Contacts of the strand formed by residues 168 - 172 (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 GLU 168 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B HIS* 4.3 5.7 - - - +
137B ARG* 3.1 33.0 + - - +
168B GLU* 3.7 31.0 - - + +
135D HIS* 3.2 45.1 + - - +
136D GLY 2.9 9.8 + - - +
137D ARG* 3.1 16.3 - - + +
138D ILE 2.9 25.6 + - - -
159D LYS* 3.6 23.7 + - - -
165D ILE 5.4 0.5 - - - +
167D PHE* 1.3 77.7 - - - +
169D SER* 1.3 59.3 + - - +
193D PHE* 3.7 5.1 - - + -
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Residues in contact with SER 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ARG* 2.9 27.8 + - - +
192B LEU 5.0 0.7 - - - +
138D ILE* 3.3 15.3 - - - -
151D HIS 4.7 4.3 - - - -
152D GLY* 4.1 23.4 - - - -
153D PHE 4.4 0.2 + - - -
154D MSE 4.0 12.5 - - - +
163D THR* 5.2 3.1 - - - -
164D SER* 3.3 28.6 - - - +
167D PHE 3.7 3.2 + - - -
168D GLU* 1.3 74.9 - - - +
170D MSE 1.3 61.2 + - - +
171D PRO* 4.8 1.6 - - - +
193D PHE* 4.1 0.9 - - - -
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Residues in contact with MSE 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ARG* 4.8 1.6 - - - +
170B MSE 3.8 26.0 - - - +
189B ASN* 5.5 1.1 - - - +
192B LEU* 3.7 20.4 - - + +
193B PHE* 4.4 11.4 - - - +
138D ILE 3.1 4.2 + - - -
139D MSE 3.2 59.5 - - + +
140D GLY 3.6 1.5 + - - -
169D SER* 1.3 77.6 - - - +
171D PRO* 1.3 76.5 - - + +
189D ASN* 3.6 26.7 - - + +
193D PHE* 3.6 39.9 - - + -
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Residues in contact with PRO 171 (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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192B LEU* 3.7 41.1 - - + +
194B HIS* 5.7 2.7 - - + -
139D MSE 4.1 6.0 - - - +
140D GLY 3.0 15.0 - - - +
141D LEU 4.5 0.2 - - - -
142D ASP* 3.6 38.1 - - + +
154D MSE 6.3 2.2 - - + -
169D SER 4.8 0.9 - - - +
170D MSE 1.3 99.5 - - + +
172D TYR* 1.3 60.7 + - - +
189D ASN* 5.0 1.4 + - - -
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Residues in contact with TYR 172 (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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192B LEU* 6.0 0.2 - - - -
139D MSE 4.1 11.0 - - + -
140D GLY* 2.9 35.3 + - - -
141D LEU* 3.5 35.3 + - + +
142D ASP* 3.1 22.5 + - - +
171D PRO* 1.3 74.1 - - - +
173D LYS* 1.3 68.1 + - - +
181D ILE* 4.2 29.2 - - + +
182D ASN 5.7 0.9 - - - +
185D GLN* 4.9 4.3 - - - +
186D LEU* 3.7 55.0 - - + +
189D ASN* 5.8 2.9 - - - +
198D ILE* 4.5 4.3 - - + -
199D ILE 2.6 25.8 + - - -
200D ALA* 4.2 5.7 - - - -
201D GLY 4.9 1.2 + - - -
209D LEU* 5.8 1.0 - - - +
214D LEU* 4.7 8.6 - - + +
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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