Contacts of the helix formed by residues 66 - 76 (chain C) in PDB entry 1GMO
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 THR 66 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64C VAL* 3.3 18.0 - - - +
65C ASN* 1.3 90.1 - - + +
67C ALA* 1.3 65.1 + - - +
68C ASP* 3.1 32.0 + - - +
69C GLN* 3.1 22.3 + - - +
70C CYS 3.8 0.2 + - - -
89C PHE* 4.1 4.3 - - - -
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Residues in contact with ALA 67 (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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39C ILE* 3.9 19.3 - - + -
66C THR* 1.3 72.0 - - - +
68C ASP* 1.3 65.8 + - - +
70C CYS* 2.8 16.5 + - - +
71C ALA* 3.0 11.3 + - - +
87C PHE* 4.1 2.4 - - + -
89C PHE* 3.6 46.3 - - + -
119C TYR* 4.5 10.8 - - + +
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Residues in contact with ASP 68 (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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37C ASN* 4.2 17.0 + - + +
39C ILE* 4.1 24.6 - - - +
66C THR* 3.1 28.4 + - - +
67C ALA* 1.3 78.4 + - - +
69C GLN* 1.3 62.9 + - + +
71C ALA* 3.0 9.5 + - - +
72C ASP* 2.8 31.3 + - - +
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Residues in contact with GLN 69 (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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64C VAL* 3.6 19.2 - - + +
65C ASN* 2.7 45.7 + - - +
66C THR* 3.1 17.8 + - - +
67C ALA 3.1 0.4 - - - -
68C ASP* 1.3 80.7 - - - +
70C CYS* 1.3 62.9 + - - +
72C ASP* 3.3 7.4 + - - +
73C ARG* 3.2 24.4 + - - +
96C CYS* 4.7 0.7 - - - -
98C TRP* 5.2 1.3 - - - -
8L IDS 3.6 34.4 + - - +
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Residues in contact with CYS 70 (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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64C VAL* 4.1 3.1 - - - -
67C ALA* 2.8 12.6 + - - +
69C GLN* 1.3 79.2 - - - +
71C ALA* 1.3 62.8 + - - +
74C CYS* 3.1 12.6 + - - +
87C PHE* 3.5 23.3 - - + -
89C PHE* 3.5 29.8 - - - -
96C CYS* 2.0 52.7 - - + -
98C TRP* 3.0 23.7 + - - +
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Residues in contact with ALA 71 (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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38C THR 4.3 0.2 - - - -
39C ILE* 3.8 36.6 - - + +
42C PHE* 3.9 4.0 - - + -
67C ALA 3.0 11.0 + - - +
68C ASP* 3.2 10.5 - - - +
70C CYS* 1.3 73.5 - - - +
72C ASP* 1.3 69.4 + - - +
74C CYS* 2.9 4.9 + - - +
75C THR* 2.8 26.7 + - - -
87C PHE* 3.4 21.7 - - + -
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Residues in contact with ASP 72 (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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37C ASN* 4.4 5.9 - - - +
38C THR* 2.9 28.1 + - - -
68C ASP* 2.8 27.3 + - - +
69C GLN* 3.7 7.2 - - - +
71C ALA* 1.3 71.1 - - - +
73C ARG* 1.3 64.9 + - - +
75C THR* 2.9 14.9 + - - -
76C ARG* 2.9 27.8 + - - +
9L SGN 4.2 23.0 + - - +
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Residues in contact with ARG 73 (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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60C LYS* 3.8 5.5 - - - +
69C GLN 3.2 12.6 + - - +
72C ASP* 1.3 78.5 - - - +
74C CYS* 1.3 58.0 + - - +
76C ARG* 4.6 4.7 - - - +
77C ASN* 2.8 23.2 + - - -
78C LYS* 2.4 34.5 + - + +
79C GLY* 3.0 32.1 + - - -
80C LEU* 3.8 11.9 - - + +
98C TRP* 3.9 28.8 - - + -
6L IDS 2.8 39.0 + - - -
7L SGN 3.1 18.6 + - - -
8L IDS 2.9 35.9 + - - +
9L SGN 5.0 5.1 + - - +
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Residues in contact with CYS 74 (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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42C PHE* 3.8 23.1 - - + -
70C CYS 3.1 14.3 + - - +
71C ALA 2.9 8.8 + - - +
73C ARG* 1.3 74.4 - - - +
75C THR* 1.3 68.3 + - - +
77C ASN* 2.8 16.3 + - - +
80C LEU* 4.4 0.2 - - - -
84C CYS* 2.0 65.0 - - - +
86C ALA 4.7 2.2 - - - -
87C PHE* 4.0 9.9 - - + -
98C TRP* 3.8 7.4 - - + +
121C ASN* 4.7 2.6 + - - -
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Residues in contact with THR 75 (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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38C THR* 2.5 39.5 - - + +
41C GLU* 5.5 3.4 - - + -
42C PHE* 3.6 12.0 - - + -
71C ALA 2.8 12.0 + - - -
72C ASP* 3.4 5.8 - - - -
74C CYS* 1.3 79.1 - - - +
76C ARG* 1.3 65.5 + - + +
77C ASN* 4.4 2.4 - - - +
121C ASN* 5.5 6.5 - - - +
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Residues in contact with ARG 76 (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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38C THR* 6.0 0.2 + - - -
72C ASP* 2.9 23.5 + - - +
73C ARG* 4.3 2.0 - - - +
75C THR* 1.3 79.0 - - + +
77C ASN* 1.3 70.9 + - - +
78C LYS* 3.0 16.6 + - + +
142D ILE* 5.6 1.7 - - - +
9L SGN 3.5 30.8 + - - -
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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