Contacts of the helix formed by residues 60 - 72 (chain C) in PDB entry 5DDP
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 GLU 60 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C HIS* 4.4 2.9 - - - -
37C GLY* 6.3 0.2 - - - -
38C GLN* 5.9 2.5 - - + +
58C PHE* 3.6 7.0 - - - +
59C LYS* 1.3 113.8 + - + +
61C VAL* 1.3 61.1 + - - +
62C SER* 3.9 14.8 - - - +
63C SER* 3.0 40.5 + - - +
64C ALA 3.2 4.2 + - - -
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Residues in contact with VAL 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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7C PRO* 4.0 27.4 - - + -
8C ASN* 4.0 9.6 - - - +
9C HIS* 3.2 47.2 + - + +
60C GLU* 1.3 72.7 + - - +
62C SER* 1.3 57.5 + - - +
64C ALA* 3.2 8.9 + - - +
65C THR* 2.9 30.2 + - - +
85C TYR* 5.4 0.2 - - + -
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Residues in contact with SER 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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60C GLU* 3.9 12.7 + - - +
61C VAL* 1.3 75.6 - - - +
63C SER* 1.3 67.3 + - - +
65C THR* 3.8 6.9 - - - -
66C ASN* 3.0 37.3 + - - +
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Residues in contact with SER 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C PHE* 2.8 29.3 + - - +
37C GLY* 3.3 10.9 - - - -
38C GLN 4.4 0.2 + - - -
58C PHE* 3.5 24.9 - - - -
60C GLU* 3.0 27.3 + - - +
62C SER* 1.3 80.9 + - - +
64C ALA* 1.3 62.7 + - - +
66C ASN* 3.4 3.8 + - - +
67C ALA* 2.9 24.6 + - - +
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Residues in contact with ALA 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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8C ASN 3.4 25.6 - - - +
9C HIS 3.6 17.5 - - - +
11C ILE* 3.7 18.6 - - + +
58C PHE* 3.7 13.8 - - + -
60C GLU 3.2 2.7 + - - +
61C VAL 3.2 8.8 + - - +
63C SER* 1.3 79.6 - - - +
65C THR* 1.3 56.4 + - - +
67C ALA* 3.3 3.1 + - - +
68C LEU* 3.0 30.0 + - - +
85C TYR* 4.4 3.6 - - + -
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Residues in contact with THR 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C PRO* 4.8 3.6 - - - +
61C VAL* 2.9 24.8 + - - +
62C SER* 3.8 8.0 - - - -
63C SER 3.2 0.2 - - - -
64C ALA* 1.3 73.0 - - - +
66C ASN* 1.3 72.7 + - - +
68C LEU* 3.1 4.0 + - - +
69C ARG* 3.1 55.7 + - - +
85C TYR* 2.8 30.6 + - - +
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Residues in contact with ASN 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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36C PHE* 3.7 17.6 + - + +
62C SER* 3.0 22.5 + - - +
63C SER* 3.9 5.2 - - - +
65C THR* 1.3 82.4 - - - +
67C ALA* 1.3 61.2 + - - +
69C ARG* 4.3 6.8 + - - +
70C SER* 3.1 28.8 + - - -
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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
----------------------------------------------------------
11C ILE* 4.7 3.6 - - + -
33C PHE* 3.8 26.7 - - + -
36C PHE* 3.9 18.5 - - + -
58C PHE* 3.9 15.5 - - + -
63C SER 2.9 18.5 + - - +
64C ALA 3.5 5.6 - - - +
65C THR 3.2 0.2 - - - -
66C ASN* 1.3 75.3 - - - +
68C LEU* 1.3 58.5 + - - +
71C MET* 2.9 36.1 + - - +
83C ILE* 4.0 0.6 - - - +
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Residues in contact with LEU 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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4C GLU 5.4 0.2 - - - +
5C THR* 6.5 0.4 - - + -
11C ILE* 4.7 1.5 - - + +
64C ALA 3.0 15.9 + - - +
65C THR* 3.1 6.9 + - - +
67C ALA* 1.3 77.8 - - - +
69C ARG* 1.3 75.8 + - + +
72C GLN* 3.3 38.8 + - + +
83C ILE* 3.7 30.3 - - + +
84C GLN* 3.5 37.5 - - - +
85C TYR* 3.7 28.3 - - + +
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Residues in contact with ARG 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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65C THR* 3.1 38.9 + - - +
66C ASN* 4.5 5.9 + - - +
68C LEU* 1.3 88.4 - - + +
70C SER* 1.3 60.3 + - - +
72C GLN* 4.2 8.9 + - - +
85C TYR* 5.2 2.4 + - - -
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Residues in contact with SER 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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35C ARG* 4.1 9.9 + - - -
36C PHE* 3.5 27.0 - - - -
66C ASN 3.1 20.3 + - - -
69C ARG* 1.3 80.2 - - - +
71C MET* 1.3 62.9 + - - +
72C GLN 3.4 2.5 + - - +
74C PHE* 5.5 1.6 - - - +
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Residues in contact with MET 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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32C ILE* 3.5 35.0 - - + -
33C PHE* 3.4 27.4 - - + -
35C ARG* 3.6 25.4 - - - -
36C PHE* 3.7 13.9 - - + -
67C ALA 2.9 15.5 + - - +
70C SER* 1.3 79.8 - - - +
72C GLN* 1.3 65.5 + - - +
73C GLY 3.3 0.9 + - - -
74C PHE* 3.1 59.8 + - + +
81C MET* 4.0 11.5 - - + +
83C ILE* 3.5 12.7 - - + +
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Residues in contact with GLN 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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68C LEU* 3.3 27.4 + - - +
69C ARG* 4.4 8.3 - - - +
70C SER 3.4 4.3 - - - +
71C MET* 1.3 75.8 - - - +
73C GLY* 1.3 61.2 + - - +
74C PHE* 3.1 5.4 + - - -
81C MET 3.5 1.7 - - - +
82C ARG* 3.4 10.7 + - - +
83C ILE* 2.8 55.8 + - - +
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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