Contacts of the helix formed by residues 72 - 83 (chain C) in PDB entry 3GTU
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 SER 72 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12C LEU* 3.4 46.1 - - - +
16C ILE* 4.5 13.0 - - - -
60C PRO* 4.0 12.4 - - - +
71C GLN* 1.3 69.6 + - - +
73C ASN* 1.3 69.8 + - - +
75C ILE* 3.0 7.1 + - - +
76C LEU* 2.9 32.6 + - - +
104C MET* 4.9 7.4 - - - -
107C ARG* 5.7 2.5 - - - -
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Residues in contact with ASN 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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71C GLN* 3.4 0.8 - - - +
72C SER* 1.3 80.4 - - - +
74C ALA* 1.3 56.1 + - - +
76C LEU* 3.7 8.8 - - - +
77C ARG* 2.9 37.8 + - - +
100C GLU* 3.3 41.2 + - - +
101C ASN* 6.1 0.4 - - - +
104C MET* 3.8 31.3 - - - +
107C ARG* 5.1 2.3 + - - -
158C ILE* 4.4 10.7 - - - +
105D ASN* 2.9 31.6 + - - +
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Residues in contact with ALA 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ILE* 3.7 12.1 - - + +
70C THR 3.2 22.9 - - - +
71C GLN* 2.9 8.8 + - + +
73C ASN* 1.3 75.8 - - - +
75C ILE* 1.3 60.3 + - - +
77C ARG* 3.4 2.9 + - - +
78C TYR* 2.9 29.8 + - - +
81C ARG* 4.6 0.3 + - - -
101D ASP* 3.8 40.0 - - + +
102D ILE 4.1 2.5 - - - +
105D ASN* 3.9 1.8 - - - +
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Residues in contact with ILE 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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4C LEU* 4.9 0.9 - - + -
16C ILE* 3.9 40.2 - - + -
60C PRO* 3.7 29.4 - - + +
61C TYR* 3.8 17.5 - - - -
62C LEU* 3.8 29.8 - - + +
69C ILE* 4.1 15.3 - - + +
70C THR 4.1 7.0 - - - +
71C GLN 2.9 19.2 + - - +
72C SER 3.5 5.6 - - - +
74C ALA* 1.3 72.8 - - - +
76C LEU* 1.3 65.6 + - - +
78C TYR* 3.2 5.5 + - - +
79C ILE* 3.1 24.4 + - + +
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Residues in contact with LEU 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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15C SER* 3.7 30.7 - - - +
16C ILE* 3.8 21.8 - - + -
19C LEU* 3.7 24.4 - - + +
72C SER* 2.9 26.5 + - - +
73C ASN* 3.7 7.9 - - - +
75C ILE* 1.3 77.1 - - - +
77C ARG* 1.3 53.1 + - - +
79C ILE* 3.2 3.8 + - - +
80C ALA* 2.7 38.6 + - - +
107C ARG* 6.2 0.4 - - - +
154C PHE* 4.0 13.0 - - + +
157C PHE* 5.3 2.9 - - + -
158C ILE* 3.8 34.1 - - + -
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Residues in contact with ARG 77 (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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73C ASN* 2.9 21.3 + - - +
74C ALA 3.7 1.8 - - - +
76C LEU* 1.3 75.5 - - - +
78C TYR* 1.3 57.6 + - - +
80C ALA* 3.5 6.9 - - - +
81C ARG* 2.8 41.8 + - - +
86C CYS* 4.4 2.0 - - - -
96C GLU* 4.3 11.9 + - - +
97C ASP* 3.1 28.3 + - - +
100C GLU* 2.8 38.7 + - - +
154C PHE* 3.6 27.8 - - + -
81D ARG* 3.7 27.2 - - - +
101D ASP* 3.6 33.8 + - - +
104D GLU* 4.6 1.7 + - - -
105D ASN* 5.9 0.4 - - - +
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Residues in contact with TYR 78 (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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62C LEU* 3.9 16.6 - - + -
64C ASP* 2.7 41.2 + - + -
67C HIS* 3.1 24.9 + + - -
69C ILE* 3.6 24.2 - - + -
74C ALA 2.9 17.8 + - - +
75C ILE* 3.4 6.3 - - - +
76C LEU 3.2 0.4 - - - -
77C ARG* 1.3 77.0 - - - +
79C ILE* 1.3 59.1 + - + +
81C ARG* 3.3 12.0 + - - +
82C LYS* 2.9 48.5 + - + +
94D GLU* 3.2 30.5 - - + -
98D ILE* 4.1 17.9 - - + -
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Residues in contact with ILE 79 (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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16C ILE* 4.0 10.8 - - + +
19C LEU* 4.1 22.2 - - + -
20C LEU* 3.5 36.3 - - + -
23C THR* 4.3 4.0 - - - +
62C LEU* 4.0 17.9 - - + -
75C ILE* 3.1 33.2 + - + +
76C LEU* 3.8 4.3 - - - +
78C TYR* 1.3 72.0 - - + +
80C ALA* 1.3 64.8 + - - +
82C LYS* 3.2 25.0 + - - +
83C HIS* 3.0 43.4 + - + +
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Residues in contact with ALA 80 (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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19C LEU* 4.4 4.7 - - + +
76C LEU 2.7 21.9 + - - +
77C ARG 3.5 4.3 - - - +
79C ILE* 1.3 72.5 - - - +
81C ARG* 1.3 56.9 + - - +
83C HIS 3.0 2.8 + - - -
84C ASN 2.8 9.7 + - - -
85C LEU* 2.8 36.0 + - - +
86C CYS* 3.3 20.6 - - - -
154C PHE* 3.6 28.7 - - + -
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Residues in contact with ARG 81 (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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74C ALA 4.6 0.8 + - - -
77C ARG* 2.8 19.7 + - - +
78C TYR* 3.6 26.8 - - - +
80C ALA* 1.3 75.5 - - - +
82C LYS* 1.3 60.4 + - - +
83C HIS 3.0 5.0 + - - -
84C ASN* 3.1 13.5 + - - +
86C CYS* 3.9 16.8 - - + -
94D GLU* 2.8 40.6 + - - +
97D LYS* 3.2 43.1 - - - +
98D ILE* 4.3 9.1 - - - +
101D ASP* 2.7 29.4 + - - -
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Residues in contact with LYS 82 (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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2C MET* 3.6 29.9 - - - +
64C ASP* 3.9 17.7 - - - +
78C TYR* 2.9 31.1 + - + +
79C ILE* 3.2 24.9 + - - +
81C ARG* 1.3 74.8 - - - +
83C HIS* 1.3 97.9 + - + +
84C ASN 3.7 0.2 - - - -
94D GLU* 5.7 1.3 + - - -
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Residues in contact with HIS 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C THR* 3.5 41.0 + - + -
25C SER* 2.9 26.8 + - - -
79C ILE* 3.0 27.7 + - + +
80C ALA 3.0 2.9 + - - +
81C ARG 3.0 0.6 - - - -
82C LYS* 1.3 104.8 + - + +
84C ASN* 1.3 71.6 + - - +
85C LEU* 3.2 16.8 + - + +
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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