Contacts of the helix formed by residues 965 - 980 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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962C ARG* 3.8 16.7 - - + +
963C VAL 3.7 0.6 - - - +
964C ASP* 1.3 78.0 - - - +
966C LEU* 1.3 62.8 + - + +
968C ARG* 4.3 0.2 - - - +
969C GLY* 2.9 25.8 + - - -
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Residues in contact with LEU 966 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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953C GLN* 4.6 19.2 - - + +
960C GLU* 5.2 11.9 - - + +
962C ARG* 3.7 18.7 - - + +
965C TRP* 1.3 77.8 - - + +
967C PHE* 1.3 60.3 + - - +
969C GLY* 3.8 1.5 - - - -
970C ALA* 2.9 30.7 + - - +
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Residues in contact with PHE 967 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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953C GLN* 5.9 2.2 - - - +
962C ARG 4.4 6.8 + - - +
963C VAL 3.4 21.1 - - - +
965C TRP 3.4 0.4 - - - -
966C LEU* 1.3 78.6 - - - +
968C ARG* 1.3 57.2 + - - +
970C ALA* 3.4 5.6 + - - +
971C VAL* 2.9 28.5 + - - +
818D MET* 6.5 1.3 - - + -
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Residues in contact with ARG 968 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021B PRO* 6.6 0.2 - - + -
1022B GLU* 6.0 7.0 - - + -
964C ASP* 3.2 29.7 + - + +
965C TRP 3.7 1.4 + - - +
967C PHE* 1.3 76.5 - - - +
969C GLY* 1.3 60.4 + - - +
971C VAL* 3.6 8.7 - - + +
972C TYR* 2.9 29.3 + - - +
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Residues in contact with GLY 969 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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965C TRP 2.9 19.6 + - - -
966C LEU* 3.8 2.0 - - - -
967C PHE 3.3 0.2 - - - -
968C ARG* 1.3 77.5 - - - +
970C ALA* 1.3 55.5 + - - +
972C TYR* 3.3 7.2 + - - +
973C HIS* 2.9 26.9 + - - +
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Residues in contact with ALA 970 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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949C GLY* 5.2 4.7 - - - +
952C LYS* 6.6 0.2 - - + -
953C GLN* 3.7 31.9 - - + +
966C LEU 2.9 17.4 + - - +
967C PHE* 3.8 5.2 - - - +
969C GLY* 1.3 72.8 - - - +
971C VAL* 1.3 60.8 + - - +
973C HIS* 3.7 6.9 - - - +
974C SER* 2.9 30.7 + - - -
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Residues in contact with VAL 971 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967C PHE 2.9 19.0 + - - +
968C ARG* 3.6 10.3 - - - +
970C ALA* 1.3 76.5 - - - +
972C TYR* 1.3 57.5 + - - +
974C SER* 3.4 5.3 + - - -
975C TYR* 2.9 31.2 + - - +
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Residues in contact with TYR 972 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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968C ARG 2.9 17.6 + - - +
969C GLY* 3.3 7.4 + - - +
971C VAL* 1.3 74.4 - - - +
973C HIS* 1.3 59.2 + - - +
975C TYR* 3.4 5.6 + - - +
976C LEU* 2.9 30.0 + - - +
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Residues in contact with HIS 973 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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952C LYS* 4.3 25.7 + - - +
969C GLY 2.9 16.9 + - - +
970C ALA* 3.7 8.5 - - - +
972C TYR* 1.3 77.7 - - - +
974C SER* 1.3 56.5 + - - +
976C LEU* 3.3 7.0 + - - +
977C THR* 2.9 27.9 + - - -
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Residues in contact with SER 974 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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945C VAL* 4.7 16.7 - - - +
949C GLY* 4.6 20.6 - - - -
952C LYS* 5.2 3.8 - - - +
970C ALA 2.9 17.9 + - - -
971C VAL* 3.9 5.6 - - - -
973C HIS* 1.3 73.8 - - - +
975C TYR* 1.3 60.3 + - - +
977C THR* 3.3 7.5 + - - -
978C ILE* 2.9 28.9 + - - +
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Residues in contact with TYR 975 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029B LEU* 4.6 20.4 - - + -
971C VAL 2.9 18.5 + - - +
972C TYR* 3.8 7.2 - - - +
974C SER* 1.3 73.9 - - - +
976C LEU* 1.3 59.2 + - - +
978C ILE* 3.3 6.9 + - - +
979C PHE* 2.9 28.8 + - - +
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Residues in contact with LEU 976 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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972C TYR 2.9 18.1 + - - +
973C HIS* 3.6 7.4 - - - +
974C SER 3.3 0.2 - - - -
975C TYR* 1.3 77.2 - - - +
977C THR* 1.3 61.4 + - - +
979C PHE* 3.4 14.6 + - - +
980C GLY* 3.5 9.0 + - - -
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Residues in contact with THR 977 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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952C LYS* 4.9 11.0 - - - -
973C HIS 2.9 16.9 + - - -
974C SER* 3.7 9.0 - - - -
976C LEU* 1.3 76.3 - - - +
978C ILE* 1.3 59.9 + - - +
979C PHE 3.6 0.2 + - - -
980C GLY* 3.6 12.9 + - - -
1036C THR* 5.7 2.6 + - - +
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Residues in contact with ILE 978 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033B LEU* 4.7 19.7 - - + +
1037B ASN* 5.8 0.3 + - - -
945C VAL* 4.6 22.7 - - + -
974C SER 2.9 17.9 + - - +
975C TYR* 3.3 8.0 + - - +
976C LEU 3.3 0.2 - - - -
977C THR* 1.3 74.8 - - - +
979C PHE* 1.3 65.5 + - - +
980C GLY 3.5 3.6 + - - -
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Residues in contact with PHE 979 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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980B GLY* 6.1 1.0 - - - -
1033B LEU* 5.7 6.7 - - + -
1037B ASN* 5.7 4.0 + - - +
975C TYR 2.9 17.2 + - - +
976C LEU* 3.7 9.9 - - - +
977C THR 3.3 0.6 - - - -
978C ILE* 1.3 79.1 - - - +
980C GLY* 1.3 62.3 + - - +
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Residues in contact with GLY 980 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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976C LEU 3.5 9.3 + - - -
977C THR* 3.6 10.9 + - - -
978C ILE 3.3 5.2 - - - -
979C PHE* 1.3 82.7 - - - +
1037C ASN* 5.1 12.6 - - - -
979D PHE 6.1 0.7 - - - -
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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