Contacts of the helix formed by residues 86 - 93 (chain B) in PDB entry 5TIN
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 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ALA 4.4 4.3 - - - +
27A ARG* 3.8 47.3 + - + +
94A TRP* 5.3 1.0 - - - -
161A TYR* 4.5 13.4 + - - +
14B LEU* 6.3 1.0 - - - +
85B LEU* 1.3 73.9 - - - +
87B PRO* 1.3 69.9 - - - +
88B SER* 2.8 38.7 + - - +
89B MET* 3.0 30.2 + - + +
118B LEU* 4.7 0.9 - - - +
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Residues in contact with PRO 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASP* 6.0 3.8 - - + +
160A GLY* 6.4 0.7 - - - -
161A TYR* 5.9 5.8 - - + +
85B LEU 3.4 6.5 - - - +
86B ASP* 1.3 92.1 - - - +
88B SER* 1.3 63.0 - - - +
89B MET 3.0 0.7 - - - -
90B LEU* 3.0 32.3 + - + +
91B ASP* 4.6 1.2 + - - +
113B THR* 6.2 0.2 - - - +
114B ASP* 4.8 11.7 - - + +
116B LYS* 3.4 45.5 + - + +
117B LEU* 4.9 2.9 - - - +
118B LEU* 4.8 3.4 - - + -
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Residues in contact with SER 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ARG* 4.0 8.8 - - - +
86B ASP* 2.8 23.8 + - - -
87B PRO* 1.3 77.1 - - - +
89B MET* 1.3 81.1 + - - +
90B LEU 3.2 1.3 + - - -
91B ASP* 3.5 25.5 + - - +
92B SER* 4.6 1.2 + - - -
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Residues in contact with MET 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ARG* 3.4 41.1 - - - +
14B LEU* 4.5 15.9 - - + -
18B MET* 4.0 29.8 - - - +
85B LEU* 4.8 5.8 - - + -
86B ASP* 3.0 18.9 + - + +
88B SER* 1.3 95.5 + - - +
90B LEU* 1.3 63.4 + - - +
91B ASP 3.2 1.1 - - - -
92B SER* 3.0 31.0 + - - +
93B ILE* 3.6 10.9 + - - +
118B LEU* 4.2 12.6 - - + -
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Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B PRO* 3.0 23.6 + - + +
89B MET* 1.3 78.0 - - - +
91B ASP* 1.3 58.9 + - - +
92B SER 3.3 0.5 + - - -
93B ILE* 3.4 22.2 + - + +
95B LYS* 2.7 38.6 + - + -
116B LYS* 3.8 31.4 - - + +
117B LEU 4.7 0.9 - - - +
118B LEU* 4.0 33.6 - - + +
128B TYR* 3.5 47.1 - - + +
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Residues in contact with ASP 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ALA* 4.6 6.1 - - - +
87B PRO 5.2 0.4 - - - +
88B SER* 3.6 19.2 - - - +
89B MET 3.2 0.8 - - - -
90B LEU* 1.3 79.9 - - - +
92B SER* 1.3 60.7 + - - +
93B ILE 3.5 2.9 + - - +
95B LYS* 4.2 8.1 + - - +
116B LYS* 5.4 5.4 + - - -
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Residues in contact with SER 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B MET* 4.0 31.9 + - - +
24B TYR* 3.3 21.7 - - - -
26B ALA* 3.7 7.5 - - - +
88B SER 4.8 1.0 + - - -
89B MET* 3.0 26.5 + - - +
91B ASP* 1.3 79.9 - - - +
93B ILE* 1.3 59.7 + - - +
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Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B MET* 3.9 32.8 - - + -
24B TYR* 3.7 10.8 - - + +
26B ALA* 3.6 8.9 - - - +
68B TRP* 4.6 3.8 - - + -
73B LEU* 4.2 22.4 - - + -
89B MET 3.6 6.5 + - - +
90B LEU* 3.4 27.4 + - + +
91B ASP 4.4 1.2 - - - +
92B SER* 1.3 82.8 - - - +
94B TRP* 1.3 76.6 + - - +
95B LYS* 3.5 11.2 + - + +
118B LEU* 3.9 33.4 - - + -
120B ILE* 5.6 0.2 - - + -
126B VAL* 4.5 11.9 - - + -
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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