.7 1.6 + - - +
966A LEU 3.4 0.2 - - - -
967A PHE* 1.3 76.1 - - - +
969A GLY* 1.3 59.3 + - - +
971A VAL* 3.6 8.0 - - - +
972A TYR* 2.9 29.6 + - - +
1022D GLU* 6.0 6.5 - - + -
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Residues in contact with GLY 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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965A TRP 2.9 18.3 + - - -
966A LEU* 3.4 2.4 + - - -
967A PHE 3.3 0.2 - - - -
968A ARG* 1.3 77.9 - - - +
970A ALA* 1.3 56.1 + - - +
972A TYR* 3.3 7.0 + - - +
973A HIS* 2.9 27.3 + - - +
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Residues in contact with ALA 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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949A GLY* 5.2 5.1 - - - +
953A GLN* 3.7 31.6 - - + -
966A LEU 2.9 18.4 + - - +
967A PHE* 3.8 4.9 - - - +
969A GLY* 1.3 72.4 - - - +
971A VAL* 1.3 60.3 + - - +
973A HIS* 3.4 7.6 + - - +
974A SER* 2.9 30.7 + - - -
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Residues in contact with VAL 971 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967A PHE 2.9 17.4 + - - +
968A ARG* 3.6 10.8 - - - +
969A GLY 3.2 0.4 - - - -
970A ALA* 1.3 75.5 - - - +
972A TYR* 1.3 57.6 + - - +
974A SER* 3.8 5.7 - - - -
975A TYR* 2.9 31.1 + - - +
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Residues in contact with TYR 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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968A ARG 2.9 17.6 + - - +
969A GLY* 3.7 6.7 - - - +
971A VAL* 1.3 75.0 - - - +
973A HIS* 1.3 59.8 + - - +
975A TYR* 3.8 6.0 - - - +
976A LEU* 2.9 30.1 + - - +
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Residues in contact with HIS 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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952A LYS* 4.3 25.2 + - - +
969A GLY 2.9 16.7 + - - +
970A ALA* 3.7 8.3 - - - +
971A VAL 3.3 0.2 - - - -
972A TYR* 1.3 76.0 - - - +
974A SER* 1.3 57.0 + - - +
976A LEU* 3.3 6.8 + - - +
977A THR* 2.9 27.2 + - - -
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Residues in contact with SER 974 (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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945A VAL* 4.7 16.7 - - - +
946A VAL* 6.5 0.4 - - - -
949A GLY* 4.6 20.4 - - - -
952A LYS* 5.2 4.8 - - - +
970A ALA 2.9 18.5 + - - -
971A VAL* 3.9 5.4 - - - -
973A HIS* 1.3 73.4 - - - +
975A TYR* 1.3 59.9 + - - +
977A THR* 3.3 8.1 + - - -
978A ILE* 2.9 28.6 + - - +
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Residues in contact with TYR 975 (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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971A VAL 2.9 18.9 + - - +
972A TYR* 3.8 6.7 - - - +
974A SER* 1.3 73.0 - - - +
976A LEU* 1.3 60.0 + - - +
978A ILE* 3.3 7.3 + - - +
979A PHE* 2.9 28.9 + - - +
1029D LEU* 4.7 20.2 - - + -
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Residues in contact with LEU 976 (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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972A TYR 2.9 18.7 + - - +
973A HIS* 3.6 7.4 - - - +
975A TYR* 1.3 77.0 - - - +
977A THR* 1.3 61.6 + - - +
979A PHE* 3.4 14.8 + - - +
980A GLY* 3.5 8.5 + - - -
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Residues in contact with THR 977 (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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952A LYS* 4.9 10.8 - - - -
973A HIS 2.9 17.1 + - - -
974A SER* 3.7 8.1 - - - -
975A TYR 3.3 0.2 - - - -
976A LEU* 1.3 76.0 - - - +
978A ILE* 1.3 61.1 + - - +
979A PHE 3.6 0.2 + - - -
980A GLY* 3.6 13.2 + - - -
1036A THR* 5.7 2.6 + - - -
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Residues in contact with ILE 978 (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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945A VAL* 4.6 22.2 - - + -
974A SER 2.9 17.5 + - - +
975A TYR* 3.8 8.3 - - - +
976A LEU 3.3 0.2 - - - -
977A THR* 1.3 73.9 - - - +
979A PHE* 1.3 63.4 + - - +
980A GLY 3.3 4.1 + - - -
1033D LEU* 4.7 19.4 - - + +
1037D ASN* 5.8 0.7 + - - -
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Residues in contact with PHE 979 (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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975A TYR 2.9 16.6 + - - +
976A LEU* 3.7 9.4 - - - +
977A THR 3.3 0.8 - - - -
978A ILE* 1.3 78.5 - - - +
980A GLY* 1.3 62.6 + - - +
980D GLY* 6.1 0.7 - - - -
1033D LEU* 5.7 5.8 - - + -
1037D ASN* 5.7 3.9 + - - +
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Residues in contact with GLY 980 (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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976A LEU 3.5 9.3 + - - -
977A THR 3.6 11.1 + - - -
978A ILE 3.3 4.8 - - - -
979A PHE* 1.3 82.2 - - - +
1037A ASN* 5.1 12.9 + - - -
979B PHE 6.1 1.3 - - - -
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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