Contacts of the helix formed by residues 89 - 101 (chain C) in PDB entry 3DC6
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 89 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87C GLU 3.6 1.7 + - - -
88C PRO* 1.3 75.8 - - - +
90C ALA* 1.3 65.3 + - - +
91C GLU* 3.3 22.4 + - - +
92C LEU* 3.1 15.8 + - - +
93C LEU* 3.0 22.6 + - - +
189C SER* 2.8 30.7 + - - -
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Residues in contact with ALA 90 (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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88C PRO 3.9 0.4 + - - -
89C SER* 1.3 72.4 - - - +
91C GLU* 1.3 63.6 + - - +
93C LEU* 3.5 5.8 + - - +
94C THR* 3.1 27.4 + - - -
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Residues in contact with GLU 91 (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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89C SER* 3.3 19.9 + - - +
90C ALA* 1.3 79.5 - - - +
92C LEU* 1.3 65.0 + - - +
94C THR* 3.5 7.6 + - - -
95C ALA* 3.3 16.3 + - - +
189C SER 3.5 13.2 - - - +
192C PHE* 3.2 33.8 - - + -
193C ALA* 3.7 16.8 + - - +
196C GLN* 3.4 16.6 - - - +
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Residues in contact with LEU 92 (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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88C PRO* 3.9 15.3 - - + -
89C SER* 3.1 16.9 + - - +
91C GLU* 1.3 81.3 - - - +
93C LEU* 1.3 51.7 + - - +
95C ALA* 3.2 4.7 + - - +
96C ILE* 2.8 55.9 + - + +
125C LEU* 5.1 1.8 - - + -
134C LEU* 4.3 8.3 - - + -
154C LEU* 4.5 7.9 - - + -
185C TRP* 4.2 7.0 - - + -
188C VAL* 4.0 23.6 - - + -
189C SER* 3.6 22.7 - - - +
192C PHE* 3.6 40.4 - - + -
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Residues in contact with LEU 93 (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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88C PRO* 4.6 17.2 - - + +
89C SER 3.0 16.5 + - - +
90C ALA* 4.0 5.8 - - - +
92C LEU* 1.3 73.1 - - - +
94C THR* 1.3 57.5 + - - +
96C ILE* 3.5 24.0 - - + +
97C LYS* 2.8 71.8 + - + +
103C LEU* 4.5 17.0 - - + +
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Residues in contact with THR 94 (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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90C ALA 3.1 14.4 + - - -
91C GLU* 3.5 11.2 - - - -
93C LEU* 1.3 76.2 - - - +
95C ALA* 1.3 56.8 + - - +
97C LYS* 3.5 9.3 + - - +
98C SER* 2.9 28.7 + - - -
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Residues in contact with ALA 95 (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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91C GLU 3.3 4.1 + - - +
92C LEU 3.2 8.4 + - - +
94C THR* 1.3 77.4 - - - +
96C ILE* 1.3 61.2 + - - +
98C SER* 3.2 6.9 + - - -
99C ASP* 2.9 39.0 + - - +
127C TYR* 6.3 0.7 - - + -
134C LEU* 3.9 13.7 - - + -
192C PHE* 3.7 28.9 - - + -
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Residues in contact with ILE 96 (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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88C PRO* 4.7 2.5 - - + -
92C LEU* 2.8 47.2 + - + +
93C LEU* 3.1 15.9 + - + +
95C ALA* 1.3 71.1 - - - +
97C LYS* 1.3 58.6 + - - +
100C PHE* 2.8 34.2 + - - +
101C GLY 3.5 0.3 + - - -
102C SER 3.7 25.4 - - - +
103C LEU* 3.9 23.3 - - + +
106C LEU* 3.7 31.0 - - + -
125C LEU* 5.1 1.6 - - + -
134C LEU* 3.7 14.8 - - + -
185C TRP* 4.4 7.2 - - + -
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Residues in contact with LYS 97 (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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93C LEU* 2.8 55.4 + - + +
94C THR* 3.7 8.1 - - - +
96C ILE* 1.3 71.6 - - - +
98C SER* 1.3 59.0 + - - +
101C GLY* 2.8 44.6 + - - +
102C SER* 4.5 7.9 - - - +
103C LEU 6.1 0.2 - - - +
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Residues in contact with SER 98 (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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94C THR* 2.9 19.9 + - - -
95C ALA* 3.2 10.5 + - - -
97C LYS* 1.3 79.3 - - - +
99C ASP* 1.3 67.5 + - - +
101C GLY 4.8 0.5 + - - -
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Residues in contact with ASP 99 (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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95C ALA* 2.9 21.8 + - - +
98C SER* 1.3 88.8 + - - +
100C PHE* 1.3 79.5 + - + +
132C LYS 4.9 1.7 - - - +
133C ILE* 3.4 25.7 - - + +
134C LEU* 2.8 44.0 + - + +
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Residues in contact with PHE 100 (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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96C ILE* 2.8 17.7 + - - +
99C ASP* 1.3 84.5 - - + +
101C GLY* 1.3 58.8 + - - +
102C SER 3.2 14.1 - - - +
105C ASN* 3.0 27.3 + - + +
106C LEU* 3.9 39.0 - - + +
109C GLN* 3.4 32.6 + - - +
125C LEU* 4.1 4.9 - - + -
134C LEU* 3.7 39.9 - - + -
135C LYS* 4.2 1.1 - - - -
136C VAL* 3.6 37.2 - - + -
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Residues in contact with GLY 101 (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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96C ILE 3.5 0.2 + - - -
97C LYS* 2.8 34.7 + - - +
98C SER 4.6 0.4 + - - -
99C ASP 3.9 0.4 - - - -
100C PHE* 1.3 76.2 - - - +
102C SER* 1.3 62.4 + - - +
105C ASN* 4.3 4.9 - - - -
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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