Contacts of the helix formed by residues 297 - 308 (chain B) in PDB entry 1X3W
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 297 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B HIS* 2.6 25.2 + - - +
296B ALA* 1.3 78.1 + - + +
298B PRO* 1.3 69.7 - - - +
299B GLU* 3.4 17.0 - - - +
300B VAL* 3.0 42.3 + - + +
301B PHE* 3.1 14.6 + - - +
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Residues in contact with PRO 298 (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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15A ILE* 3.6 31.2 - - + +
18A MSE 4.6 5.4 - - + -
294B ILE* 3.2 22.6 - - + +
295B MSE 4.9 1.1 - - - +
296B ALA 3.4 8.5 - - - +
297B ASN* 1.3 84.4 - - - +
299B GLU* 1.3 71.3 + - - +
301B PHE* 2.9 22.4 - - + +
302B VAL 3.3 2.4 + - - -
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Residues in contact with GLU 299 (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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18A MSE 3.3 37.3 - - - +
22A LYS* 4.4 18.0 - - + +
297B ASN* 3.4 18.8 - - - +
298B PRO* 1.3 78.1 - - - +
300B VAL* 1.3 54.6 + - - +
302B VAL* 2.6 37.6 + - + +
303B SER* 3.3 5.9 + - - +
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Residues in contact with VAL 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B HIS* 4.6 19.3 - - + +
297B ASN* 3.0 35.7 + - + +
298B PRO 3.4 0.8 - - - -
299B GLU* 1.3 72.7 - - - +
301B PHE* 1.3 69.2 + - - +
303B SER* 3.3 18.4 + - - +
304B MSE 3.4 41.8 - - + +
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Residues in contact with PHE 301 (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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12A PHE* 5.6 0.7 - + - -
15A ILE* 4.9 9.2 - - + -
19A LEU* 5.3 0.2 - - + -
255B ILE* 4.7 5.0 - - + +
257B LEU* 5.9 2.9 - - + -
265B LEU* 6.1 0.2 - - + -
280B LEU* 3.2 45.8 - - + -
283B ILE* 5.0 9.6 - - + -
284B SER* 5.8 0.2 - - - -
290B LEU* 5.5 14.1 - - + -
293B HIS* 4.8 5.1 + - + +
294B ILE* 3.4 45.3 - - + +
297B ASN 3.1 11.1 + - - +
298B PRO* 2.9 19.2 + - + +
300B VAL* 1.3 80.5 - - - +
302B VAL* 1.3 55.9 + - + -
303B SER 3.1 0.5 + - - -
304B MSE 3.5 3.1 + - - +
305B LEU* 2.7 61.7 - - + +
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Residues in contact with VAL 302 (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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15A ILE* 3.8 27.1 - - + -
18A MSE 4.1 15.7 - - + -
19A LEU* 3.7 32.3 - - + -
22A LYS* 4.2 27.1 - - + -
298B PRO 3.9 0.2 - - - +
299B GLU* 2.6 20.3 + - + +
301B PHE* 1.3 75.6 - - + +
303B SER* 1.3 67.3 + - - +
305B LEU* 3.0 28.9 - - + +
306B LEU* 3.1 15.1 - - + +
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Residues in contact with SER 303 (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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299B GLU* 3.5 3.6 + - - +
300B VAL* 3.3 33.6 - - - +
301B PHE 3.1 0.4 + - - -
302B VAL* 1.3 77.7 - - - +
304B MSE 1.3 59.1 + - - -
305B LEU 2.4 16.5 + - - -
306B LEU* 2.8 20.0 - - - +
307B GLU* 3.1 10.8 - - - +
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Residues in contact with MSE 304 (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 SER* 3.6 36.3 - - - +
255B ILE* 3.8 35.7 - - + +
262B LEU* 5.7 0.7 - - - +
300B VAL* 3.4 40.2 - - + +
301B PHE 3.5 3.2 + - - -
302B VAL 3.3 0.4 + - - -
303B SER* 1.3 78.4 - - - +
305B LEU* 1.3 59.2 + - + +
307B GLU* 3.3 32.8 - - + +
308B ALA* 3.7 6.6 + - - +
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Residues in contact with LEU 305 (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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19A LEU* 3.9 24.5 - - + -
255B ILE* 3.6 24.5 - - + -
257B LEU* 5.5 3.6 - - + -
262B LEU* 5.6 1.3 - - - +
265B LEU* 4.7 22.1 - - + +
280B LEU* 5.1 1.1 - - + -
301B PHE* 2.7 63.3 - - + +
302B VAL* 3.0 19.3 - - + +
303B SER 2.4 16.4 + - - -
304B MSE 1.3 67.8 - - - +
306B LEU* 1.3 60.4 + - + +
307B GLU 3.1 0.4 - - - -
308B ALA* 2.8 34.4 + - - +
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Residues in contact with LEU 306 (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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19A LEU* 4.4 9.6 - - + +
22A LYS* 3.3 35.4 - - + +
23A TYR* 3.6 26.0 - - + -
26A PHE* 3.5 33.3 - - + -
302B VAL* 3.1 20.2 - - + +
303B SER* 2.8 33.7 - - - +
305B LEU* 1.3 74.4 - - - +
307B GLU* 1.3 68.8 + - - +
308B ALA 3.0 1.6 + - - -
309B VAL* 3.1 29.6 - - - +
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Residues in contact with GLU 307 (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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26A PHE* 4.6 3.6 - - - -
254B SER* 6.0 1.6 - - - -
303B SER 3.1 20.6 + - - +
304B MSE 3.3 27.5 - - + +
306B LEU* 1.3 76.7 - - - +
308B ALA* 1.3 64.5 + - - +
309B VAL* 3.2 6.1 + - - +
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Residues in contact with ALA 308 (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 ILE* 6.0 2.0 - - + -
262B LEU* 3.9 33.7 - - + +
266B ARG* 3.9 13.9 + - - +
304B MSE 4.0 5.8 - - - +
305B LEU* 2.8 21.1 + - - +
306B LEU 3.3 2.7 - - - -
307B GLU* 1.3 80.2 + - - +
309B VAL* 1.3 58.9 + - - +
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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