Contacts of the helix formed by residues 252 - 260 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A LYS 3.7 1.5 + - - +
215A THR* 3.3 28.3 + - - +
216A PHE* 4.2 1.8 - - + -
217A THR* 5.3 0.4 - - - +
250A SER* 3.2 6.1 + - - +
251A THR* 1.3 77.4 - - + +
253A GLY* 1.3 59.2 + - - +
254A GLU* 2.6 29.3 + - - +
255A LYS* 3.0 43.6 + - + +
256A VAL* 3.0 23.6 + - - +
266A MET* 3.9 3.6 - - - -
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Residues in contact with GLY 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A THR 3.2 7.7 + - - -
252A ASN* 1.3 73.4 + - - +
254A GLU* 1.3 51.0 + - - +
256A VAL* 4.2 1.8 - - - -
257A THR* 2.5 47.3 + - - +
263A PRO* 4.9 5.4 - - - -
266A MET* 3.7 19.9 - - - +
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Residues in contact with GLU 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A ASN* 2.6 31.1 + - - +
253A GLY* 1.3 76.6 + - - +
255A LYS* 1.3 56.2 + - + +
257A THR* 2.4 20.8 + - - -
258A ALA* 2.8 24.1 + - - +
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Residues in contact with LYS 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A THR 4.3 4.0 - - - +
216A PHE* 4.0 21.5 - - + +
217A THR* 3.6 26.7 - - + +
252A ASN* 3.0 38.8 + - + +
254A GLU* 1.3 80.1 - - + +
256A VAL* 1.3 57.5 + - - +
258A ALA* 3.4 7.5 + - - +
259A PHE* 3.0 28.6 + - - +
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Residues in contact with VAL 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A PHE* 3.8 33.0 - - + -
248A ALA* 3.9 14.4 - - + -
250A SER* 4.0 2.5 - - - +
252A ASN 3.0 20.2 + - - +
253A GLY* 3.8 6.1 - - - +
255A LYS* 1.3 74.9 - - - +
257A THR* 1.3 65.9 + - - +
259A PHE* 3.2 4.3 + - - +
260A GLY 3.2 5.2 + - - -
261A ILE* 3.1 52.2 + - + +
263A PRO* 4.6 6.1 - - + -
266A MET* 3.8 25.6 - - + -
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Residues in contact with THR 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A GLY 2.5 23.3 + - - +
254A GLU* 2.4 27.0 + - - -
256A VAL* 1.3 73.5 - - - +
258A ALA* 1.3 54.2 + - - -
260A GLY* 2.9 21.8 + - - -
261A ILE 3.3 8.5 - - - +
263A PRO* 3.3 41.7 - - + -
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Residues in contact with ALA 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A LYS* 4.8 2.4 + - - -
254A GLU 2.8 20.1 + - - +
255A LYS* 3.7 8.7 - - - +
256A VAL 3.3 0.2 - - - -
257A THR* 1.3 74.4 + - - +
259A PHE* 1.3 61.1 + - - +
260A GLY* 3.2 0.7 - - - -
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Residues in contact with PHE 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A ILE* 4.8 2.0 - - + -
216A PHE* 3.9 17.7 - + + -
222A ILE* 5.6 4.0 - - + -
225A ALA* 3.5 32.8 - - + -
226A THR* 3.8 32.3 - - + -
229A LYS* 2.8 56.5 + - + +
242A VAL* 4.0 2.3 - - + +
246A PHE* 3.7 28.0 - + - -
255A LYS 3.0 16.7 + - - +
256A VAL 3.5 5.8 - - - +
257A THR 3.2 0.2 - - - -
258A ALA* 1.3 77.6 - - - +
260A GLY* 1.3 58.1 + - - +
261A ILE* 3.6 22.2 - - + -
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Residues in contact with GLY 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A PRO 5.2 3.1 - - - +
242A VAL* 3.6 13.3 - - - +
243A SER* 3.5 26.9 + - - -
257A THR 2.9 13.3 + - - -
258A ALA 3.2 0.9 - - - -
259A PHE* 1.3 78.9 - - - +
261A ILE* 1.3 64.2 + - - +
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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