Contacts of the helix formed by residues 187 - 198 (chain E) in PDB entry 4U8T
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 SER 187 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E SER* 2.7 21.2 + - - -
186E SER* 1.3 87.2 - - - +
188E LEU* 1.3 62.8 + - - +
189E GLU* 3.2 9.9 + - - +
190E HIS* 3.2 44.9 + - - -
191E VAL* 3.6 6.2 - - - +
229E VAL* 4.3 4.2 - - - +
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Residues in contact with LEU 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E SER* 1.3 72.1 + - - +
189E GLU* 1.3 62.9 + - - +
191E VAL* 3.1 6.6 + - + +
192E LYS* 3.0 39.4 + - - +
229E VAL* 3.9 30.6 - - + +
234E ARG* 6.3 1.1 - - - +
236E CYS* 5.3 3.1 - - + -
323E PHE* 3.7 34.1 - - + -
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Residues in contact with GLU 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E SER* 3.2 8.1 + - - +
188E LEU* 1.3 78.0 - - - +
190E HIS* 1.3 63.7 + - + +
192E LYS* 3.1 28.4 + - - +
193E LYS* 2.9 60.1 + - + +
196E TYR* 6.1 1.2 - - - -
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Residues in contact with HIS 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185E SER* 4.0 7.4 - - - +
186E SER* 5.6 0.7 - - - -
187E SER* 3.2 27.9 + - - +
188E LEU 3.3 0.2 - - - -
189E GLU* 1.3 82.8 - - + +
191E VAL* 1.3 57.8 + - - +
193E LYS* 3.5 1.7 + - + -
194E SER* 2.9 25.8 + - - -
200E TRP* 3.6 8.5 - - + -
253E ILE 5.1 0.9 - - - -
254E TRP* 3.4 65.9 + + + +
260E TYR* 4.3 8.5 - + - -
0S 6MZ 3.0 31.1 + + - +
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Residues in contact with VAL 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185E SER* 3.6 22.0 - - - -
187E SER 3.6 15.5 - - - +
188E LEU* 3.1 9.8 + - + +
189E GLU 3.1 0.6 - - - -
190E HIS* 1.3 75.9 - - - +
192E LYS* 1.3 63.1 + - - +
194E SER* 3.3 4.4 + - - -
195E PHE* 3.2 18.9 + - - +
200E TRP* 4.2 6.7 - - + -
227E PHE* 3.9 18.4 - - + -
228E SER 5.9 0.2 - - - -
229E VAL* 4.1 13.0 - - + +
236E CYS* 4.0 10.1 - - - -
268E TRP* 3.6 27.4 - - + -
323E PHE* 4.0 16.1 - - + -
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Residues in contact with LYS 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188E LEU* 3.0 37.5 + - + +
189E GLU* 3.1 32.8 + - - +
191E VAL* 1.3 74.0 - - - +
193E LYS* 1.3 61.0 + - - +
195E PHE* 2.8 21.0 + - - +
196E TYR* 3.1 28.8 + - + -
323E PHE* 3.5 47.4 + - + +
324E LEU* 5.5 2.7 - - + -
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Residues in contact with LYS 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189E GLU* 2.9 46.4 + - + +
190E HIS* 3.9 5.8 - - + +
192E LYS* 1.3 71.3 - - - +
194E SER* 1.3 65.9 + - - +
196E TYR* 4.4 7.4 - - + +
197E ASN* 2.9 42.9 + - - +
253E ILE* 3.2 50.8 - - + +
254E TRP* 4.5 2.7 - - + +
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Residues in contact with SER 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E HIS 2.9 15.7 + - - -
191E VAL* 3.4 11.0 - - - -
192E LYS 3.1 0.4 - - - -
193E LYS* 1.3 77.4 - - - +
195E PHE* 1.3 56.6 + - - +
198E GLY* 2.8 29.9 + - - +
199E ILE 2.6 28.8 + - - +
200E TRP* 3.6 21.8 - - - +
227E PHE* 4.6 0.3 - - - -
253E ILE* 5.1 0.7 - - - -
254E TRP* 4.6 4.0 - - - +
266E VAL* 3.9 2.9 - - - +
268E TRP* 3.4 20.3 + - - -
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Residues in contact with PHE 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E ILE* 3.6 32.3 - - + -
191E VAL 3.2 11.1 + - - +
192E LYS 2.8 11.1 + - - +
194E SER* 1.3 79.5 - - - +
196E TYR* 1.3 86.4 + + - +
197E ASN 3.6 0.2 + - - -
198E GLY* 4.1 3.8 + - - -
268E TRP* 3.6 37.8 - + + +
271E VAL* 3.9 15.7 - - + -
323E PHE* 4.1 14.1 - + + -
324E LEU* 3.5 22.4 - - + -
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Residues in contact with TYR 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189E GLU* 6.1 0.7 - - - -
192E LYS* 3.1 32.4 + - + +
193E LYS* 3.4 5.8 + - + -
195E PHE* 1.3 100.1 - + - +
197E ASN* 1.3 73.5 + - - +
324E LEU* 3.6 20.6 - - + +
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Residues in contact with ASN 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193E LYS* 2.9 36.5 + - - +
196E TYR* 1.3 90.0 - - - +
198E GLY* 1.3 62.0 + - - +
199E ILE* 3.4 13.4 + - + +
250E ASP* 5.5 2.8 - - + +
253E ILE* 4.0 36.6 - - + +
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Residues in contact with GLY 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E SER 2.8 14.7 + - - -
195E PHE 4.1 3.7 + - - -
196E TYR 3.7 1.4 - - - -
197E ASN* 1.3 77.4 - - - +
199E ILE* 1.3 60.8 + - - +
265E LYS* 3.5 5.5 - - - +
266E VAL* 2.8 40.0 + - - +
268E TRP* 5.3 2.0 - - - -
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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