Contacts of the helix formed by residues 56 - 68 (chain C) in PDB entry 2RD9
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 ASN 56 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-10B HIS* 2.9 32.0 + - - +
-9B HIS* 3.4 22.2 + - - -
-6B GLU* 5.2 0.2 + - - -
52C ALA* 3.2 16.1 + - + +
54C LYS 3.8 0.8 - - - -
55C THR* 1.3 77.8 - - + +
57C TRP* 1.3 96.3 + - + +
58C ILE 3.6 1.1 - - - -
59C PRO* 3.5 2.5 - - - +
60C ARG* 3.0 36.6 + - - +
76C PHE* 3.5 21.5 - - + -
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Residues in contact with TRP 57 (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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-9B HIS* 5.1 2.2 - + - -
52C ALA* 3.5 35.2 + - + +
53C GLU* 4.1 4.0 + - - -
56C ASN* 1.3 97.0 - - - +
58C ILE* 1.3 61.3 + - - +
60C ARG* 6.3 0.4 - - - -
61C LEU* 3.0 28.1 + - - +
104C ASN* 6.3 0.2 - - - +
135C LEU* 3.6 42.6 - - + +
138C ALA* 3.6 24.5 - - + -
139C TRP* 3.4 67.9 - + + -
142C HIS* 3.4 35.7 + + + -
165D TRP* 5.3 9.6 - + - -
169D LEU* 5.4 2.7 - - + -
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Residues in contact with ILE 58 (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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52C ALA 5.2 0.2 + - - -
53C GLU* 5.3 1.9 + - - +
57C TRP* 1.3 74.0 - - - +
59C PRO* 1.3 77.1 - - + +
61C LEU* 3.2 21.4 + - + +
62C ARG* 3.0 51.5 + - - +
104C ASN* 3.4 56.9 - - + +
107C THR* 3.8 12.8 - - + -
108C LEU* 4.3 7.9 - - + +
111C LEU* 4.5 2.9 - - + -
139C TRP* 3.9 21.1 - - + -
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Residues in contact with PRO 59 (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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53C GLU 4.8 4.0 - - - +
54C LYS 3.4 26.5 - - - +
55C THR* 3.8 16.6 - - - +
56C ASN 3.5 13.0 - - - +
57C TRP 3.9 0.4 - - - +
58C ILE* 1.3 94.0 - - + +
60C ARG* 1.3 60.2 + - + +
62C ARG* 3.6 11.8 + - + +
63C PHE* 3.2 22.0 + - - +
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Residues in contact with ARG 60 (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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-6B GLU* 2.9 27.1 + - - -
-5B ASN* 5.3 1.0 + - - -
55C THR 5.4 0.7 - - - +
56C ASN* 3.0 33.5 + - - +
57C TRP* 3.9 2.4 - - - +
59C PRO* 1.3 74.5 - - + +
61C LEU* 1.3 59.7 + - - +
63C PHE* 3.3 7.0 + - - +
64C ILE* 2.9 34.2 + - + +
73C PHE* 3.5 45.6 - - + -
74C PRO* 3.3 24.5 + - + +
75C ALA* 4.2 6.5 - - - +
76C PHE* 3.3 40.0 - - + -
124C HIS* 4.4 3.6 + - - -
125C PRO* 4.8 1.6 - - - +
135C LEU* 4.2 18.4 - - + -
165D TRP* 3.9 12.3 - - - +
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Residues in contact with LEU 61 (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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57C TRP 3.0 19.5 + - - +
58C ILE* 3.2 16.8 + - + +
60C ARG* 1.3 74.4 - - - +
62C ARG* 1.3 63.7 + - - +
64C ILE* 3.7 2.5 - - + +
65C LEU* 3.1 46.6 + - + +
108C LEU* 3.6 31.6 - - + -
111C LEU* 3.9 17.7 - - + -
112C VAL* 3.9 7.2 - - + -
132C VAL* 3.8 35.4 - - + -
135C LEU* 3.6 16.6 - - + +
136C LEU* 4.4 7.0 - - + -
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Residues in contact with ARG 62 (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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58C ILE* 3.0 30.3 + - - +
59C PRO* 3.7 12.3 - - - +
61C LEU* 1.3 73.7 - - - +
63C PHE* 1.3 61.6 + - - +
65C LEU* 3.4 4.8 + - - +
66C GLN* 2.8 35.1 + - + +
107C THR* 3.7 28.2 + - - +
111C LEU* 4.0 24.9 - - + +
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Residues in contact with PHE 63 (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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59C PRO 3.2 12.2 + - - +
60C ARG* 3.5 8.3 - - - +
62C ARG* 1.3 77.4 - - - +
64C ILE* 1.3 56.3 + - - +
66C GLN* 4.7 1.8 - - - -
67C GLU* 2.7 62.9 + - + +
68C GLY 5.5 0.4 - - - -
71C LYS* 3.6 35.4 - - + -
72C PRO 3.4 26.9 - - - -
73C PHE* 3.5 22.7 - + + -
74C PRO* 3.9 23.3 - - + -
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Residues in contact with ILE 64 (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 ARG 2.9 20.3 + - - +
61C LEU* 3.7 5.8 - - - +
63C PHE* 1.3 76.8 - - - +
65C LEU* 1.3 59.2 + - + +
68C GLY* 2.9 30.5 + - - +
73C PHE* 3.7 33.0 - - + -
120C ARG* 4.5 3.5 + - + +
121C THR 3.8 7.4 - - - +
122C GLY* 3.7 27.1 - - - +
130C VAL* 4.4 10.8 - - + -
131C LYS 5.1 0.7 - - - +
132C VAL* 3.9 29.2 - - + +
135C LEU* 3.9 30.5 - - + -
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Residues in contact with LEU 65 (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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61C LEU* 3.1 34.4 + - + +
62C ARG* 3.9 3.6 - - - +
64C ILE* 1.3 77.0 - - - +
66C GLN* 1.3 59.6 + - - +
68C GLY 4.5 1.6 + - - -
111C LEU* 3.7 50.3 - - + +
112C VAL* 4.6 2.2 - - + -
117C ASP* 4.7 4.0 - - + +
120C ARG* 2.9 57.3 + - + +
132C VAL* 4.1 19.5 - - + -
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Residues in contact with GLN 66 (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 ARG 2.8 22.1 + - - +
63C PHE* 4.1 1.8 - - - +
65C LEU* 1.3 74.8 - - - +
67C GLU* 1.3 77.3 + - + +
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Residues in contact with GLU 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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63C PHE* 2.7 60.9 + - + +
66C GLN* 1.3 95.6 - - + +
68C GLY* 1.3 62.9 + - - +
70C HIS* 2.8 31.1 + - - +
71C LYS* 3.4 37.9 + - + +
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Residues in contact with GLY 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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63C PHE* 5.5 0.5 - - - -
64C ILE* 2.9 20.9 + - - +
65C LEU 4.5 1.6 + - - -
66C GLN 3.8 1.0 - - - -
67C GLU* 1.3 82.6 - - - +
69C GLU* 1.3 60.2 + - - -
70C HIS* 3.4 6.2 + - - -
71C LYS 3.6 12.5 - - - +
121C THR 3.4 14.8 - - - -
122C GLY* 3.6 9.0 - - - -
123C ALA 4.1 0.2 + - - -
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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
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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