Contacts of the helix formed by residues 59 - 74 (chain F) in PDB entry 3PJV
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 59 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56F ASN* 3.0 19.8 + - + +
57F ILE 3.3 0.4 - - - -
58F ASP* 1.3 78.0 - - - +
60F PRO* 1.3 69.2 - - - +
61F ALA* 3.4 10.1 + - - +
62F MSE 3.1 33.6 + - + +
63F VAL* 3.0 19.9 + - - +
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Residues in contact with PRO 60 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57F ILE 5.5 1.6 - - - +
58F ASP 3.4 10.8 - - - +
59F ASP* 1.3 86.0 - - - +
61F ALA* 1.3 62.3 + - - +
63F VAL* 3.4 10.0 + - + +
64F GLU* 3.1 24.1 + - - +
90F ILE* 6.0 6.9 - - + +
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Residues in contact with ALA 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F ASP* 3.3 9.5 + - - +
60F PRO* 1.3 79.4 - - + +
62F MSE 1.3 57.4 + - - +
64F GLU* 3.4 6.9 + - - +
65F LEU* 3.0 28.4 + - - +
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Residues in contact with MSE 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F ASN* 3.5 34.3 - - + +
59F ASP* 3.1 35.4 + - + +
61F ALA* 1.3 77.0 - - - +
63F VAL* 1.3 66.4 + - - +
65F LEU* 3.2 21.5 + - + +
66F LEU* 2.9 42.8 + - + +
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Residues in contact with VAL 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F LEU* 3.9 28.3 - - + -
56F ASN* 3.4 24.0 - - - +
57F ILE* 4.1 22.9 - - + +
59F ASP 3.0 12.6 + - - +
60F PRO* 3.6 11.4 - - + +
62F MSE 1.3 77.3 - - - +
64F GLU* 1.3 56.8 + - - +
66F LEU* 3.3 1.6 + - - +
67F VAL* 3.0 31.9 + - + +
81F VAL* 4.9 5.2 - - + -
90F ILE* 4.6 14.6 - - + -
91F VAL* 4.1 21.3 - - + -
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Residues in contact with GLU 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F PRO 3.1 13.6 + - - +
61F ALA* 3.7 7.9 - - - +
62F MSE 3.2 0.2 - - - -
63F VAL* 1.3 80.3 - - - +
65F LEU* 1.3 63.0 + - - +
67F VAL* 3.8 1.3 - - - +
68F SER* 3.0 34.1 + - - +
90F ILE 5.5 0.9 - - - +
91F VAL* 4.1 31.9 - - + +
93F ARG* 6.6 0.2 - - - -
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Residues in contact with LEU 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F ALA 3.0 16.5 + - - +
62F MSE 3.2 25.3 + - + +
64F GLU* 1.3 77.8 - - - +
66F LEU* 1.3 61.9 + - + +
68F SER* 3.8 5.1 - - - -
69F SER* 2.9 35.2 + - - +
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Residues in contact with LEU 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F LEU* 4.3 5.8 - - + -
52F SER* 3.5 34.5 - - - +
53F LEU* 3.9 18.4 - - + -
56F ASN* 3.5 17.3 - - + +
62F MSE 2.9 37.7 + - + +
63F VAL 3.8 3.1 - - - +
65F LEU* 1.3 80.8 - - + +
67F VAL* 1.3 63.7 + - - +
69F SER* 3.4 8.2 + - - -
70F ILE* 3.3 27.7 + - - +
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Residues in contact with VAL 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F LEU* 4.1 20.0 - - + -
53F LEU* 4.6 2.2 - - + -
63F VAL* 3.0 24.3 + - + +
64F GLU* 3.8 3.6 - - - +
66F LEU* 1.3 76.2 - - - +
68F SER* 1.3 58.9 + - - +
70F ILE* 3.3 4.2 + - - +
71F PHE* 3.0 25.6 + - - +
79F ILE* 3.9 26.6 - - + +
81F VAL* 3.8 26.7 - - + -
91F VAL* 3.8 20.0 - - + -
93F ARG* 4.1 20.9 - - + +
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Residues in contact with SER 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F GLU* 3.0 23.6 + - - +
65F LEU* 3.8 5.4 - - - -
67F VAL* 1.3 78.6 - - - +
69F SER* 1.3 57.9 + - - +
71F PHE* 4.3 1.3 - - - -
72F ASP* 2.7 42.5 + - - -
93F ARG* 3.2 35.1 + - - +
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Residues in contact with SER 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F LEU* 2.9 28.5 + - - +
66F LEU* 3.7 11.0 - - - -
67F VAL 3.3 0.2 - - - -
68F SER* 1.3 78.3 - - - +
70F ILE* 1.3 62.9 + - - +
72F ASP* 4.2 4.3 - - - +
73F SER* 2.9 26.2 + - - -
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Residues in contact with ILE 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F ALA* 4.9 9.9 - - + +
48F ALA* 6.2 4.0 - - + -
49F LEU* 4.4 22.9 - - + +
52F SER* 5.7 1.1 - - - +
66F LEU 3.3 13.0 + - - +
67F VAL 3.8 5.4 - - - +
68F SER 3.2 0.4 - - - -
69F SER* 1.3 79.3 - - - +
71F PHE* 1.3 67.7 + - - +
73F SER* 3.3 16.5 + - - +
74F GLY* 3.3 9.9 + - - -
76F TYR* 3.5 27.4 - - + +
79F ILE* 3.9 12.6 - - + -
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Residues in contact with PHE 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F VAL 3.0 17.5 + - - +
68F SER* 3.8 3.6 - - - +
70F ILE* 1.3 79.3 - - - +
72F ASP* 1.3 65.2 + - - +
73F SER 3.4 0.3 + - - -
74F GLY 3.5 16.1 - - - +
76F TYR* 3.6 37.6 + - + +
78F SER* 4.0 6.3 - - - -
79F ILE* 3.9 24.4 - - + +
93F ARG* 3.6 64.8 - - + -
94F ASN 3.6 28.7 - - - -
95F GLY* 3.8 4.9 - - - -
143F LYS* 5.6 0.7 + - - -
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Residues in contact with ASP 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D GLN* 3.0 16.8 - - - +
68F SER* 2.7 29.9 + - - +
69F SER* 4.2 3.9 - - - +
71F PHE* 1.3 77.0 - - - +
73F SER* 1.3 58.1 + - - +
74F GLY 3.5 2.7 + - - +
93F ARG* 3.2 33.9 + - - -
143F LYS* 4.1 21.6 + - - +
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Residues in contact with SER 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D GLN* 3.8 13.0 - - - +
41D HIS* 5.3 9.0 - - - -
69F SER 2.9 19.3 + - - -
70F ILE* 3.3 11.5 + - - +
72F ASP* 1.3 78.3 - - - +
74F GLY* 1.3 56.8 + - - +
75F TYR* 5.7 2.2 - - - -
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Residues in contact with GLY 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D HIS* 6.5 0.2 - - - -
41F HIS* 6.0 0.4 - - - -
70F ILE 3.3 4.9 + - - -
71F PHE 3.5 10.1 + - - +
72F ASP 3.5 2.1 - - - +
73F SER* 1.3 80.8 + - - +
75F TYR* 1.3 72.0 + - - -
76F TYR* 3.6 24.6 + - - -
139F PHE* 4.1 8.7 - - - -
143F LYS* 6.0 0.3 + - - -
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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