Contacts of the helix formed by residues 148 - 152 (chain D) in PDB entry 1EJI
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 HIS 148 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75C GLU* 4.5 6.7 + - - -
302C GLY* 5.7 0.4 - - - -
121D SER* 4.1 6.7 - - - -
141D LEU 5.3 0.2 - - - +
143D LEU* 3.7 4.5 - - - -
147D GLY* 1.3 75.1 - - - -
149D LEU* 1.3 70.8 + - + +
150D THR* 2.7 51.0 + - + +
151D HIS* 2.7 31.3 + - + +
152D GLY 4.8 1.6 - - - +
203D SER* 4.2 5.4 - - - -
503D PLG 3.4 70.7 + + + -
602D THF 3.3 32.6 + - - -
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Residues in contact with LEU 149 (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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75C GLU* 5.6 0.4 - - - +
297C PHE* 4.5 5.8 - - + -
298C PRO* 3.5 40.4 - - + +
143D LEU* 3.4 22.9 - - + +
148D HIS* 1.3 75.8 + - + +
150D THR* 1.3 59.2 + - + +
152D GLY* 2.8 23.0 + - - -
153D PHE* 3.6 34.1 - - + -
160D ILE* 5.1 0.9 - - + -
161D SER* 3.3 24.9 + - - +
602D THF 3.2 45.7 + - + +
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Residues in contact with THR 150 (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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300C LEU 5.5 1.1 - - - +
121D SER* 3.2 46.2 - - - +
124D ASN* 3.0 27.2 + - + +
125D PHE 5.9 0.2 - - - +
128D TYR* 2.7 24.0 + - - -
148D HIS* 2.7 31.6 + - + -
149D LEU* 1.3 73.2 - - + +
151D HIS* 1.3 57.1 + - - +
152D GLY 3.0 2.3 + - - -
161D SER* 4.5 1.8 - - - -
163D THR* 2.9 22.8 + - - +
503D PLG 3.8 1.0 + - - -
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Residues in contact with HIS 151 (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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128D TYR* 4.1 4.3 - - - -
138D ILE* 4.7 4.2 - - - +
140D GLY* 4.1 21.3 + - - -
141D LEU 4.7 10.1 + - - +
147D GLY* 4.2 3.4 - - - -
148D HIS* 2.7 32.8 + - + +
150D THR* 1.3 82.5 - - - +
152D GLY* 1.3 63.0 + - - +
163D THR* 4.1 4.7 - - - +
169D SER* 4.7 4.2 - - - -
199D ILE* 3.6 43.0 + - + +
201D GLY 3.1 35.3 + - - -
202D THR 4.2 0.4 - - - -
228D ASP* 3.1 26.9 + - - +
503D PLG 3.6 15.0 - - + +
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Residues in contact with GLY 152 (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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140D GLY 6.1 0.3 - - - -
141D LEU 5.4 3.3 - - - +
142D ASP* 5.8 1.6 - - - +
143D LEU 5.4 3.5 + - - -
148D HIS 4.8 1.6 - - - +
149D LEU 2.8 8.4 + - - +
150D THR 3.0 4.2 + - - -
151D HIS* 1.3 85.8 - - - +
153D PHE* 1.3 61.7 + - - +
163D THR* 3.6 22.9 - - - +
164D SER 4.1 0.9 - - - -
169D SER* 4.1 17.6 - - - -
171D PRO* 5.7 4.5 - - - +
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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