Contacts of the helix formed by residues 54 - 69 (chain C) in PDB entry 1USK
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 ASP 54 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51C ASP 3.1 11.3 + - - +
52C ALA* 3.9 7.0 - - + +
53C CYS* 1.3 77.9 - - - +
55C PRO* 1.3 76.9 - - - +
56C LYS* 3.2 11.4 + - - +
57C GLN* 3.2 31.4 + - + +
58C ALA* 2.9 23.0 + - - +
81C SER* 4.1 3.0 - - - -
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Residues in contact with PRO 55 (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 CYS 4.4 1.1 - - - +
54C ASP* 1.3 93.7 - - - +
56C LYS* 1.3 60.2 + - - +
58C ALA* 3.5 7.0 + - + +
59C VAL* 3.3 26.7 + - - +
80C SER* 3.7 42.4 - - - +
81C SER* 4.4 0.4 - - - -
84C PRO* 4.3 8.0 - - + +
148C GLN* 5.8 2.7 - - - +
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Residues in contact with LYS 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ASP* 3.2 11.6 + - - +
55C PRO* 1.3 76.5 - - - +
57C GLN* 1.3 64.6 + - - +
59C VAL* 3.6 8.0 + - + +
60C ALA* 3.3 18.9 + - - +
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Residues in contact with GLN 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C SER* 5.0 0.8 + - - -
50C ASP* 3.7 24.8 + - - +
51C ASP* 3.4 18.4 - - - +
52C ALA* 3.4 23.5 - - - +
54C ASP* 3.2 15.7 + - - +
56C LYS* 1.3 77.3 - - - +
58C ALA* 1.3 59.8 + - - +
60C ALA* 3.3 10.0 + - + +
61C VAL* 3.0 33.5 + - + +
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Residues in contact with ALA 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ASP* 3.8 17.0 - - - +
54C ASP 2.9 17.6 + - - +
55C PRO 3.6 6.3 - - - +
56C LYS 3.2 0.4 - - - -
57C GLN* 1.3 75.3 - - - +
59C VAL* 1.3 59.9 + - - +
61C VAL* 3.5 2.9 + - - +
62C ALA* 3.1 27.5 + - - +
76C HIS* 3.8 8.2 - - - +
81C SER* 3.3 39.5 - - - +
84C PRO* 5.0 1.1 - - + -
85C ALA* 3.9 2.5 - - - +
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Residues in contact with VAL 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C PRO 3.3 12.7 + - - +
56C LYS* 3.8 10.1 - - + +
57C GLN 3.3 0.2 - - - -
58C ALA* 1.3 75.8 - - - +
60C ALA* 1.3 65.6 + - - +
62C ALA* 3.2 3.1 + - - +
63C ASN* 3.1 36.6 + - - +
84C PRO* 3.9 30.5 - - + +
85C ALA* 5.1 0.4 - - - +
88C ILE* 3.8 16.6 - - + -
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Residues in contact with ALA 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LYS 3.3 11.7 + - - +
57C GLN* 3.4 16.2 - - + +
59C VAL* 1.3 81.1 - - - +
61C VAL* 1.3 61.8 + - + +
63C ASN* 3.6 6.9 + - - +
64C LYS* 3.2 21.1 + - - +
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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
----------------------------------------------------------
8C VAL* 3.8 15.3 - - + -
49C TYR* 3.5 35.7 - - + -
50C ASP 3.5 26.0 - - - +
51C ASP* 4.0 7.0 - - + -
57C GLN* 3.0 21.7 + - + +
58C ALA 3.7 5.6 - - - +
59C VAL 3.3 0.2 - - - -
60C ALA* 1.3 74.1 - - + +
62C ALA* 1.3 61.0 + - - +
64C LYS* 3.1 8.7 + - - +
65C ILE* 2.9 34.7 + - + +
76C HIS* 4.2 4.7 - - + -
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Residues in contact with ALA 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ALA 3.1 17.3 + - - +
59C VAL 3.2 5.8 + - - +
61C VAL* 1.3 77.3 - - - +
63C ASN* 1.3 61.0 + - - +
65C ILE* 3.3 4.1 + - - +
66C VAL* 3.1 26.7 + - - +
85C ALA* 3.9 12.3 - - + -
88C ILE* 3.9 20.0 - - + -
89C TYR* 3.5 33.0 + - + +
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Residues in contact with ASN 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C VAL* 3.1 34.8 + - - +
60C ALA* 4.0 6.1 - - - +
61C VAL 3.4 0.2 - - - -
62C ALA* 1.3 75.3 - - - +
64C LYS* 1.3 61.9 + - - +
66C VAL* 3.4 8.8 + - - +
67C ASN* 3.1 23.4 + - - +
88C ILE* 3.6 25.4 - - - +
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Residues in contact with LYS 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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49C TYR* 4.0 19.1 - - + -
60C ALA 3.2 13.5 + - - +
61C VAL* 3.1 13.3 + - - +
63C ASN* 1.3 75.9 - - - +
65C ILE* 1.3 51.8 + - - +
67C ASN* 3.2 7.6 + - + +
68C ASP* 2.8 67.4 + - - +
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Residues in contact with ILE 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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6C ALA* 3.6 20.0 - - + -
8C VAL* 3.7 16.6 - - + -
49C TYR* 3.6 23.6 - - + +
61C VAL* 2.9 20.2 + - + +
62C ALA 3.3 7.2 + - - +
64C LYS* 1.3 74.3 - - - +
66C VAL* 1.3 63.9 + - - +
68C ASP* 3.3 14.3 + - - +
69C GLY 3.3 8.0 + - - -
70C ILE* 3.4 33.7 + - + +
73C VAL* 4.0 19.7 - - + -
89C TYR* 3.6 26.9 - - + +
94C ILE* 4.8 1.8 - - + -
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Residues in contact with VAL 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ALA 3.1 16.3 + - - +
63C ASN* 3.6 11.2 - - - +
64C LYS 3.3 0.2 - - - -
65C ILE* 1.3 74.6 - - - +
67C ASN* 1.3 64.0 + - - +
69C GLY* 3.3 13.0 + - - -
70C ILE 4.9 0.4 - - - -
71C LYS* 4.8 9.2 + - - +
88C ILE* 3.8 22.9 - - + -
89C TYR* 4.8 0.9 - - + -
92C GLU* 3.8 31.0 - - + +
94C ILE* 3.5 27.4 - - + -
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Residues in contact with ASN 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ASN 3.1 11.1 + - - +
64C LYS* 3.6 9.6 - - - +
66C VAL* 1.3 82.5 - - - +
68C ASP* 1.3 65.0 + - - +
69C GLY* 3.1 2.2 + - - -
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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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4C LYS* 4.7 12.7 + - - +
49C TYR* 2.5 29.2 + - - +
64C LYS* 2.8 50.7 + - - +
65C ILE* 3.8 6.1 - - - +
66C VAL 3.3 0.6 - - - -
67C ASN* 1.3 76.4 - - - +
69C GLY* 1.3 59.6 + - - +
70C ILE* 3.3 12.2 + - + +
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Residues in contact with GLY 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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4C LYS* 6.0 1.9 - - - +
65C ILE 3.3 0.2 + - - -
66C VAL 3.3 10.6 + - - -
67C ASN 3.1 6.1 - - - -
68C ASP* 1.3 78.9 - - - +
70C ILE* 1.3 63.7 + - - +
71C LYS* 3.7 20.6 + - - +
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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