Contacts of the strand formed by residues 153 - 159 (chain D) in PDB entry 5E5R
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 LEU 153 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146D PRO* 4.0 21.3 - - + -
147D PRO 3.4 24.0 - - - +
148D PRO* 4.2 13.2 + - + +
151D GLY* 4.7 3.8 - - - -
152D GLU* 1.3 102.6 + - + +
154D SER* 1.3 59.4 + - - +
155D TYR* 3.7 25.4 - - + +
176D GLN* 4.8 2.1 - - - +
198D VAL* 3.8 24.9 - - + -
199D THR 3.4 1.8 - - - -
200D SER* 3.8 23.1 - - - +
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Residues in contact with SER 154 (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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152D GLU 4.4 0.2 + - - -
153D LEU* 1.3 73.9 - - - +
155D TYR* 1.3 64.7 + - - +
176D GLN* 3.6 10.3 - - - -
197D VAL 3.8 0.2 - - - +
198D VAL* 3.6 4.7 - - - +
199D THR* 2.9 50.6 + - - +
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Residues in contact with TYR 155 (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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144D CYS* 3.7 24.0 - - - -
146D PRO* 2.6 30.5 + - + -
147D PRO* 2.9 22.9 + - - +
148D PRO* 3.0 6.9 - - + +
153D LEU* 3.7 25.3 - - + +
154D SER* 1.3 77.6 - - - +
156D ALA* 1.3 62.8 + - - +
174D VAL* 4.4 5.8 - - + +
175D SER 4.4 1.1 - - - +
176D GLN* 2.8 58.8 + - - +
178D THR 4.6 0.2 - - - -
179D GLY* 3.3 40.4 - - - +
196D CYS* 4.9 1.6 - - - -
197D VAL 3.5 2.7 - - - -
198D VAL* 4.0 15.5 - - + -
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Residues in contact with ALA 156 (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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155D TYR* 1.3 76.4 - - - +
157D TRP* 1.3 72.7 + - - +
165D PHE* 3.6 30.7 - - + -
174D VAL* 5.0 2.9 - - - -
196D CYS* 3.6 1.4 - - - -
197D VAL* 2.7 40.7 + - + +
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Residues in contact with TRP 157 (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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129D ARG* 4.4 6.3 - - - -
142D LEU* 3.1 31.4 - - + -
143D LEU 3.4 17.7 - - - -
144D CYS* 3.6 19.5 - - + -
156D ALA* 1.3 80.2 - - - +
158D VAL* 1.3 57.0 + - - +
165D PHE* 3.3 8.0 - - - +
166D VAL* 2.7 45.1 + - + +
174D VAL* 3.8 23.7 - - + +
179D GLY 2.8 22.8 + - - -
181D LEU* 3.5 28.1 - - + +
194D TYR* 3.8 27.8 - - + -
195D THR 3.3 23.8 - - - -
196D CYS* 3.7 23.1 - - + -
212D THR* 4.6 3.8 - - + -
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Residues in contact with VAL 158 (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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157D TRP* 1.3 77.4 - - - +
159D PHE* 1.3 59.5 + - - +
160D ASN 4.1 13.5 - - - +
162D TYR* 3.5 37.2 - - + -
163D PRO 4.1 3.1 - - - -
164D SER 3.1 18.4 - - - +
165D PHE* 3.7 21.5 - - + -
166D VAL* 3.9 5.3 - - - +
193D ASN 3.5 1.0 - - - +
194D TYR* 3.4 6.6 - - - -
195D THR* 3.1 54.9 + - + +
197D VAL* 4.0 5.6 - - + -
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Residues in contact with PHE 159 (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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158D VAL* 1.3 72.9 - - - +
160D ASN* 1.3 96.2 + - - +
161D GLU 3.3 2.5 + - - -
164D SER* 2.6 32.2 + - - +
165D PHE 5.2 0.4 - - - +
166D VAL* 4.0 14.5 - - + +
189D SER 3.7 15.9 - - - -
190D ASP* 3.5 4.7 - - - -
191D VAL 3.4 21.8 - - - -
192D GLY* 3.8 11.2 - - - -
193D ASN 3.5 5.8 - - - -
194D TYR* 3.2 42.4 - + - -
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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