Contacts of the helix formed by residues 950 - 967 (chain C) in PDB entry 6V3O
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 GLY 950 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C PRO* 4.0 23.2 - - - +
95C ALA* 5.4 2.3 - - - +
96C ILE* 4.1 14.4 - - - +
948C PRO 3.3 0.8 + - - -
949C PRO* 1.3 71.8 - - - +
951C LEU* 1.3 59.2 + - - +
952C GLU 3.6 1.8 - - - +
953C ASP* 3.7 7.8 + - - -
954C THR* 3.1 29.1 + - - +
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Residues in contact with LEU 951 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ALA* 6.3 2.0 - - + -
904C PHE* 6.5 0.2 - - + -
908C THR* 3.6 25.4 - - + +
911C ARG* 3.6 57.2 - - + +
912C ILE* 3.9 20.6 - - + +
947C TYR* 4.9 2.2 - - + -
948C PRO* 3.3 38.5 + - + +
949C PRO 4.1 5.6 - - - +
950C GLY* 1.3 75.2 - - - +
952C GLU* 1.3 68.4 + - - +
953C ASP 3.2 1.1 - - - -
954C THR* 3.2 8.6 - - + +
955C LEU* 2.9 27.4 + - - +
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Residues in contact with GLU 952 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754C MET* 3.8 26.8 - - - +
945C SER* 2.2 44.1 + - - +
946C GLU* 3.8 7.6 + - - +
947C TYR* 3.7 37.2 - - + +
948C PRO 4.5 0.6 + - - +
951C LEU* 1.3 76.8 - - - +
953C ASP* 1.3 70.1 + - - +
955C LEU* 3.8 4.8 - - - +
956C ILE* 3.1 34.1 + - + +
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Residues in contact with ASP 953 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ILE* 3.3 27.1 - - + +
230C ILE* 4.8 21.6 - - + +
942C ASN* 3.0 40.1 + - - +
945C SER* 5.7 0.2 - - - -
950C GLY* 3.7 6.3 + - - +
951C LEU 3.2 0.8 - - - -
952C GLU* 1.3 87.4 - - - +
954C THR* 1.3 57.4 + - - +
956C ILE* 3.5 9.2 + - - +
957C LEU* 3.1 31.9 + - + +
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Residues in contact with THR 954 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ALA* 4.8 16.4 - - + -
96C ILE* 4.4 1.7 - - - +
99C ALA* 4.0 11.3 - - - +
904C PHE* 3.8 26.3 - - + -
908C THR* 3.7 17.3 + - + +
950C GLY 3.1 21.8 + - - +
951C LEU* 3.2 21.8 - - + +
953C ASP* 1.3 74.4 - - - +
955C LEU* 1.3 60.6 + - - +
957C LEU* 3.1 10.7 + - - +
958C THR* 2.9 32.2 + - - +
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Residues in contact with LEU 955 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747C PRO* 5.3 1.6 - - + -
750C GLU* 3.8 32.3 - - + -
754C MET* 3.8 14.6 - - + -
905C GLN* 3.7 36.8 - - + +
908C THR* 4.6 9.2 - - + -
909C LEU* 3.9 24.0 - - + +
912C ILE* 4.0 14.6 - - + -
951C LEU 2.9 18.1 + - - +
952C GLU* 3.8 3.8 - - - +
954C THR* 1.3 78.8 - - - +
956C ILE* 1.3 61.3 + - - +
958C THR* 2.8 19.3 + - - +
959C MET* 3.0 20.1 + - + +
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Residues in contact with ILE 956 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C ILE* 4.9 12.3 - - + -
754C MET* 3.6 24.0 - - + -
756C ILE* 3.4 34.1 - - + -
952C GLU* 3.1 23.5 + - + +
953C ASP* 3.7 11.2 - - - +
954C THR 3.3 0.2 - - - -
955C LEU* 1.3 75.0 - - - +
957C LEU* 1.3 58.7 + - - +
959C MET* 3.3 6.6 + - + +
960C LYS* 2.9 51.4 + - + +
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Residues in contact with LEU 957 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ILE* 3.7 35.9 - - + +
99C ALA* 4.0 20.2 - - + +
100C SER* 4.1 13.0 - - - +
103C LEU* 4.0 28.0 - - + +
229C GLU* 4.0 17.3 - - + +
230C ILE* 4.3 19.7 - - + -
901C LEU* 4.5 4.2 - - - +
953C ASP 3.1 19.5 + - - +
954C THR* 3.1 11.4 + - - +
956C ILE* 1.3 76.6 - - - +
958C THR* 1.3 57.6 + - - +
960C LYS* 3.4 7.5 + - + +
961C GLY* 2.9 25.8 + - - -
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Residues in contact with THR 958 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ALA* 5.1 0.9 - - + -
901C LEU* 3.8 40.8 - - + +
904C PHE* 4.0 19.1 - - + +
905C GLN* 3.1 27.7 + - - +
908C THR* 5.7 0.7 - - - +
954C THR* 2.9 21.6 + - - +
955C LEU* 2.8 18.3 + - - -
957C LEU* 1.3 75.8 - - - +
959C MET* 1.3 56.2 + - - +
962C ILE* 2.8 38.4 + - - +
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Residues in contact with MET 959 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C THR* 4.1 4.4 + - - +
747C PRO* 4.9 11.4 - - + +
