Contacts of the helix formed by residues 253 - 264 (chain B) in PDB entry 3JW8
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 ASP 253 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160B LEU* 4.4 18.4 - - + +
163B PRO* 6.1 5.8 - - + -
245B GLN* 4.3 1.4 + - - +
249B ASP 3.8 14.1 + - - +
250B ARG 5.2 0.9 - - - -
251B LEU 3.9 3.0 + - - -
252B CYS* 1.3 74.2 - - - +
254B SER* 1.3 67.3 + - - +
255B LYS* 3.0 55.3 + - - +
256B GLY* 2.9 16.8 + - - -
257B ALA 4.1 1.4 + - - -
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Residues in contact with SER 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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262A GLU* 5.3 1.6 + - - +
245B GLN* 3.6 20.0 - - - +
246B GLY 3.8 18.8 + - - -
247B SER* 4.3 17.0 + - - -
249B ASP 4.6 2.6 + - - +
252B CYS 3.4 2.4 + - - -
253B ASP* 1.3 72.8 + - - +
255B LYS* 1.3 81.9 + - - +
257B ALA* 3.0 16.5 + - - +
258B TYR* 3.3 26.8 - - - -
273B ILE* 4.8 2.5 - - - -
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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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262A GLU* 3.6 26.2 + - - +
160B LEU* 4.5 9.4 - - + +
253B ASP* 3.0 36.0 + - + +
254B SER* 1.3 89.6 + - - +
256B GLY* 1.3 61.6 + - - +
258B TYR* 3.4 16.0 + - + +
259B LEU* 3.1 23.7 + - - +
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Residues in contact with GLY 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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159B VAL* 3.7 19.5 - - - +
160B LEU* 3.7 30.3 - - - +
253B ASP 2.9 10.7 + - - -
255B LYS* 1.3 78.3 - - - +
257B ALA* 1.3 56.6 + - - +
259B LEU* 3.3 4.0 + - - +
260B LEU* 2.9 29.6 + - - +
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Residues in contact with ALA 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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157B PRO* 5.9 1.1 - - + -
159B VAL* 5.2 1.3 - - - +
243B LEU* 3.3 31.0 - - + +
245B GLN* 3.6 38.5 + - + +
253B ASP 4.1 1.6 + - - -
254B SER 3.0 11.7 + - - +
256B GLY* 1.3 74.3 - - - +
258B TYR* 1.4 64.1 + - - +
260B LEU* 3.3 3.1 + - - -
261B MSE 3.2 20.5 + - - +
271B LEU* 4.3 6.5 - - + -
273B ILE* 5.1 2.0 - - + -
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Residues in contact with TYR 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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258A TYR* 3.7 36.9 - + + -
261A MSE 3.6 16.1 + - + -
262A GLU* 3.4 40.5 + - + +
247B SER* 6.1 0.2 - - - -
254B SER* 3.3 42.4 + - - -
255B LYS* 3.4 14.5 + - + +
257B ALA* 1.4 75.6 - - + +
259B LEU* 1.3 62.8 + - - +
261B MSE 3.3 7.8 + - - +
262B GLU* 3.0 24.1 + - - +
271B LEU* 3.8 22.2 - - + -
273B ILE* 3.5 24.7 - - + +
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Residues in contact with LEU 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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159B VAL* 4.6 7.2 - - + -
160B LEU* 4.3 20.6 - - + -
231B GLU* 5.9 6.5 - - + -
234B LEU* 4.4 12.1 - - + -
255B LYS 3.1 14.3 + - - +
256B GLY 3.5 6.5 - - - +
257B ALA 3.3 0.2 - - - -
258B TYR* 1.3 77.4 - - - +
260B LEU* 1.3 57.5 + - - +
262B GLU* 3.3 12.5 + - - +
263B LEU* 2.9 62.8 + - + +
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Residues in contact with LEU 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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139B ILE* 4.2 8.1 - - + -
154B LEU* 3.7 27.6 - - + -
157B PRO* 4.2 9.6 - - + -
159B VAL* 4.3 7.4 - - + -
234B LEU* 3.4 37.4 - - + +
237B LEU* 3.8 19.7 - - + -
241B PHE* 4.2 9.6 - - + -
243B LEU* 3.8 23.8 - - + -
256B GLY 2.9 16.3 + - - +
257B ALA* 3.3 5.4 + - - +
259B LEU* 1.3 75.9 - - - +
261B MSE 1.3 60.3 + - - +
264B ALA* 3.1 35.4 + - + +
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Residues in contact with MSE 261 (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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258A TYR* 3.6 17.8 + - + -
271A LEU* 3.6 27.6 - - + +
273A ILE* 3.7 32.9 - - + +
241B PHE* 3.9 22.9 - - - -
243B LEU* 3.9 4.9 - - + -
257B ALA 3.2 16.9 + - - +
258B TYR 3.5 8.5 - - - +
260B LEU* 1.3 76.3 - - - +
262B GLU* 1.3 54.9 + - - +
269B LYS* 2.7 58.1 + - + +
270B THR 3.9 6.1 - - - -
271B LEU* 3.6 34.5 - - + +
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Residues in contact with GLU 262 (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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254A SER* 5.5 2.8 + - - +
258A TYR* 3.4 26.5 - - + +
273A ILE* 6.0 0.2 - - - -
275A GLU* 4.2 8.8 - - - +
258B TYR 3.0 16.6 + - - +
259B LEU* 3.9 12.5 - - - +
260B LEU 3.2 0.2 - - - -
261B MSE 1.3 81.0 - - - +
263B LEU* 1.3 74.3 + - + +
264B ALA 4.1 0.9 - - - +
265B LYS* 5.4 0.9 + - - -
269B LYS* 4.0 6.5 + - - -
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Residues in contact with LEU 263 (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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231B GLU* 5.5 6.5 - - + +
234B LEU* 3.5 31.5 - - + +
235B PRO* 3.6 14.1 - - + +
259B LEU* 2.9 51.6 + - + +
262B GLU* 1.3 84.5 - - + +
264B ALA* 1.3 62.6 + - - +
265B LYS* 2.9 29.5 + - - +
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Residues in contact with ALA 264 (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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275A GLU* 3.7 5.0 - - - +
234B LEU* 3.4 13.5 - - - +
237B LEU* 4.3 7.0 - - + +
241B PHE* 3.7 29.8 - - + -
260B LEU* 3.1 28.1 + - + +
262B GLU 3.6 0.2 - - - -
263B LEU* 1.3 78.1 - - - +
265B LYS* 1.3 60.5 + - - +
266B SER* 3.3 4.5 - - - +
269B LYS* 2.7 30.0 + - + -
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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