Contacts of the strand formed by residues 81 - 89 (chain N) in PDB entry 5HJD
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 PHE 81 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17J ARG* 3.4 14.2 - - - +
18J KCR 3.4 44.4 - - + +
20J LEU* 6.0 0.9 - - + -
32N TRP* 3.3 30.5 - + - -
55N LEU* 4.1 0.9 - - + -
56N HIS* 3.9 34.8 - - + -
79N ALA 3.5 12.8 - - - -
80N GLY* 1.3 87.1 - - - +
82N ILE* 1.3 77.1 + - - +
83N LEU* 3.3 36.6 - - + -
103N ASP* 3.7 5.5 - - - +
104N LEU* 3.1 35.0 + - + -
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Residues in contact with ILE 82 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J ARG* 4.0 22.9 - - - +
20J LEU* 4.5 29.8 - - + +
54N HIS 4.5 1.0 - - - +
55N LEU 5.8 0.2 - - - -
56N HIS* 5.7 0.5 + - - -
81N PHE* 1.3 81.1 - - - +
83N LEU* 1.3 61.2 + - - +
84N PRO* 3.2 15.3 - - + +
101N ASP* 3.9 35.4 - - + +
102N TYR 3.8 2.2 - - - +
103N ASP* 3.9 29.4 - - + +
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Residues in contact with LEU 83 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34N VAL* 3.5 32.1 - - + -
53N PHE* 4.0 10.5 - - + -
54N HIS 3.4 33.0 - - - +
55N LEU* 3.6 13.5 - - + -
81N PHE* 3.3 29.5 + - + -
82N ILE* 1.3 71.4 - - - +
84N PRO* 1.3 70.7 - - - +
85N ILE* 3.3 18.2 + - + +
102N TYR* 2.7 39.7 + - + +
104N LEU* 3.6 12.1 - - + -
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Residues in contact with PRO 84 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J LEU* 6.2 2.2 - - + -
52N VAL 3.7 0.2 - - - +
54N HIS* 2.9 66.3 + - + +
82N ILE* 3.2 16.4 - - + +
83N LEU* 1.3 81.8 - - - +
85N ILE* 1.3 59.6 + - - +
99N ARG* 3.3 31.0 - - + +
100N PHE 3.4 8.5 - - - +
101N ASP* 4.0 4.9 - - - +
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Residues in contact with ILE 85 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13N LEU* 3.8 27.6 - - + -
34N VAL* 4.4 6.3 - - + -
36N VAL* 3.8 16.4 - - + -
51N VAL* 3.7 27.1 - - + -
52N VAL 3.4 5.6 - - - +
53N PHE* 4.1 18.4 - - + -
83N LEU* 3.5 22.4 - - + +
84N PRO* 1.3 74.6 - - - +
86N GLU* 1.3 65.1 + - - +
87N VAL* 4.2 4.2 + - + -
98N VAL 3.7 0.7 - - - +
99N ARG* 3.3 4.0 - - - +
100N PHE* 2.8 39.3 + - + +
102N TYR* 3.8 23.6 - - + -
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Residues in contact with GLU 86 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51N VAL* 3.3 3.2 - - - -
52N VAL* 2.7 43.1 + - + +
54N HIS* 3.5 28.6 + - + +
85N ILE* 1.3 78.1 - - - +
87N VAL* 1.3 62.4 + - - +
88N TYR* 3.2 34.3 + - + -
97N LYS* 3.5 24.2 + - + +
98N VAL 3.3 4.9 - - - +
99N ARG* 4.0 24.9 + - + +
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Residues in contact with VAL 87 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N LEU* 4.5 14.4 - - + -
13N LEU* 6.0 0.2 - - + -
36N VAL* 4.3 16.4 - - + -
48N VAL* 3.8 28.7 - - + -
50N LYS 3.9 2.5 - - - -
51N VAL* 3.9 23.6 - - + -
85N ILE* 4.7 6.3 - - + -
86N GLU* 1.3 72.8 - - - +
88N TYR* 1.3 65.4 + - - +
89N PHE* 3.8 15.3 - - + -
97N LYS* 3.4 3.3 - - - -
98N VAL* 2.9 47.6 + - + +
100N PHE* 4.7 8.7 - - + -
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Residues in contact with TYR 88 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48N VAL* 3.3 13.2 - - - +
49N GLU* 3.2 23.9 + - + -
50N LYS* 2.8 54.0 + - + +
52N VAL* 3.7 23.1 - - + +
86N GLU* 3.2 29.4 + - + -
87N VAL* 1.3 76.0 - - - +
89N PHE* 1.3 61.6 + - - +
96N ARG* 3.7 15.9 - - + -
97N LYS* 2.8 38.7 + - + -
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Residues in contact with PHE 89 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47N PHE* 3.4 24.5 - + - +
49N GLU* 3.9 10.9 - - - +
87N VAL* 3.8 11.4 - - + -
88N TYR* 1.3 77.1 - - - +
90N LYS* 1.3 59.0 + - - +
91N ASN* 2.8 33.0 + - - +
95N PRO* 3.9 7.6 - - + -
96N ARG* 3.2 27.7 + - - +
97N LYS* 3.6 24.7 - - - -
98N VAL* 3.6 25.6 - - + -
122N LEU* 3.7 18.4 - - + -
124N PHE* 3.6 36.8 - + - -
131N PHE* 3.9 8.7 - - + -
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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