Contacts of the helix formed by residues 961 - 980 (chain C) in PDB entry 3O37
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 961 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898C VAL* 6.2 0.2 - - + -
900C LEU* 3.3 11.7 - - - +
959C TYR 3.6 0.6 - - - -
960C SER* 1.3 86.0 + - - +
962C PRO* 1.3 79.3 - - + +
963C GLU* 3.8 27.6 - - - +
964C ASP* 2.8 53.4 + - - +
965C PHE 3.8 1.9 + - - -
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Residues in contact with PRO 962 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900C LEU* 3.5 3.8 - - + -
904C ASP* 3.5 36.6 - - + +
961C LYS* 1.3 86.7 - - + +
963C GLU* 1.3 73.0 + - - +
964C ASP 2.9 1.2 + - - -
965C PHE* 3.0 29.1 + - + -
966C VAL* 3.0 18.4 + - + +
1005C TYR* 3.6 26.5 - - + +
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Residues in contact with GLU 963 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961C LYS* 3.2 28.6 + - - +
962C PRO* 1.3 90.1 - - - +
964C ASP* 1.3 58.0 + - - +
966C VAL* 3.8 8.8 - - - +
967C ALA* 3.0 30.1 + - - +
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Residues in contact with ASP 964 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958C MET 4.8 2.8 - - - +
959C TYR* 3.6 27.6 - - + -
960C SER* 2.9 36.4 + - - -
961C LYS* 2.8 42.3 + - - +
963C GLU* 1.3 81.1 - - - +
965C PHE* 1.3 59.3 + - - +
967C ALA* 3.5 11.4 + - - +
968C ASP* 3.6 9.2 + - - -
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Residues in contact with PHE 965 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900C LEU* 3.8 27.1 - - + -
904C ASP 3.7 16.4 - - - -
908C CYS* 3.5 35.2 - - + -
911C LEU* 3.9 22.7 - - + -
948C ILE* 4.7 0.8 - - + +
959C TYR* 3.7 27.5 - + + +
962C PRO* 3.0 32.5 + - + -
964C ASP* 1.3 76.5 - - - +
966C VAL* 1.3 78.0 + - + +
967C ALA 3.2 0.4 - - - -
968C ASP* 3.1 4.7 + - - +
969C PHE* 3.1 33.3 + + + -
1005C TYR* 3.4 26.0 - + - -
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Residues in contact with VAL 966 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962C PRO* 3.0 24.7 + - + +
963C GLU* 3.8 9.2 - - - +
965C PHE* 1.3 88.7 - - + +
967C ALA* 1.3 65.0 + - - +
969C PHE* 3.1 9.5 + - - +
970C ARG* 2.9 57.1 + - - +
997C PHE* 4.4 3.8 - - + -
1001C LEU* 3.8 36.3 - - + -
1005C TYR* 5.6 0.9 - - + -
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Residues in contact with ALA 967 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963C GLU 3.0 17.9 + - - +
964C ASP* 3.6 8.5 - - - +
965C PHE 3.2 0.2 - - - -
966C VAL* 1.3 78.7 - - - +
968C ASP* 1.3 59.4 + - - +
970C ARG* 3.4 7.6 + - - +
971C LEU* 3.0 26.9 + - - +
974C GLN* 5.5 0.5 + - - -
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Residues in contact with ASP 968 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943C MET* 3.2 33.4 - - - +
948C ILE* 3.8 12.3 - - + -
951C ARG* 2.9 29.9 + - - -
958C MET* 5.1 0.2 - - - +
959C TYR* 2.5 38.7 + - - +
964C ASP 3.6 3.5 + - - +
965C PHE 3.1 9.8 + - - +
967C ALA* 1.3 78.6 - - - +
969C PHE* 1.3 64.7 + - - +
971C LEU* 3.3 16.5 + - - +
972C ILE* 3.3 3.6 + - - +
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Residues in contact with PHE 969 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908C CYS* 3.8 23.3 - - - -
911C LEU* 4.3 7.2 - - + -
912C LEU* 3.5 48.7 - - + -
915C LEU* 3.6 31.2 - - + -
945C LEU* 4.0 4.7 - - + -
948C ILE* 3.5 16.6 - - + -
965C PHE* 3.1 32.2 + + - -
966C VAL* 3.1 5.0 + - - +
968C ASP* 1.3 75.4 - - - +
970C ARG* 1.3 63.6 + - - +
972C ILE* 3.1 17.7 + - + +
973C PHE* 3.2 18.7 - + + -
997C PHE* 3.4 37.9 - + + -
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Residues in contact with ARG 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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966C VAL* 2.9 38.2 + - - +
967C ALA* 3.8 7.6 - - - +
969C PHE* 1.3 74.8 - - - +
971C LEU* 1.3 58.5 + - - +
973C PHE* 3.2 11.9 + - + +
974C GLN* 2.8 36.1 + - - +
994C GLU* 5.7 3.1 - - - +
997C PHE* 4.4 5.8 - - + -
998C GLU* 2.9 41.7 + - - +
1001C LEU* 3.6 14.5 - - - +
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Residues in contact with LEU 971 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941C ASN* 3.3 38.6 - - + +
943C MET* 3.7 27.6 - - + -
