Contacts of the helix formed by residues 90 - 95 (chain B) in PDB entry 1EJD
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 MET 90 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B LEU* 4.5 1.3 - - - -
30B PHE* 3.9 20.9 - - + -
49B ASP* 3.5 49.6 - - - +
52B THR* 3.9 25.4 - - + -
53B THR* 3.3 22.2 - - - +
56B LEU* 4.5 3.6 - - + -
86B LEU 5.4 0.4 - - - +
87B VAL 2.8 11.2 + - - +
88B LYS 3.4 1.2 + - - -
89B THR* 1.3 82.2 - - - +
91B ARG* 1.3 59.0 + - - +
92B ALA* 3.8 18.6 - - + +
93B SER* 2.7 46.4 + - - +
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Residues in contact with ARG 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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90B MET* 1.3 67.5 - - - +
92B ALA* 1.3 57.6 + - - +
93B SER* 2.9 13.3 + - - -
94B ILE* 3.2 22.6 + - + +
120B ARG* 6.1 1.2 - - - +
121B PRO* 3.5 43.7 - - + +
122B VAL* 5.8 6.3 - - + -
2424B PO4 5.5 3.6 + - - -
2427B PO4 5.4 1.0 + - - -
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Residues in contact with ALA 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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26B LEU* 4.2 16.6 - - + -
30B PHE* 3.5 8.6 - - + -
49B ASP* 5.7 0.4 - - - +
90B MET* 3.1 18.9 - - + +
91B ARG* 1.3 76.4 - - - +
93B SER* 1.3 62.2 + - - +
94B ILE* 3.0 4.3 - - - -
95B TRP* 3.0 51.9 + - + +
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Residues in contact with SER 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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30B PHE* 4.0 11.9 - - - -
56B LEU* 3.9 10.0 - - - +
82B ALA* 5.3 0.6 - - - +
87B VAL* 3.4 36.6 + - - +
90B MET* 2.7 28.8 + - - +
91B ARG* 2.9 2.8 + - - -
92B ALA* 1.3 77.5 - - - +
94B ILE* 1.3 63.6 + - - +
95B TRP 3.0 1.7 + - - -
96B ALA* 3.0 21.0 + - - +
109B VAL* 4.0 9.5 - - - +
110B SER 5.0 2.9 + - - -
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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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91B ARG* 3.2 20.7 + - + +
92B ALA* 3.0 5.3 - - - +
93B SER* 1.3 79.1 + - - +
95B TRP* 1.3 65.8 + - + +
96B ALA 3.1 5.1 + - - -
97B LEU* 3.1 33.3 + - + +
98B GLY 4.5 0.9 + - - -
109B VAL* 3.6 28.7 - - + -
111B LEU* 4.5 2.7 - - + -
122B VAL* 4.1 28.3 - - + -
125B HIS* 3.6 44.0 - - + +
126B ILE* 4.7 4.5 - - + -
143B VAL* 4.4 4.5 - - + -
168B THR* 4.5 2.9 + - - -
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Residues in contact with TRP 95 (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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23B ASN* 4.9 8.7 - - + -
26B LEU* 3.9 14.1 - - + -
27B PRO* 3.6 37.5 - - + -
30B PHE* 3.6 22.5 - + + +
92B ALA* 3.0 35.7 + - + +
94B ILE* 1.3 79.3 - - + +
96B ALA* 1.3 55.8 + - - +
97B LEU 3.3 0.4 - - - -
98B GLY 4.6 0.4 - - - -
99B PRO* 3.0 25.5 - - - +
125B HIS* 3.9 6.6 - + - -
163B VAL* 4.8 8.1 - - + -
164B GLY* 3.0 40.3 + - - -
167B VAL* 3.4 34.5 - - + +
168B THR* 3.4 21.0 - - - -
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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