Contacts of the helix formed by residues 185 - 195 (chain E) in PDB entry 3IFS
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 185 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145E LYS 5.1 0.2 - - - -
146E SER* 3.8 13.0 - - - -
184E ARG* 1.3 81.4 - - - +
186E ALA* 1.3 61.9 + - - -
187E LEU 3.3 2.5 - - - -
188E LYS 4.1 0.4 - - - -
189E THR* 2.7 32.3 + - - -
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Residues in contact with ALA 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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146E SER 3.0 11.9 + - - +
147E GLY 4.1 5.2 - - - +
148E THR* 4.1 16.2 - - + +
185E GLY* 1.3 71.6 - - - +
187E LEU* 1.3 58.0 + - - +
189E THR* 3.6 4.9 + - - -
190E LEU* 3.1 27.2 + - - +
348F LEU* 3.3 42.6 - - - +
349F ASP* 4.1 5.8 - - + -
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Residues in contact with LEU 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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142E VAL* 4.0 42.2 - - + +
144E SER* 3.5 34.5 - - - +
146E SER 3.4 2.4 + - - -
147E GLY* 3.7 17.0 - - - +
156E PHE* 4.5 17.9 - - + -
178E ALA* 4.2 9.2 - - + -
180E THR* 3.8 22.7 - - + +
185E GLY 3.3 0.8 - - - -
186E ALA* 1.3 77.6 - - - +
188E LYS* 1.3 59.7 + - - +
190E LEU* 3.1 11.2 + - + +
191E ALA* 2.8 28.0 + - + +
196E TYR* 5.5 1.3 - - + -
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Residues in contact with LYS 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 THR* 4.0 10.3 + - + +
181E ASP 3.6 20.0 - - - +
182E LYS* 3.4 22.6 + - - +
183E ALA* 3.8 19.1 + - - +
184E ARG* 3.6 22.7 - - - +
185E GLY 3.6 1.8 + - - -
186E ALA 3.5 0.2 - - - -
187E LEU* 1.3 78.2 - - - +
189E THR* 1.3 57.8 + - - +
191E ALA* 3.3 1.5 + - + -
192E ASP* 2.6 67.5 + - - +
198E THR* 4.1 29.4 - - + +
200E VAL* 6.2 0.9 - - - -
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Residues in contact with THR 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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183E ALA 5.6 0.5 + - - -
184E ARG* 4.9 2.6 - - - -
185E GLY 2.7 27.6 + - - -
186E ALA* 3.8 5.4 - - - -
188E LYS* 1.3 77.7 - - - +
190E LEU* 1.3 61.4 + - - +
192E ASP* 3.5 7.7 + - + +
193E ASN* 3.1 45.3 + - - +
348F LEU* 4.1 19.3 - - + -
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Residues in contact with LEU 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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156E PHE* 3.7 31.0 - - + -
160E ARG* 4.3 19.1 - - - +
186E ALA 3.1 18.1 + - - +
187E LEU* 3.1 8.5 + - + +
189E THR* 1.3 74.5 - - - +
191E ALA* 1.3 56.8 + - - +
193E ASN* 3.1 5.8 + - + -
194E GLU* 2.7 60.4 + - + +
196E TYR* 4.0 16.2 - - + +
344F GLU* 5.9 2.0 - - - +
346F ASN* 6.0 5.6 - - + +
348F LEU* 3.9 20.1 - - + +
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Residues in contact with ALA 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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178E ALA* 4.1 11.2 - - + -
187E LEU 2.8 17.1 + - - +
188E LYS* 3.6 8.1 - - + +
190E LEU* 1.3 75.1 - - - +
192E ASP* 1.3 56.8 + - - +
195E GLY* 2.7 30.0 + - - -
196E TYR* 3.0 33.3 + - + +
198E THR* 3.4 25.4 - - - +
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Residues in contact with ASP 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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183E ALA 5.0 3.1 - - - +
188E LYS* 2.6 57.5 + - - +
189E THR* 3.7 8.5 - - + +
191E ALA* 1.3 79.8 - - - +
193E ASN* 1.3 64.9 + - - +
195E GLY* 3.6 7.7 + - - -
198E THR* 5.2 1.4 + - - -
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Residues in contact with ASN 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 THR* 3.1 35.6 + - - +
190E LEU* 3.1 6.0 + - + +
192E ASP* 1.3 81.7 - - - +
194E GLU* 1.3 68.5 + - + +
346F ASN* 5.3 8.5 - - - +
348F LEU* 4.3 11.3 - - - +
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Residues in contact with GLU 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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160E ARG* 4.7 8.9 + - - +
164E GLU* 5.2 0.5 - - - +
169E LYS* 4.1 28.1 + - - +
173E ARG* 3.1 25.9 - - + +
190E LEU* 2.7 42.5 + - + +
193E ASN* 1.3 79.6 - - - +
195E GLY* 1.3 58.8 + - - +
196E TYR* 3.5 34.5 + - + +
346F ASN* 5.4 5.4 + - - -
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Residues in contact with GLY 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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173E ARG* 2.9 31.9 + - - +
191E ALA 2.7 12.0 + - - -
192E ASP 3.6 6.5 + - - -
193E ASN 3.3 2.6 + - - -
194E GLU* 1.3 80.4 - - - +
196E TYR* 1.3 61.2 + - - -
197E GLU 3.9 0.2 + - - -
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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