Contacts of the helix formed by residues 252 - 260 (chain B) in PDB entry 4WMJ
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 252 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214B LYS 3.7 1.1 + - - +
215B THR* 3.0 32.3 + - - +
216B PHE* 4.1 2.0 - - + -
217B THR* 4.8 1.0 - - - +
250B SER* 3.2 7.1 + - - +
251B THR* 1.3 78.2 + - - +
253B GLY* 1.3 60.3 + - - +
254B GLU* 3.3 12.5 + - - +
255B LYS* 3.1 39.8 + - - +
256B VAL* 3.0 25.6 + - - +
266B MET* 3.8 2.5 - - - -
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Residues in contact with GLY 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B THR 3.3 7.5 + - - -
252B ASN* 1.3 73.7 - - - +
254B GLU* 1.4 57.6 + - - +
256B VAL* 4.3 1.8 - - - -
257B THR* 2.7 40.2 + - - +
263B PRO* 5.4 3.6 - - - -
266B MET* 3.6 21.9 - - - +
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Residues in contact with GLU 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B ASN* 3.1 8.9 + - - +
253B GLY* 1.4 77.0 - - - +
255B LYS* 1.3 74.9 + - + +
257B THR* 2.9 19.5 + - - -
258B ALA* 2.9 18.8 + - + +
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Residues in contact with LYS 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B THR 4.2 0.2 - - - +
216B PHE* 3.8 22.1 - - + +
217B THR* 3.6 29.4 - - + +
252B ASN* 3.1 35.5 + - - +
254B GLU* 1.3 87.9 + - + +
256B VAL* 1.3 65.1 + - - +
258B ALA* 3.4 7.0 + - + +
259B PHE* 3.1 23.2 + - - +
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Residues in contact with VAL 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B PHE* 3.7 26.0 - - + -
248B ALA* 3.7 25.4 - - + -
250B SER* 3.9 3.8 - - - +
252B ASN 3.0 22.0 + - - +
253B GLY* 4.0 3.1 - - - +
255B LYS* 1.3 76.1 - - - +
257B THR* 1.3 66.9 + - + +
259B PHE* 3.1 10.4 + - - +
260B GLY 3.3 0.2 + - - -
261B ILE* 3.1 51.7 + - + +
262B ASP 4.9 1.8 - - - +
263B PRO* 5.0 0.7 - - + -
266B MET* 3.8 24.9 - - + -
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Residues in contact with THR 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B GLY* 2.7 27.8 + - - +
254B GLU* 2.9 12.5 + - - -
256B VAL* 1.3 77.0 - - + +
258B ALA* 1.3 58.5 + - - +
260B GLY* 2.9 19.6 + - - -
261B ILE 3.3 9.9 - - - +
263B PRO* 3.6 40.8 - - + -
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Residues in contact with ALA 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B LYS* 4.8 2.6 + - - -
254B GLU* 2.9 20.3 + - + +
255B LYS* 3.7 8.3 - - + +
256B VAL 3.2 0.2 - - - -
257B THR* 1.3 79.1 + - - +
259B PHE* 1.4 59.3 + - - +
260B GLY 3.5 0.5 + - - -
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Residues in contact with PHE 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B ILE* 4.8 2.7 - - + -
216B PHE* 4.0 17.5 - + + -
222B ILE* 5.3 5.2 - - + -
225B ALA* 3.6 37.0 - - + -
226B THR* 3.8 28.0 - - + -
229B LYS* 2.7 53.7 + - + +
242B VAL* 4.2 2.7 - - + +
246B PHE* 3.8 26.2 - + - -
255B LYS 3.1 12.5 + - - +
256B VAL 3.1 10.7 + - - +
258B ALA* 1.4 77.8 - - - +
260B GLY* 1.3 56.6 + - - +
261B ILE* 3.8 22.7 - - + -
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Residues in contact with GLY 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B PRO 4.9 3.8 - - - +
242B VAL* 3.4 25.2 - - - +
243B SER* 3.8 13.5 + - - -
257B THR 2.9 11.8 + - - -
258B ALA 3.2 1.0 - - - -
259B PHE* 1.3 80.0 - - - +
261B ILE* 1.3 63.5 + - - +
262B ASP 3.8 0.5 + - - -
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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