Contacts of the helix formed by residues 254 - 262 (chain E) in PDB entry 1MDU
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 254 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229E MET* 4.0 24.6 + - - +
232E ALA* 3.9 18.3 - - + +
233E ALA 6.0 0.2 - - - +
239E GLU* 4.6 1.0 + - - -
253E GLY* 1.3 71.3 - - - +
255E GLU* 1.3 65.4 + - - +
256E ARG 3.0 0.6 + - - -
257E PHE* 3.2 32.3 + - + -
258E ARG* 2.9 56.1 + - - +
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Residues in contact with GLU 255 (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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191E LEU* 4.3 10.7 - - + +
194E ILE* 3.6 24.6 - - + +
195E LEU* 4.8 2.8 - - + +
198E ARG* 2.6 41.8 + - - +
219E CYS* 4.2 2.3 - - - -
252E ILE* 4.0 13.2 - - + -
253E GLY 2.7 31.4 + - - -
254E ASN* 1.3 89.3 + - - +
256E ARG* 1.3 62.0 + - - +
258E ARG* 3.4 25.8 + - - +
259E CYS* 3.3 26.5 + - - +
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Residues in contact with ARG 256 (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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217E LYS 5.7 0.4 + - - -
218E LEU* 2.8 31.0 + - - +
219E CYS* 3.1 13.9 - - - +
220E TYR* 3.0 54.2 + - + -
237E SER 5.3 0.2 + - - -
238E LEU* 3.0 38.4 + - - +
240E LYS* 3.3 42.8 - - - +
252E ILE* 3.4 32.3 - - + +
253E GLY 3.2 11.2 - - - +
255E GLU* 1.3 78.2 - - - +
257E PHE* 1.3 57.5 + - - +
260E PRO* 3.2 9.2 - - - +
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Residues in contact with PHE 257 (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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220E TYR* 3.1 49.0 - + + +
221E VAL* 5.1 0.3 - - - -
222E ALA* 4.2 9.5 + - + +
225E PHE* 3.7 20.0 - + - -
228E GLU* 3.3 40.6 - - + -
229E MET* 3.6 24.2 - - - -
232E ALA* 4.2 0.7 - - + -
238E LEU* 3.8 22.9 - - + -
253E GLY 4.3 3.6 - - - -
254E ASN* 3.5 33.4 - - + -
256E ARG* 1.3 75.0 - - - +
258E ARG* 1.3 60.9 + - - +
259E CYS 3.2 2.2 - - - -
260E PRO* 3.2 2.5 - - - +
261E GLU* 3.1 29.1 + - - +
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Residues in contact with ARG 258 (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 TYR* 3.6 31.2 + - + +
194E ILE* 4.0 20.9 - - + +
225E PHE* 4.0 22.4 - - + -
229E MET* 4.2 16.2 - - - -
254E ASN* 2.9 48.3 + - - +
255E GLU* 3.4 26.2 + - - +
257E PHE* 1.3 75.1 - - + +
259E CYS* 1.3 66.8 + - - +
261E GLU* 3.3 17.6 + - - +
268E PHE* 3.6 12.1 - - + -
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Residues in contact with CYS 259 (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 LEU* 3.4 42.0 - - - +
190E TYR* 3.6 17.8 - - + -
191E LEU* 4.2 15.7 - - + -
194E ILE* 5.4 1.3 - - + +
215E LYS* 4.5 6.1 - - - -
219E CYS* 4.1 16.6 - - - -
255E GLU 3.3 16.1 + - - +
258E ARG* 1.3 79.7 - - - +
260E PRO* 1.3 67.4 - - + +
262E THR* 2.8 26.2 + - - -
308E TYR* 4.8 0.2 - - - -
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Residues in contact with PRO 260 (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 LEU* 4.5 11.4 - - + -
219E CYS* 3.8 15.5 - - + -
220E TYR 3.6 15.0 - - - +
221E VAL* 3.8 23.7 - - + +
256E ARG 3.2 15.0 - - - +
257E PHE 3.2 13.0 - - - +
259E CYS* 1.3 90.3 - - + +
261E GLU* 1.3 63.3 + - - +
262E THR 2.9 4.3 + - - -
263E LEU* 3.1 22.4 + - + +
264E PHE* 4.2 5.2 - - - -
308E TYR* 3.9 22.9 - - + -
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Residues in contact with GLU 261 (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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221E VAL* 4.7 4.4 - - - +
222E ALA 4.8 3.1 + - - -
225E PHE* 3.5 28.2 - - + +
257E PHE 3.1 19.2 + - - +
258E ARG 3.4 9.6 - - - +
259E CYS 3.2 1.0 - - - -
260E PRO* 1.3 76.5 - - - +
262E THR* 1.3 52.5 + - - +
264E PHE* 2.8 29.9 + - - +
265E GLN* 2.9 35.6 + - - +
268E PHE* 3.4 23.8 - - + -
314E ARG* 2.7 45.8 + - - -
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Residues in contact with THR 262 (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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182E LEU* 3.6 19.3 - - + +
187E LEU* 4.1 8.5 - - + -
190E TYR* 3.8 15.8 - - - -
258E ARG 3.7 6.9 + - - -
259E CYS 2.8 21.4 + - - -
261E GLU* 1.3 77.8 - - - +
263E LEU* 1.3 60.9 + - - +
265E GLN 3.0 31.0 - - - +
266E PRO* 3.0 9.3 - - + +
268E PHE* 3.8 8.3 - - + +
269E ILE* 3.6 35.2 - - + -
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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