Contacts of the strand formed by residues 53 - 67 (chain C) in PDB entry 2PT9
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 GLN 53 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B TRP* 3.6 8.4 - - - -
56B PHE* 4.3 13.6 - - + -
57B SER 3.3 10.3 - - - +
58B LEU* 4.0 11.9 - - + -
82B TYR* 2.9 29.8 + - + -
45C GLU 4.2 1.0 - - - +
46C PHE* 4.4 4.2 - - - -
47C SER 5.1 0.2 + - - -
50C TRP* 3.4 48.3 - - + +
51C PRO 4.6 2.3 - - - +
52C GLY* 1.3 80.6 + - - +
54C ALA* 1.3 64.4 + - - +
234C ILE* 3.8 14.0 - - - +
264C PRO* 4.3 5.3 - - - +
265C CYS* 3.6 31.5 - - - +
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Residues in contact with ALA 54 (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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43B TRP* 4.0 4.9 - - + -
55B ALA 3.9 0.3 - - - +
56B PHE* 3.5 8.6 - - - -
57B SER* 2.9 39.9 + - - +
45C GLU 3.8 12.3 - - - +
46C PHE* 3.4 36.1 - - + -
50C TRP* 5.3 0.9 - - - -
53C GLN* 1.3 78.3 - - - +
55C PHE* 1.3 63.8 + - - +
56C SER* 4.9 3.8 + - - +
702C 1PG 5.3 0.2 - - - +
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Residues in contact with PHE 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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54B GLN* 3.9 31.9 - - + -
55B ALA 3.4 17.7 - - - -
56B PHE* 4.7 13.0 - + + +
266B CYS* 5.9 2.5 - - - -
43C PHE* 4.2 0.5 - - - +
45C GLU* 2.7 48.6 + - - +
50C TRP* 6.0 0.2 - - - -
54C ALA* 1.3 75.0 - - - +
56C SER* 1.3 59.4 + - - +
57C LEU* 3.7 29.8 - - + -
81C TYR* 4.8 4.3 - - - -
91C ILE* 4.3 16.9 - - + +
261C PRO* 4.3 11.4 - - + -
262C THR* 3.7 41.3 - - + -
263C TYR 5.8 2.7 - - - +
264C PRO* 6.0 4.0 - - + -
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Residues in contact with SER 56 (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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54B GLN* 3.3 5.7 - - - +
55B ALA* 2.8 40.2 + - - -
57B SER* 4.8 3.5 + - - -
42C TRP* 3.8 17.0 - - - -
43C PHE 3.1 8.7 - - - -
44C SER* 2.6 29.1 + - - -
54C ALA* 4.9 2.8 + - - +
55C PHE* 1.3 77.4 - - - +
57C LEU* 1.3 66.5 + - - +
91C ILE* 6.3 0.4 - - - -
702C 1PG 3.4 17.3 + - - -
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Residues in contact with LEU 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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53B GLY 3.4 11.0 - - - +
54B GLN* 4.0 1.3 - - + -
42C TRP* 3.4 4.0 - - - -
43C PHE* 2.8 37.0 + - + +
55C PHE* 3.7 29.2 - - + -
56C SER* 1.3 76.6 - - - +
58C LYS* 1.3 61.1 + - - +
59C ILE* 4.2 0.7 - - - +
76C PHE* 4.6 8.5 - - + -
78C SER* 4.4 12.8 - - - -
80C THR* 4.9 0.2 - - - +
81C TYR* 3.5 32.8 - - + -
84C VAL* 4.0 27.4 - - + -
91C ILE* 4.2 21.7 - - + +
94C THR* 4.3 10.3 - - + -
262C THR* 4.5 0.2 - - + -
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Residues in contact with LYS 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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53B GLY* 2.9 22.6 + - - +
41C LYS 3.9 15.7 - - - +
42C TRP* 3.4 35.9 - - + +
57C LEU* 1.3 72.9 - - - +
59C ILE* 1.3 62.0 + - - +
78C SER* 3.1 8.6 - - - -
79C THR* 2.8 58.7 + - + +
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Residues in contact with ILE 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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41C LYS* 3.0 31.2 + - + +
42C TRP 3.7 7.4 - - - +
43C PHE* 3.6 32.8 - - + +
58C LYS* 1.3 75.9 - - - +
60C LYS* 1.3 64.8 + - - +
61C LYS* 3.6 30.5 - - - +
62C ILE* 3.9 23.1 - - + +
74C LEU* 6.5 0.7 - - + -
76C PHE* 3.9 20.4 - - + -
77C GLU 3.6 4.9 - - - +
78C SER* 4.3 1.1 - - - +
79C THR* 3.9 6.0 - - - +
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Residues in contact with LYS 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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58C LYS 3.8 2.4 + - - -
59C ILE* 1.3 74.3 - - - +
61C LYS* 1.3 66.7 + - + +
77C GLU* 2.6 46.3 + - + +
78C SER 4.1 6.8 + - - +
79C THR* 3.7 42.7 + - + +
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Residues in contact with LYS 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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59C ILE* 3.6 9.2 - - - -
60C LYS* 1.3 83.9 - - + +
62C ILE* 1.3 66.3 + - - +
63C LEU* 3.7 26.2 - - + -
76C PHE* 3.4 1.9 - - - +
77C GLU* 2.8 44.1 + - + +
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Residues in contact with ILE 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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59C ILE* 3.9 24.8 - - + +
61C LYS* 1.3 80.0 - - - +
63C LEU* 1.3 66.2 + - - +
64C TYR* 3.9 5.4 - - - +
65C GLU* 3.8 29.2 - - + +
74C LEU* 3.7 26.2 - - + -
76C PHE* 3.8 8.5 - - + -
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Residues in contact with LEU 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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61C LYS* 3.6 34.1 + - + +
62C ILE* 1.3 73.5 - - - +
64C TYR* 1.3 65.2 + - - +
75C VAL* 3.0 15.5 + - + +
76C PHE 4.3 1.8 - - - -
77C GLU* 4.1 20.2 - - + +
83C LYS* 3.8 36.6 - - + -
158C TYR* 3.3 36.1 + - + -
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Residues in contact with TYR 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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62C ILE* 3.7 2.8 - - - +
63C LEU* 1.3 80.0 - - - +
65C GLU* 1.3 69.6 + - - +
66C THR* 3.6 37.2 + - + +
73C VAL* 4.8 3.6 - - + -
74C LEU* 3.4 5.7 - - - +
75C VAL* 2.8 43.4 + - + +
150C THR* 4.9 4.3 - - + +
153C GLU* 5.7 1.2 + - - -
154C VAL* 3.5 32.5 - - + -
157C ILE* 6.4 2.9 - - + -
158C TYR* 3.7 29.4 - + + -
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Residues in contact with GLU 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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62C ILE* 3.8 27.0 - - + +
64C TYR* 1.3 85.7 - - - +
66C THR* 1.3 66.0 + - - +
73C VAL 3.4 6.6 - - - +
74C LEU* 3.6 25.8 - - + +
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Residues in contact with THR 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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64C TYR* 3.6 33.7 + - + +
65C GLU* 1.3 77.0 + - - +
67C LYS* 1.3 70.9 + - - +
68C SER* 5.1 0.2 - - - -
72C ASN* 3.6 4.7 + - - +
73C VAL* 2.9 49.3 + - + +
150C THR* 3.9 16.4 - - + -
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Residues in contact with LYS 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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66C THR* 1.3 82.2 + - - +
68C SER* 1.3 67.3 + - - +
71C GLN 4.0 3.1 - - - +
72C ASN* 3.1 30.4 + - - +
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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