Contacts of the helix formed by residues 87 - 95 (chain o) in PDB entry 3J7Y
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 87 (chain o).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118g TRP* 3.9 27.8 - + + -
142g GLU* 3.7 15.5 - - + -
143g VAL* 3.7 11.5 - - - +
85o HIS* 3.5 33.7 - - + -
86o ARG* 1.3 79.1 - - - +
88o ILE* 1.3 66.4 + - - +
89o ALA* 3.2 11.6 + - + +
90o ASP* 3.8 37.5 + - - +
91o GLN* 4.1 6.6 + - - +
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Residues in contact with ILE 88 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F ALA* 5.9 2.7 - - + -
91F PRO* 5.2 6.1 - - + -
12M ALA* 3.7 33.0 - - + +
15M LEU* 5.2 2.5 - - + -
142g GLU* 3.2 33.5 - - - +
143g VAL* 3.7 32.1 - - + +
87o PHE* 1.3 74.3 - - - +
89o ALA* 1.3 59.1 + - - +
91o GLN* 3.2 11.3 + - - +
92o LEU* 2.9 49.6 + - + +
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Residues in contact with ALA 89 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M LEU* 5.5 7.4 - - + -
87o PHE* 3.2 11.0 - - + +
88o ILE* 1.3 79.0 - - - +
90o ASP* 1.3 63.1 + - - +
92o LEU* 3.2 9.2 + - - +
93o ASP* 2.9 29.2 + - - +
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Residues in contact with ASP 90 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28M LYS* 5.5 2.5 + - - +
87o PHE* 3.8 31.2 + - - +
88o ILE 3.3 0.6 - - - -
89o ALA* 1.3 78.3 - - - +
91o GLN* 1.3 58.2 + - - +
93o ASP* 3.2 9.6 + - - +
94o HIS* 2.9 27.0 + - - +
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Residues in contact with GLN 91 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F PRO* 5.0 1.4 - - - +
92F ARG 4.5 4.5 + - - -
93F LEU* 3.8 40.1 + - + +
94F ASP* 2.6 38.8 + - - +
28M LYS* 5.2 7.9 - - - +
143g VAL* 3.7 32.0 - - + +
87o PHE 4.1 5.3 + - - +
88o ILE* 3.2 20.1 + - - +
90o ASP* 1.3 77.0 - - - +
92o LEU* 1.3 67.0 + - - +
94o HIS* 3.2 22.1 + - - +
95o LEU 3.7 2.9 + - - -
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Residues in contact with LEU 92 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F PRO* 4.8 5.4 - - + -
93F LEU* 4.0 15.0 - - + -
12M ALA 3.8 10.1 - - - +
15M LEU* 3.4 44.9 - - + -
16M LEU* 3.6 28.9 - - + +
19M LEU* 3.8 22.9 - - + +
88o ILE* 2.9 33.6 + - + +
89o ALA* 3.2 8.9 + - - +
91o GLN* 1.3 80.2 - - - +
93o ASP* 1.3 63.9 + - - +
95o LEU* 3.0 24.7 + - + +
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Residues in contact with ASP 93 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M LEU* 5.4 1.7 - - - +
41b ARG* 5.5 0.5 + - - -
89o ALA 2.9 13.0 + - - +
90o ASP* 3.2 13.0 + - - +
92o LEU* 1.3 76.2 - - - +
94o HIS* 1.3 53.8 + - - +
96o ASN* 2.6 62.7 + - - +
97o VAL 4.5 0.2 + - - -
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Residues in contact with HIS 94 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2287A U 3.2 34.9 + - - -
2288A A 4.5 1.8 - - - -
26M ASN 3.2 26.6 + - - -
28M LYS* 3.2 49.8 - - + +
90o ASP 2.9 13.7 + - - +
91o GLN 3.2 12.9 + - - +
93o ASP* 1.3 75.2 - - - +
95o LEU* 1.3 60.4 + - + +
96o ASN 3.2 1.0 + - - -
97o VAL* 3.5 26.4 + - + +
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Residues in contact with LEU 95 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F LEU* 3.9 25.4 - - + -
16M LEU* 3.6 32.5 - - + -
19M LEU* 4.4 6.1 - - + -
20M PRO* 3.4 30.3 - - + +
22M VAL* 3.7 25.1 - - + -
26M ASN* 2.7 53.9 + - + +
27M LEU* 5.8 1.6 - - + -
91o GLN 3.7 0.4 + - - -
92o LEU* 3.0 18.5 + - + +
93o ASP 2.9 2.6 + - - -
94o HIS* 1.3 75.7 - - + +
96o ASN* 1.3 55.8 + - - +
97o VAL 3.1 3.5 + - - -
98o THR 3.4 0.2 + - - -
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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