751C TYR* 3.6 25.4 - - + -
754C MET* 3.8 23.6 - - - -
756C ILE* 3.8 18.4 - - + -
779C PHE* 3.4 31.6 - - + -
783C GLN* 3.2 17.5 + - + +
905C GLN* 3.4 18.6 - - - +
955C LEU* 3.0 23.3 + - + +
956C ILE* 3.6 6.5 - - - +
958C THR* 1.3 82.8 + - - +
960C LYS* 1.3 61.8 + - - +
963C ALA* 3.1 27.7 + - - +
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Residues in contact with LYS 960 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LEU* 4.4 12.5 - - + +
179C THR* 3.2 38.8 + - + +
180C GLN* 3.0 26.1 + - - +
229C GLU* 4.0 14.3 + - + +
230C ILE* 4.9 5.8 - - - +
231C ARG* 2.8 45.5 - - - +
956C ILE* 2.9 35.2 + - + +
957C LEU* 3.7 8.5 - - + +
959C MET* 1.3 77.5 - - - +
961C GLY* 1.3 56.8 + - - +
963C ALA* 3.5 1.7 + - - +
964C ALA* 3.0 29.2 + - - +
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Residues in contact with GLY 961 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LEU* 3.4 25.3 - - - +
106C LEU* 3.1 12.2 - - - +
901C LEU* 3.6 20.2 - - - -
957C LEU 2.9 10.7 + - - -
960C LYS* 1.3 75.4 - - - +
962C ILE* 1.3 64.3 + - - +
964C ALA* 3.2 1.1 + - - +
965C GLY 3.0 18.7 + - - -
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Residues in contact with ILE 962 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782C THR* 4.4 0.9 - - + +
783C GLN* 3.8 34.3 - - - +
785C ARG* 5.3 0.4 - - - -
898C ILE* 4.4 19.2 - - + +
901C LEU* 3.9 28.2 - - + +
902C ASN* 3.6 22.9 - - - +
905C GLN* 3.6 27.8 - - - +
958C THR 2.8 25.0 + - - +
961C GLY* 1.3 72.1 - - - -
963C ALA* 1.3 58.4 + - - +
965C GLY* 3.2 1.6 + - - +
966C MET* 2.9 42.8 + - + +
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Residues in contact with ALA 963 (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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177C HIS* 5.8 1.7 - - + -
178C PRO* 5.8 2.7 - - + -
179C THR* 3.8 24.0 - - + -
675C GLU* 5.3 3.3 - - - +
779C PHE* 4.1 12.8 - - + -
782C THR* 6.1 1.3 - - - -
783C GLN* 3.6 12.6 - - - +
959C MET 3.1 20.4 + - - +
962C ILE* 1.3 76.9 - - - +
964C ALA* 1.3 62.5 + - - +
966C MET* 4.5 3.8 - - - +
967C GLN* 3.0 24.4 + - - +
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Residues in contact with ALA 964 (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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103C LEU* 4.7 3.4 - - + -
106C LEU* 4.6 4.9 - - + -
107C ASN* 4.4 17.3 - - - +
110C ASN* 3.7 17.8 + - - +
177C HIS* 5.9 5.4 - - + -
179C THR* 5.2 2.2 - - + +
960C LYS 3.0 18.8 + - - +
961C GLY* 3.2 7.6 + - - +
963C ALA* 1.3 76.3 - - - +
965C GLY* 1.3 60.4 - - - +
967C GLN* 3.5 19.1 + - - +
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Residues in contact with GLY 965 (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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106C LEU* 3.8 18.1 - - - +
835C LYS* 5.0 0.3 - - - -
894C ARG* 3.1 34.2 + - - -
898C ILE* 3.8 24.1 - - - +
961C GLY 3.0 10.7 + - - -
962C ILE 3.2 2.2 + - - -
964C ALA* 1.3 79.2 - - - +
966C MET* 1.3 59.7 + - - +
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Residues in contact with MET 966 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782C THR* 3.7 26.0 - - + +
785C ARG* 3.9 18.8 - - - +
787C HIS* 3.8 20.4 - - - -
835C LYS* 2.6 78.5 + - + +
895C ASN* 4.8 2.9 - - - +
898C ILE* 3.8 23.6 - - + -
962C ILE* 2.9 30.5 + - + +
963C ALA* 4.3 2.7 - - - +
965C GLY* 1.3 79.2 - - - +
967C GLN* 1.3 63.2 + - - +
968C ASN 3.7 1.4 - - - +
969C THR* 4.2 1.5 - - + +
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Residues in contact with GLN 967 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ASN* 4.5 12.3 - - - +
675C GLU* 3.6 40.9 - - - +
676C VAL* 4.9 1.7 - - - -
679C PHE* 4.0 24.4 - - - +
782C THR* 5.2 1.7 - - - +
894C ARG* 3.6 29.8 - - - +
963C ALA* 3.0 15.0 + - - +
964C ALA* 3.5 20.4 + - - +
966C MET* 1.3 81.7 - - - +
968C ASN* 1.3 66.5 + - - +
969C THR* 3.8 5.5 + - - +
1003C FLC 3.5 22.2 - - - +
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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
------------------------------------------------------------
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