Contacts of the helix formed by residues 249 - 260 (chain B) in PDB entry 3ANX
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 SER 249 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248B PHE* 1.3 87.0 - - - +
250B GLU* 1.4 61.2 + - - +
251B GLY* 3.0 15.2 + - - -
252B VAL* 3.2 27.8 + - - +
253B ILE* 3.8 15.6 + - - +
273B GLU* 3.9 3.3 - - - +
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Residues in contact with GLU 250 (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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249B SER* 1.4 70.2 + - - +
251B GLY* 1.3 62.9 + - - +
252B VAL 3.3 1.7 + - - -
253B ILE* 4.1 4.3 - - + +
254B GLU* 3.4 24.1 + - - +
269B ALA* 4.1 14.7 - - + +
270B PRO* 3.6 32.8 - - + +
273B GLU* 3.1 34.2 + - - +
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Residues in contact with GLY 251 (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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249B SER* 3.0 9.2 + - - -
250B GLU* 1.3 76.4 - - - +
252B VAL* 1.3 57.2 + - - +
254B GLU* 3.4 8.2 - - - +
255B ALA* 3.2 22.3 + - - +
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Residues in contact with VAL 252 (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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248B PHE* 6.1 0.4 - - + -
249B SER* 3.2 34.8 - - - +
250B GLU 3.3 0.4 - - - -
251B GLY* 1.3 76.9 - - - +
253B ILE* 1.3 69.1 + - + +
255B ALA* 2.9 25.3 - - + +
256B ARG* 3.0 45.5 + - + +
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Residues in contact with ILE 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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73B LEU* 4.3 29.0 - - + +
74B THR* 4.5 7.6 - - + -
248B PHE* 3.6 43.1 - - + -
249B SER 3.8 9.0 + - - +
250B GLU* 3.8 5.6 + - - +
251B GLY 3.6 0.2 - - - -
252B VAL* 1.3 86.6 - - + +
254B GLU* 1.3 65.1 + - - +
256B ARG* 3.0 8.4 + - - +
257B ILE* 3.0 34.1 + - + +
269B ALA* 3.5 29.8 - - + +
272B LEU* 4.5 17.0 - - + -
273B GLU* 6.0 1.6 - - + -
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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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250B GLU* 3.4 14.8 + - - +
251B GLY* 3.4 13.7 - - - +
253B ILE* 1.3 76.2 - - - +
255B ALA* 1.3 71.2 + - - +
257B ILE* 3.8 7.7 - - - +
258B ARG* 2.6 78.9 + - - +
269B ALA* 3.4 20.4 + - + +
270B PRO* 4.8 3.3 - - - +
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Residues in contact with ALA 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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251B GLY 3.2 9.7 + - - +
252B VAL* 2.9 20.0 - - + +
254B GLU* 1.3 83.0 - - - +
256B ARG* 1.3 58.9 + - + +
258B ARG* 3.6 3.3 - - - +
259B GLU* 2.7 38.6 + - + +
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Residues in contact with ARG 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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73B LEU* 3.0 42.3 + - + +
74B THR* 3.6 14.6 + - - +
76B PRO* 3.6 39.6 + - - +
252B VAL* 3.0 38.8 + - - +
253B ILE* 3.0 5.7 + - - +
255B ALA* 1.3 80.4 - - + +
257B ILE* 1.3 58.1 + - - +
259B GLU* 3.6 9.6 - - + -
260B ARG* 3.0 52.0 + - - +
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Residues in contact with ILE 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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73B LEU* 3.8 26.9 - - + -
253B ILE* 3.0 28.6 + - + +
254B GLU* 3.8 7.4 - - - +
256B ARG* 1.3 77.5 - - - +
258B ARG* 1.3 70.3 + - + +
260B ARG 3.1 0.2 + - - -
261B ASN* 3.1 17.2 + - - -
262B LEU* 3.6 23.8 + - + +
264B LEU* 4.1 31.2 - - + -
267B LEU* 6.0 0.2 - - + -
268B THR* 4.6 4.7 - - - -
269B ALA* 4.3 19.1 - - + +
272B LEU* 5.5 2.5 - - + -
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Residues in contact with ARG 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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254B GLU* 2.6 54.5 + - + +
255B ALA* 3.6 3.6 - - - +
257B ILE* 1.3 80.2 - - + +
259B GLU* 1.3 63.7 + - - +
261B ASN* 3.0 23.1 + - - +
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Residues in contact with GLU 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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255B ALA* 2.7 24.5 + - + +
256B ARG* 3.4 14.8 - - + +
258B ARG* 1.3 77.5 - - - +
260B ARG* 1.3 66.2 + - + +
261B ASN* 3.2 12.1 + - - +
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Residues in contact with ARG 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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72B MET* 3.1 20.6 + - - +
73B LEU* 3.9 10.4 - - - +
75B HIS 2.6 31.1 + - - -
76B PRO 4.0 8.9 + - - -
78B PRO* 3.3 18.6 - - - +
97B LYS 4.1 1.7 - - - +
98B HIS* 3.1 39.0 + - - -
99B PRO* 3.4 41.4 - - + +
100B THR* 4.6 11.3 + - + +
256B ARG* 3.0 35.1 + - - +
257B ILE 3.6 0.7 - - - +
259B GLU* 1.3 82.8 + - + +
261B ASN* 1.3 69.0 + - - +
262B LEU* 3.0 9.4 + - + -
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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