Contacts of the strand formed by residues 86 - 94 (chain b) in PDB entry 5EHD
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 86 (chain b).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46b THR* 4.5 14.6 - - + -
47b VAL 3.3 9.4 - - - +
48b SER* 3.4 18.0 - - - -
84b GLN* 3.5 18.7 - - - +
85b PRO* 1.3 86.7 - - - +
87b VAL* 1.3 72.9 + - - +
88b SER* 4.8 1.3 - - - +
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Residues in contact with VAL 87 (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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86a THR* 4.0 23.3 - - + -
88a SER* 4.8 7.0 - - - -
46b THR* 3.3 2.6 - - - -
47b VAL* 2.8 35.0 + - + +
77b ALA* 4.1 15.0 - - + -
79b LEU* 3.3 26.4 - - + +
84b GLN* 3.4 26.9 - - - +
86b THR* 1.3 71.7 - - - +
88b SER* 1.3 64.4 + - - +
89b LEU* 3.8 24.5 + - + -
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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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88a SER* 3.1 23.0 + - - -
45b ARG* 3.4 5.8 + - - -
46b THR* 3.9 17.4 - - - +
86b THR* 4.3 2.2 - - - -
87b VAL* 1.3 73.6 - - - +
89b LEU* 1.3 63.1 + - - +
90b GLY* 3.5 8.7 + - - -
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Residues in contact with LEU 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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45a ARG* 2.9 26.5 + - - -
46a THR* 3.5 30.3 - - + -
88a SER* 3.8 10.5 + - - -
90a GLY* 4.6 1.5 - - - -
44b LEU* 3.6 40.4 - - + +
45b ARG 2.4 28.9 + - - +
47b VAL* 3.9 24.5 - - + -
76b LEU* 4.0 15.3 - - + +
87b VAL* 3.8 19.7 - - + +
88b SER* 1.3 69.3 - - - +
90b GLY* 1.3 56.8 + - - +
91b GLY 3.3 0.6 + - - -
92b PHE* 4.0 18.6 + - + -
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Residues in contact with GLY 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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45a ARG* 3.5 9.8 + - - -
90a GLY* 5.7 2.7 - - - -
45b ARG* 3.5 30.6 + - - +
88b SER* 3.5 10.0 + - - -
89b LEU* 1.3 79.0 - - - +
91b GLY* 1.3 59.8 + - - +
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Residues in contact with GLY 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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45a ARG* 3.6 17.0 + - - -
114a GLN* 4.6 0.5 - - - +
43b SER* 3.2 21.7 + - - -
44b LEU 3.0 9.0 + - - -
45b ARG* 3.7 18.8 - - - +
90b GLY* 1.3 78.5 - - - +
92b PHE* 1.3 60.4 + - - +
93b GLU* 3.2 14.8 + - - +
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Residues in contact with PHE 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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18a LEU* 3.7 20.4 - - + -
45a ARG* 3.7 31.0 - - + +
46a THR* 5.4 0.4 - - + -
112a SER* 3.5 22.9 - - - -
113a GLY* 3.6 26.9 - - - -
114a GLN* 3.6 25.8 - - + -
42b LEU 3.3 3.6 - - - +
44b LEU* 2.8 46.0 + - + +
76b LEU* 3.6 25.8 - - + -
89b LEU* 4.0 20.5 + - + -
90b GLY 3.9 0.2 - - - -
91b GLY* 1.3 69.9 - - - +
93b GLU* 1.3 69.5 + - - +
94b ILE* 3.8 8.0 + - + +
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Residues in contact with GLU 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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16a ASN* 3.0 12.0 + - - +
18a LEU* 5.7 0.3 - - - +
114a GLN* 2.8 37.7 + - - +
41b GLN* 3.1 28.7 - - + +
42b LEU 3.0 4.7 - - - +
43b SER* 3.4 26.4 + - - +
91b GLY* 3.2 8.2 + - - +
92b PHE* 1.3 72.6 - - - +
94b ILE* 1.3 63.3 + - - +
116b LEU* 3.6 23.3 - - + +
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Residues in contact with ILE 94 (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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16a ASN* 4.0 3.1 - - - +
17a TYR 6.5 0.2 - - - -
18a LEU* 4.2 24.5 - - + +
41b GLN* 3.8 3.6 - - - -
42b LEU* 2.8 38.8 + - + +
44b LEU* 3.9 25.6 - - + -
62b ALA* 4.3 10.8 - - + -
64b ALA* 3.8 29.4 - - + -
76b LEU* 4.9 1.6 - - + -
92b PHE* 4.0 21.5 - - + +
93b GLU* 1.3 81.1 - - - +
95b THR* 1.3 68.1 + - - +
96b PRO* 3.6 1.0 - - - +
98b VAL* 3.9 24.0 - - + +
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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