Contacts of the strand formed by residues 192 - 200 (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 GLY 192 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159D PHE* 3.8 5.4 - - - -
160D ASN* 3.6 10.8 - - - -
190D ASP 3.2 4.9 + - - -
191D VAL* 1.3 76.3 - - - +
193D ASN* 1.3 68.1 + - - +
194D TYR* 3.9 4.7 - - - -
212D THR 3.9 0.2 - - - +
213D PRO* 3.4 0.7 - - - +
214D LEU 2.8 33.4 + - - +
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Residues in contact with ASN 193 (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 3.5 2.8 - - - +
159D PHE* 3.5 4.9 - - - -
160D ASN* 2.7 52.9 + - - +
192D GLY* 1.3 79.4 - - - +
194D TYR* 1.3 63.7 + - - +
195D THR* 5.1 1.1 + - - +
211D PRO* 3.9 23.5 - - + +
212D THR 3.6 2.7 - - - -
213D PRO* 3.5 22.3 - - - +
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Residues in contact with TYR 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D LEU* 3.7 13.7 - - + -
157D TRP* 3.8 19.9 - - + -
158D VAL 3.4 2.0 - - - -
159D PHE* 3.2 30.2 - + - -
166D VAL* 4.1 17.0 - - + -
172D ARG* 6.0 1.9 - - - -
181D LEU* 3.7 26.7 - - + -
183D ILE* 4.5 5.1 - - + +
190D ASP* 2.3 50.9 + - - +
192D GLY 3.9 4.0 - - - -
193D ASN* 1.3 75.2 - - - +
195D THR* 1.3 61.6 + - - +
196D CYS 4.3 0.2 + - - -
210D SER 4.2 0.9 - - - +
211D PRO* 3.2 1.3 - - - +
212D THR* 2.8 47.8 + - - +
214D LEU* 3.6 26.0 - - + -
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Residues in contact with THR 195 (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* 3.3 8.5 - - - -
158D VAL* 3.1 50.8 + - + +
160D ASN 4.9 4.2 + - - -
193D ASN* 5.1 1.6 - - - +
194D TYR* 1.3 74.0 - - - +
196D CYS* 1.3 73.8 + - - +
197D VAL* 3.6 2.3 + - + +
208D LEU* 4.0 20.6 - - + -
209D GLY 3.4 19.9 + - - +
210D SER 4.5 0.9 - - - -
211D PRO* 3.4 26.9 - - - +
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Residues in contact with CYS 196 (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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124D PHE* 3.8 7.2 - - + -
129D ARG* 4.3 5.5 - - - +
144D CYS* 2.0 52.9 - - + -
155D TYR* 4.2 7.6 - - - -
156D ALA 3.6 5.6 - - - -
157D TRP* 3.7 34.4 - - + -
179D GLY 4.0 2.2 - - - -
194D TYR 4.3 0.2 + - - -
195D THR* 1.3 73.5 - - - +
197D VAL* 1.3 62.6 + - - +
198D VAL* 4.0 2.5 - - - -
207D VAL 3.7 1.4 - - - +
208D LEU* 3.6 2.6 - - - -
209D GLY 2.9 27.7 + - - +
210D SER 4.8 4.0 + - - -
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Residues in contact with VAL 197 (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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154D SER 3.8 0.5 - - - +
155D TYR* 3.5 4.7 - - - -
156D ALA* 2.7 51.5 + - + +
158D VAL* 4.0 27.1 - - + -
162D TYR* 4.1 9.0 - - + -
165D PHE* 5.1 1.8 - - + -
195D THR* 4.2 7.6 - - + +
196D CYS* 1.3 76.2 - - - +
198D VAL* 1.3 61.5 + - - +
199D THR* 3.9 6.0 + - - +
206D ARG* 4.0 25.1 - - + -
207D VAL 3.5 2.5 - - - +
208D LEU* 3.5 31.2 - - + -
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Residues in contact with VAL 198 (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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124D PHE* 4.0 13.2 - - + -
144D CYS* 3.8 29.2 - - - -
146D PRO* 4.0 19.1 - - + -
153D LEU* 3.8 39.9 - - + -
154D SER 3.6 3.4 - - - +
155D TYR* 4.0 9.0 - - + -
197D VAL* 1.3 70.3 - - - +
199D THR* 1.3 62.8 + - - +
200D SER* 4.0 2.2 + - - +
205D THR 4.8 0.2 - - - +
206D ARG* 3.5 0.9 - - - -
207D VAL* 2.9 45.5 + - + +
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Residues in contact with THR 199 (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 3.8 0.3 - - - +
153D LEU* 3.4 3.1 - - - -
154D SER* 2.9 49.9 + - - +
197D VAL* 3.9 6.9 + - - +
198D VAL* 1.3 74.2 - - - +
200D SER* 1.3 70.9 + - - +
204D ASN* 4.3 16.4 - - - +
206D ARG* 3.6 20.8 - - + +
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Residues in contact with SER 200 (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* 3.4 13.5 + - - +
153D LEU* 3.8 17.6 - - - +
198D VAL* 4.0 2.7 + - - -
199D THR* 1.3 85.8 - - - +
201D THR* 1.3 66.2 + - - +
202D VAL* 3.1 18.9 + - - +
203D THR* 3.2 37.4 + - - +
204D ASN* 4.1 5.9 - - - +
205D THR 4.8 2.4 + - - -
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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