Contacts of the strand formed by residues 84 - 91 (chain F) in PDB entry 4YHP
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 84 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39E GLN* 5.7 0.2 + - - -
35F TYR 3.7 0.5 - - - +
36F GLN* 3.7 1.7 - - - -
37F GLN* 2.7 48.5 + - + +
83F ALA* 1.3 74.1 - - - +
85F TYR* 1.3 59.4 + - - +
86F TYR* 3.9 30.3 + - + -
102F GLY* 5.6 0.7 - - - -
103F THR 3.3 7.2 - - - +
104F LYS* 3.3 43.2 + - - +
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Residues in contact with TYR 85 (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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6F GLN* 2.7 25.8 + - - -
20F ILE* 3.8 21.3 - - + -
34F TRP* 4.9 1.8 - - + -
35F TYR 3.2 16.2 - - - +
36F GLN* 3.0 39.2 + - + -
46F VAL* 4.9 1.8 - - + -
61F PHE* 3.9 12.0 - + - -
72F LEU* 3.6 20.2 - - + -
74F ILE* 3.5 21.8 - - + +
81F ASP* 2.6 32.8 + - - +
83F ALA* 3.8 10.5 - - + -
84F ASP* 1.3 73.2 - - - +
86F TYR* 1.3 58.3 + - - +
102F GLY* 3.3 0.9 - - - -
103F THR 2.7 24.0 + - - +
105F VAL* 3.5 31.2 - - + -
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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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39E GLN* 3.3 17.7 + - - -
43E LYS 3.7 3.5 + - - -
44E GLY* 3.4 23.2 - - - -
45E LEU* 3.7 33.7 - - + -
6F GLN* 3.5 0.9 - - - -
34F TRP* 3.3 7.0 - - - -
35F TYR* 2.8 44.9 + - + -
37F GLN* 3.3 26.8 + - + -
84F ASP* 3.9 29.5 + - + -
85F TYR* 1.3 75.5 - - - +
87F CYS* 1.3 64.2 + - - +
99F PHE* 4.5 5.4 - - + -
100F GLY 3.6 13.9 - - - -
101F THR 3.7 10.4 + - - -
102F GLY* 3.5 25.8 - - - -
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Residues in contact with CYS 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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4F LEU* 4.0 3.1 - - - -
6F GLN* 3.0 26.1 + - - -
22F CYS* 2.0 48.7 - - + -
32F VAL* 4.0 3.4 - - + -
33F HIS 3.3 6.7 - - - +
34F TRP* 3.5 22.9 - - + -
86F TYR* 1.3 73.5 - - - +
88F GLN* 1.3 61.6 + - - +
99F PHE* 3.3 5.0 - - - +
100F GLY* 2.7 37.0 + - - -
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Residues in contact with GLN 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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106E TRP 3.0 22.4 + - - -
107E HIS* 3.4 11.8 - - - +
108E PHE* 4.6 0.7 - - - -
4F LEU* 4.5 0.4 - - - -
32F VAL* 3.5 1.1 - - - +
33F HIS* 2.8 47.4 + - - +
35F TYR* 2.6 43.4 + - + -
87F CYS* 1.3 78.9 - - - +
89F VAL* 1.3 86.3 + - - +
97F TYR* 3.2 26.8 - - + -
98F VAL 3.2 14.1 - - - +
99F PHE* 3.9 19.1 - - + -
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Residues in contact with VAL 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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4F LEU* 4.0 20.6 - - + -
27F ILE* 4.3 4.9 - - + -
30F ILE* 3.8 28.5 - - + -
31F SER 3.5 19.5 - - - +
32F VAL* 4.0 13.7 - - + -
33F HIS* 4.5 0.9 - - - -
88F GLN* 1.3 91.8 + - - +
90F TRP* 1.3 64.0 + - - +
91F ASP* 4.8 2.7 - - + +
97F TYR* 3.6 0.7 - - - -
98F VAL* 2.9 54.1 + - + +
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Residues in contact with TRP 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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50E ASP* 5.0 5.2 + - - -
59E TYR* 6.1 0.7 - + - -
99E GLU* 5.0 1.5 + - - -
106E TRP* 3.9 51.7 + + + +
30F ILE* 5.7 3.9 - - - +
31F SER 4.9 1.6 + - - -
33F HIS* 5.0 2.4 + - - -
88F GLN* 3.7 1.0 - - - +
89F VAL* 1.3 77.4 - - - +
91F ASP* 1.3 63.9 + - - +
92F ASP* 3.4 37.7 + - + +
95F ASN* 3.8 30.0 - - + -
96F ALA 3.6 19.7 - - - +
97F TYR* 3.5 45.3 - + + -
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Residues in contact with ASP 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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89F VAL* 4.1 4.6 - - + +
90F TRP* 1.3 72.3 - - - +
92F ASP* 1.3 62.8 + - - +
93F SER* 3.1 25.5 + - - -
94F ILE* 3.7 28.9 - - + +
95F ASN* 2.8 25.6 + - - -
96F ALA 2.9 23.3 + - - +
98F VAL* 4.8 8.3 - - + +
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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