967C ALA 3.0 13.7 + - - +
968C ASP* 3.4 16.6 - - - +
969C PHE 3.2 0.2 - - - -
970C ARG* 1.3 77.1 - - - +
972C ILE* 1.3 56.9 + - - +
974C GLN* 3.7 28.0 - - - +
975C ASN* 2.8 56.1 + - - +
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Residues in contact with ILE 972 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924C PHE* 4.0 33.0 - - + -
943C MET* 3.5 27.8 - - + +
944C ASP 3.5 26.0 - - - -
945C LEU* 3.7 16.8 - - + +
948C ILE* 3.6 21.1 - - + -
968C ASP 3.4 10.8 - - - +
969C PHE* 3.1 11.6 + - + +
971C LEU* 1.3 79.6 - - - +
973C PHE* 1.3 69.1 + - + +
975C ASN* 3.4 4.1 + - - +
976C CYS* 3.1 25.6 + - - +
993C LEU* 5.8 0.4 - - + -
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Residues in contact with PHE 973 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915C LEU* 4.5 9.4 - - + -
924C PHE* 6.0 1.3 - + - -
945C LEU* 6.6 0.2 - - + -
969C PHE* 3.2 25.6 - + + -
970C ARG* 3.2 13.5 + - + +
972C ILE* 1.3 83.7 - - + +
974C GLN* 1.3 60.5 + - - +
976C CYS* 3.3 7.1 + - + +
977C ALA* 3.0 30.1 + - - +
990C GLY* 3.8 12.3 - - - +
993C LEU* 3.8 24.5 - - + -
994C GLU* 3.5 64.6 - - + +
997C PHE* 3.6 40.2 - + + -
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Residues in contact with GLN 974 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967C ALA 5.5 0.4 + - - -
970C ARG* 2.8 16.9 + - - +
971C LEU* 3.6 35.0 - - - +
973C PHE* 1.3 78.1 - - - +
975C ASN* 1.3 64.3 + - - +
977C ALA* 4.0 4.9 - - - +
978C GLU* 3.1 39.9 + - - +
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Residues in contact with ASN 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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935C TYR* 3.2 19.5 + - - +
939C ILE* 3.3 32.4 - - + +
941C ASN 3.0 22.9 + - - -
942C PRO* 3.5 0.8 - - - +
943C MET* 3.5 19.1 + - - +
971C LEU* 2.8 37.5 + - - +
972C ILE* 3.6 4.9 - - - +
974C GLN* 1.3 81.1 - - - +
976C CYS* 1.3 62.4 + - - +
978C GLU* 3.4 0.6 + - - -
979C PHE* 3.0 28.9 + - - +
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Residues in contact with CYS 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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924C PHE* 3.4 33.9 - - + -
935C TYR* 4.8 2.4 + - - -
972C ILE 3.1 13.9 + - - +
973C PHE* 3.5 11.7 - - - +
975C ASN* 1.3 77.6 - - - +
977C ALA* 1.3 58.2 + - - +
980C ASN* 2.9 50.5 + - - +
986C VAL* 3.5 21.1 - - - -
987C ALA* 4.0 7.9 - - - -
990C GLY* 3.8 10.8 - - - -
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Residues in contact with ALA 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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973C PHE 3.0 16.8 + - - +
974C GLN* 4.0 5.8 - - - +
976C CYS* 1.3 77.7 - - - +
978C GLU* 1.3 61.2 + - - +
980C ASN 3.4 14.8 - - - +
987C ALA* 5.7 4.5 - - - -
991C ILE* 5.5 11.4 - - + -
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Residues in contact with GLU 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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938C ILE* 5.8 1.5 - - + +
939C ILE* 4.6 11.9 - - + +
974C GLN* 3.1 32.8 + - - +
975C ASN 4.1 1.6 - - - +
977C ALA* 1.3 77.2 - - - +
979C PHE* 1.3 60.2 + - - +
980C ASN 4.9 0.2 - - - +
10H SER* 2.5 44.4 + - - +
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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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932C VAL* 5.3 9.2 - - + -
934C ASP* 4.0 8.7 - - + -
935C TYR* 3.4 62.6 - + + -
938C ILE* 3.8 30.7 - - + +
939C ILE* 4.0 7.0 - - + -
975C ASN 3.0 17.7 + - - +
978C GLU* 1.3 80.7 - - - +
980C ASN* 1.3 83.6 - - - +
981C GLU 3.9 1.4 + - - -
10H SER* 4.5 6.2 - - - +
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Residues in contact with ASN 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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935C TYR* 5.4 2.0 - - - -
976C CYS* 2.9 34.1 + - - +
977C ALA 3.4 16.6 - - - +
978C GLU 4.8 0.6 - - - +
979C PHE* 1.3 99.3 - - - +
981C GLU* 1.3 66.1 + - - +
982C PRO* 3.6 2.9 - - - +
984C SER* 3.6 16.4 + - - +
986C VAL* 3.4 35.8 - - - +
987C ALA* 4.1 10.1 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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