Contacts of the strand formed by residues 85 - 94 (chain F) in PDB entry 6P59
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 THR 85 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13F ARG* 3.4 30.6 + - + +
14F VAL 4.8 4.0 - - - +
75F ASN 3.2 8.5 + - - -
76F LEU* 2.8 38.0 + - + +
77F THR 2.9 23.6 + - - -
78F THR* 4.1 0.2 - - - -
79F GLU* 3.9 16.3 + - + +
83F LEU 4.6 0.5 + - - -
84F GLY* 1.3 74.3 - - - -
86F TYR* 1.3 76.6 + - - +
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Residues in contact with TYR 86 (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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13F ARG* 3.8 2.1 - - - -
14F VAL* 3.3 29.8 + - - +
16F ARG* 3.6 51.1 - - + -
19F ILE* 3.7 21.1 - - + -
55F HIS* 3.9 19.7 - + - -
73F TYR 3.3 8.7 - - - +
74F TRP* 3.7 38.6 - + + -
75F ASN 5.4 0.2 - - - -
76F LEU* 3.6 6.3 - - - +
83F LEU* 6.0 3.9 - - + +
84F GLY 3.5 17.0 - - - -
85F THR* 1.3 90.6 - - - +
87F GLY* 1.3 58.8 + - - +
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Residues in contact with GLY 87 (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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11F VAL* 4.2 4.0 - - - -
12F TRP 3.1 13.2 - - - -
14F VAL* 4.3 7.6 - - - -
19F ILE* 4.2 2.7 - - - +
72F THR* 3.3 5.7 - - - -
73F TYR* 2.6 42.4 + - - +
76F LEU* 3.7 12.2 - - - +
86F TYR* 1.3 76.5 - - - +
88F ALA* 1.3 57.2 + - - +
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Residues in contact with ALA 88 (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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11F VAL* 3.6 4.8 - - - +
12F TRP* 2.8 38.7 + - - +
14F VAL* 4.6 8.0 - - + +
19F ILE* 5.7 0.4 - - + -
70F VAL* 5.2 2.2 - - + -
71F THR 3.3 8.1 - - - +
72F THR* 4.9 5.6 - - + -
73F TYR* 4.8 0.9 - - - -
87F GLY* 1.3 74.8 - - - +
89F ALA* 1.3 61.7 + - - +
90F LEU* 4.7 2.2 - - + -
215F LEU* 4.2 28.0 - - + -
216F CYS* 4.3 15.9 - - - -
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Residues in contact with ALA 89 (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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9F ARG* 3.5 35.3 + - - +
10F PRO 3.7 15.5 - - - +
11F VAL* 4.3 1.6 - - + -
12F TRP* 4.8 0.9 - - - -
69F LYS 3.8 1.2 - - - +
70F VAL* 3.7 4.5 - - - +
71F THR 2.8 31.5 + - - +
73F TYR* 3.8 17.7 - - + -
88F ALA* 1.3 76.6 - - - +
90F LEU* 1.3 66.1 + - - +
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Residues in contact with LEU 90 (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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9F ARG* 3.8 0.9 - - - -
10F PRO 5.0 1.6 + - - -
12F TRP* 4.0 8.8 - - + +
68F ILE* 6.0 0.9 - - + -
69F LYS 4.0 2.2 - - - -
70F VAL* 5.0 4.9 - - + +
88F ALA* 4.5 2.9 - - + -
89F ALA* 1.3 86.3 - - - +
91F ALA* 1.3 60.2 + - - +
104F ASP* 3.3 29.7 + - - +
105F ILE* 3.2 29.2 + - + +
106F ASP 3.9 1.8 - - - +
107F PRO* 3.3 41.3 - - + -
110F ALA* 4.0 10.8 - - + -
212F LEU* 4.1 22.9 - - + -
216F CYS* 3.5 24.7 - - - -
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Residues in contact with ALA 91 (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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9F ARG* 3.3 22.0 - - - +
68F ILE* 3.4 14.3 - - - +
69F LYS* 3.1 41.1 + - + +
90F LEU* 1.3 73.3 - - - +
92F TYR* 1.3 60.4 + - - +
93F ILE* 4.4 2.2 - - + -
102F PHE* 3.5 27.4 - - + -
103F THR 3.4 5.2 - - - -
105F ILE* 3.9 5.2 - - - +
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Residues in contact with TYR 92 (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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142C ALA 5.0 1.9 + - - -
143C PHE* 3.4 47.0 + + + -
146C ALA* 5.1 7.9 - - + +
62F LEU* 4.1 15.9 - - + -
66F THR* 3.2 38.1 + - + +
67F LYS 3.8 5.4 - - - -
68F ILE* 4.4 3.1 - - + -
91F ALA* 1.3 73.6 - - - +
93F ILE* 1.3 59.5 + - - +
94F ASP* 4.2 21.1 + - + -
101F TYR* 3.3 12.2 - + - +
102F PHE* 3.6 1.6 - - - -
103F THR* 2.9 46.4 + - + +
105F ILE* 4.2 9.8 - - + +
113F LEU* 3.8 22.7 - - + -
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Residues in contact with ILE 93 (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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77C GLN* 3.2 41.5 - - + +
66F THR* 3.2 7.8 - - - +
67F LYS* 2.8 70.5 + - + +
69F LYS* 4.0 16.4 - - + -
91F ALA* 4.4 4.5 - - + -
92F TYR* 1.3 76.8 - - - +
94F ASP* 1.3 61.2 + - - +
95F GLN* 3.8 25.4 + - + -
100F PRO* 4.7 6.3 - - + -
101F TYR 3.3 5.4 - - - +
102F PHE* 4.0 17.3 - - + -
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Residues in contact with ASP 94 (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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139C ALA* 3.5 23.7 - - - +
142C ALA* 5.2 4.0 - - - +
66F THR* 3.5 17.7 + - - +
92F TYR* 4.1 17.7 + - + -
93F ILE* 1.3 72.7 - - - +
95F GLN* 1.3 63.8 + - - +
96F LYS* 3.1 39.4 + - - +
97F CYS* 3.7 4.2 - - - -
100F PRO* 3.4 2.4 - - - +
101F TYR* 2.6 55.7 + - + -
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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