Contacts of the helix formed by residues 185 - 199 (chain E) in PDB entry 3SDI
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 ASN 185 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45E HIS* 4.8 1.3 - - - -
180E ILE* 3.5 21.0 + - - -
183E ASP* 3.2 6.4 - - - +
184E GLY* 1.3 80.6 + - - +
186E PRO* 1.3 70.6 - - - +
187E ASP* 3.9 15.8 + - - +
188E GLU* 3.1 34.4 + - - +
189E LEU* 3.3 9.2 + - - +
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Residues in contact with PRO 186 (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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45E HIS* 4.0 22.6 - - + +
184E GLY 3.5 8.1 - - - +
185E ASN* 1.3 88.1 - - - +
187E ASP* 1.3 70.3 + - - +
189E LEU* 3.2 8.0 + - + +
190E ILE* 3.1 28.8 + - + +
214E ILE* 3.8 25.3 - - + +
219E THR* 5.9 1.6 - - + +
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Residues in contact with ASP 187 (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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185E ASN* 3.1 11.2 + - - +
186E PRO* 1.3 85.4 - - - +
188E GLU* 1.3 59.9 + - + +
190E ILE* 3.6 4.4 + - - +
191E LYS* 3.1 31.9 + - - +
231E LYS* 5.7 2.1 - - - -
232E TYR* 3.1 35.8 + - + -
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Residues in contact with GLU 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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180E ILE* 3.8 25.7 - - - +
185E ASN* 3.1 28.5 + - + +
187E ASP* 1.3 78.3 - - + +
189E LEU* 1.3 58.8 + - - +
191E LYS* 3.4 33.9 + - - +
192E ALA* 3.1 25.5 + - - +
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Residues in contact with LEU 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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40E LEU* 3.6 33.8 - - + +
41E ARG* 4.5 2.9 - - - -
42E SER* 3.9 16.8 - - - +
45E HIS* 3.7 37.2 - - + +
46E ALA 4.4 0.2 - - - +
47E VAL* 3.7 22.1 - - + +
180E ILE* 3.7 34.9 - - + +
185E ASN 3.3 7.8 + - - +
186E PRO* 3.2 11.3 + - + +
188E GLU* 1.3 76.7 - - - +
190E ILE* 1.3 64.9 + - - +
192E ALA* 3.5 1.4 + - + +
193E GLY* 3.2 16.8 + - - -
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Residues in contact with ILE 190 (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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47E VAL* 4.1 24.9 - - + -
49E VAL* 4.7 0.6 - - + +
186E PRO* 3.1 22.6 + - + +
187E ASP* 3.9 5.8 - - - +
188E GLU 3.4 0.2 - - - -
189E LEU* 1.3 75.8 - - - +
191E LYS* 1.3 51.5 + - - +
193E GLY* 2.8 5.2 + - - -
194E VAL* 2.7 35.5 + - + +
212E ILE* 3.6 43.1 - - + -
214E ILE* 4.5 13.2 - - + -
224E TYR* 4.8 13.5 - - + -
232E TYR* 3.7 36.6 - - + +
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Residues in contact with LYS 191 (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 ASP* 3.1 17.7 + - - +
188E GLU* 3.4 32.7 + - - +
190E ILE* 1.3 75.6 - - - +
192E ALA* 1.3 51.9 + - - +
194E VAL* 3.2 8.9 + - - +
195E GLU* 2.8 38.9 + - - +
231E LYS 5.4 5.8 + - - -
232E TYR* 4.6 19.6 - - + +
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Residues in contact with ALA 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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40E LEU* 4.3 15.9 - - + +
175E TYR* 3.8 15.6 - - + +
179E THR* 5.5 3.1 - - + -
180E ILE* 4.4 22.0 - - + -
188E GLU 3.1 13.1 + - - +
189E LEU 3.8 5.4 - - - +
190E ILE 3.3 0.4 - - - -
