Contacts of the strand formed by residues 90 - 95 (chain D) in PDB entry 1EJH
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 90 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46D TRP 4.5 0.2 - - - -
47D PHE* 3.3 11.4 - - - -
48D PHE* 2.8 55.9 + - + +
56D TRP* 5.3 4.2 + - - -
85D LEU* 4.9 2.2 - - - -
89D CYS* 1.3 77.7 - - - +
91D TYR* 1.3 64.8 + - - +
92D SER* 4.9 2.9 - - - +
153D VAL* 4.6 5.1 - - + +
154D VAL* 3.3 9.2 - - - +
155D ASN* 2.9 18.4 + - - +
157D ARG* 2.5 47.0 + - - -
1004D M7G 4.5 1.7 + - - -
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Residues in contact with TYR 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D LEU* 4.0 9.6 - - + -
46D TRP 3.4 12.1 - - - -
47D PHE* 3.8 19.6 - + - -
63D ILE* 4.0 18.8 - - + +
79D ILE* 3.6 23.2 - - + +
80D GLN* 2.8 44.1 + - - +
82D SER* 3.2 24.0 - - - -
85D LEU* 3.7 22.7 - - + +
90D ASP* 1.3 73.4 - - - +
92D SER* 1.3 64.9 + - - +
130D TRP* 3.7 16.9 - + + -
153D VAL* 3.6 0.9 - - - +
154D VAL* 3.1 44.6 + - + +
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Residues in contact with SER 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D ALA 3.3 1.4 - - - +
45D LEU* 3.2 8.3 - - - +
46D TRP* 2.7 47.0 + - - -
60D LEU* 5.6 2.7 - - - +
90D ASP* 4.9 3.6 - - - +
91D TYR* 1.3 76.0 + - - +
93D LEU* 1.3 60.4 + - - +
94D PHE* 3.7 9.0 - - - -
100D PRO* 3.7 27.6 - - - +
130D TRP* 4.5 1.3 - - - -
152D ALA 3.3 4.0 - - - -
153D VAL* 3.2 23.4 - - - +
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Residues in contact with LEU 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D TRP* 3.8 23.5 - - + -
44D ALA 3.4 18.6 - - - +
45D LEU* 4.0 12.6 - - + -
66D PHE* 3.7 27.4 - - + -
72D PHE* 5.5 0.9 - - + -
92D SER* 1.3 72.1 - - - +
94D PHE* 1.3 62.0 + - - +
130D TRP* 4.4 2.6 - - + -
134D LEU* 3.6 35.4 - - + +
137D LEU* 3.7 16.9 - - + +
138D ILE* 3.9 23.6 - - + -
151D GLY* 2.9 4.2 - - - -
152D ALA 2.8 34.0 + - - +
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Residues in contact with PHE 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D TRP* 3.5 6.9 - - - -
44D ALA* 2.9 33.0 + - - +
46D TRP* 4.6 5.2 - + - +
92D SER* 3.7 6.1 - - - -
93D LEU* 1.3 79.3 - - - +
95D LYS* 1.3 63.7 + - - +
98D ILE* 3.4 35.2 - - + +
100D PRO* 3.6 27.1 - - + -
107D ASN* 3.9 10.8 - - - -
150D CYS 3.3 18.6 - - - -
151D GLY* 3.8 3.8 - - - -
152D ALA 3.4 8.3 - - - -
153D VAL* 3.4 26.7 - - + -
166D TRP* 3.6 51.6 - + + -
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Residues in contact with LYS 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ASN* 3.9 32.8 + - + +
42D ARG 3.8 6.3 - - - +
43D TRP* 3.6 29.3 - - + -
44D ALA* 5.4 0.9 - - - +
94D PHE* 1.3 75.6 - - - +
96D ASP* 1.3 69.5 + - - +
97D GLY 3.0 0.3 + - - -
98D ILE* 2.9 36.6 + - + +
140D GLU* 5.1 3.3 + - - -
146D SER 3.1 20.8 + - - -
147D ASP* 3.4 20.2 + - - +
149D VAL* 2.9 29.1 + - - +
150D CYS 2.9 16.7 + - - +
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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