191E LYS* 1.3 77.9 - - - +
193E GLY* 1.3 57.6 + - - +
195E GLU* 3.9 7.0 - - - -
196E ALA* 3.1 27.0 + - - +
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Residues in contact with GLY 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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38E VAL* 4.6 2.9 - - - +
40E LEU* 3.7 24.0 - - - +
49E VAL* 3.7 16.3 - - - +
189E LEU 3.2 7.2 + - - -
190E ILE 2.8 7.5 + - - -
192E ALA* 1.3 75.8 - - - +
194E VAL* 1.3 58.7 + - - +
196E ALA* 3.1 6.7 + - - +
197E ILE* 2.9 29.3 + - - +
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Residues in contact with VAL 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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49E VAL* 4.5 7.4 - - + -
190E ILE* 2.7 38.3 + - + +
191E LYS* 3.7 6.5 - - - +
193E GLY* 1.3 71.4 - - - +
195E GLU* 1.3 52.8 + - - +
197E ILE* 3.2 16.7 - - - +
198E SER* 2.7 24.9 + - - +
207E LEU* 3.9 21.9 - - + +
210E LEU* 4.4 9.2 - - + -
212E ILE* 4.0 15.7 - - + -
232E TYR* 3.7 31.2 - - + +
233E ILE* 5.3 2.0 - - - +
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Residues in contact with GLU 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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175E TYR* 3.1 36.4 + - + +
191E LYS* 2.8 22.7 + - - +
192E ALA* 3.9 4.3 - - - +
194E VAL* 1.3 75.4 - - - +
196E ALA* 1.3 59.3 + - - +
198E SER* 3.0 17.0 + - - +
199E GLN* 2.8 24.7 + - - +
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Residues in contact with ALA 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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38E VAL* 4.3 9.0 - - + -
172E ALA* 3.0 24.8 - - + +
175E TYR* 3.5 26.6 - - + -
176E LEU* 3.9 22.0 - - + -
192E ALA 3.1 20.1 + - - +
193E GLY 3.1 6.0 + - - +
195E GLU* 1.3 77.2 - - - +
197E ILE* 1.3 59.6 + - - +
198E SER 3.3 0.9 + - - -
199E GLN* 3.4 9.2 + - - +
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Residues in contact with ILE 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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36E VAL* 3.9 22.2 - - + +
38E VAL* 3.8 19.9 - - + +
49E VAL* 3.8 31.0 - - + +
50E ALA 3.8 3.4 - - - -
51E LEU* 3.6 34.1 - - + +
172E ALA* 4.6 1.3 - - - -
193E GLY 2.9 10.8 + - - +
194E VAL* 3.2 26.0 - - - +
196E ALA* 1.3 76.3 - - - +
198E SER* 1.3 62.0 + - - +
200E SER* 3.2 16.5 + - - -
201E LEU* 3.9 9.9 - - + +
207E LEU* 3.9 19.3 - - + -
210E LEU* 4.9 2.5 - - + -
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Residues in contact with SER 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 VAL* 2.7 18.9 + - - +
195E GLU* 3.0 13.2 + - - +
196E ALA 3.2 0.6 - - - -
197E ILE* 1.3 73.5 - - - +
199E GLN* 1.3 60.0 + - - +
200E SER 2.9 10.6 + - - -
201E LEU* 3.2 37.8 + - - +
207E LEU* 4.4 10.0 - - - +
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Residues in contact with GLN 199 (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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168E ARG 4.5 0.2 - - - +
171E GLY* 3.3 33.1 - - - +
172E ALA* 4.2 1.3 - - - -
175E TYR* 3.5 35.2 - - + -
195E GLU* 2.8 32.9 + - - +
196E ALA 3.7 8.5 - - - +
197E ILE 3.3 1.0 - - - -
198E SER* 1.3 75.9 - - - +
200E SER* 1.3 56.0 + - - +
201E LEU 3.7 1.8 - - - -
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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