Contacts of the helix formed by residues 251 - 266 (chain B) in PDB entry 2JG1
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 GLY 251 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ASN* 4.8 0.4 - - - -
250B VAL* 1.3 73.9 - - - +
252B SER* 1.3 59.7 + - - +
253B GLY 3.3 2.7 - - - -
254B ASP* 3.4 18.1 + - - +
255B SER* 2.8 30.5 + - - -
284B ASN* 3.1 8.7 + - - +
290B THR* 3.9 11.7 - - - -
291B GLY* 4.5 2.6 - - - -
1312B ANP 3.0 20.8 + - - -
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Residues in contact with SER 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B PRO 3.0 19.0 + - - -
251B GLY* 1.3 77.3 - - - +
253B GLY* 1.3 61.1 + - - +
255B SER* 4.2 0.2 - - - -
256B THR* 2.8 32.7 + - - -
281B GLY* 2.8 25.9 + - - -
284B ASN* 3.1 12.2 + - - +
285B ALA* 3.5 12.3 + - - +
1312B ANP 3.3 30.5 + - - -
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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
----------------------------------------------------------
163B ASP* 4.3 3.8 - - - -
183B LYS* 3.5 13.9 - - - +
252B SER* 1.3 78.1 - - - +
254B ASP* 1.3 57.3 + - - +
256B THR* 3.2 3.3 + - - -
257B VAL* 2.9 32.4 + - - +
1311B MG 4.6 0.2 - - - -
1312B ANP 2.9 40.6 + - - -
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Residues in contact with ASP 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LYS* 3.0 49.3 + - - +
41B ASN* 2.9 41.7 + - + -
42B VAL* 3.4 23.2 - - + +
45B VAL* 6.3 0.2 - - + -
134B SER* 5.0 0.5 - - - -
163B ASP* 3.9 6.6 - - - +
251B GLY* 3.5 13.9 - - - +
252B SER 3.3 0.4 - - - -
253B GLY* 1.3 75.7 - - - +
255B SER* 1.3 57.3 + - - +
257B VAL* 3.4 3.2 + - - -
258B ALA* 3.0 24.1 + - - +
1312B ANP 3.0 7.0 + - - -
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Residues in contact with SER 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B VAL* 3.8 21.7 - - - +
251B GLY 2.8 21.1 + - - -
252B SER 3.7 4.0 - - - -
254B ASP* 1.3 72.8 - - - +
256B THR* 1.3 60.7 + - - +
258B ALA* 3.3 9.4 + - - +
259B GLY 3.0 22.9 + - - -
280B LEU* 3.3 39.0 - - - +
284B ASN* 3.3 18.3 + - - +
291B GLY* 4.3 1.2 - - - -
293B VAL* 4.4 0.8 - - - +
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Residues in contact with THR 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LYS* 3.8 22.9 - - + -
220B ILE* 5.1 5.2 - - + -
222B SER* 5.4 2.7 - - - -
252B SER 2.8 24.2 + - - -
253B GLY* 3.2 7.4 + - - -
255B SER* 1.3 74.7 - - - +
257B VAL* 1.3 58.4 + - - +
259B GLY* 3.1 2.9 + - - -
260B ILE* 2.8 36.4 + - + +
277B ALA* 3.3 37.6 + - + +
278B ASN* 4.9 2.9 - - - +
281B GLY* 3.7 1.7 - - - -
1312B ANP 3.4 20.5 - - - +
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Residues in contact with VAL 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 3.9 22.0 - - + -
132B ALA* 4.4 5.2 - - + -
134B SER* 4.4 7.6 - - - +
161B ILE* 3.9 22.2 - - + +
163B ASP* 3.4 31.0 - - + +
183B LYS* 3.7 19.1 - - + -
253B GLY 2.9 17.2 + - - +
254B ASP 3.5 8.3 - - - +
255B SER 3.3 0.2 - - - -
256B THR* 1.3 76.8 - - - +
258B ALA* 1.3 57.0 + - - +
260B ILE* 3.3 8.2 + - + +
261B THR* 2.9 38.6 + - - +
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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
----------------------------------------------------------
42B VAL* 3.7 28.7 - - + +
45B VAL* 3.6 26.2 - - + -
46B LEU* 3.3 20.2 - - + +
49B VAL* 5.9 0.4 - - + -
254B ASP 3.0 12.5 + - - +
255B SER 3.3 9.6 + - - +
257B VAL* 1.3 75.0 - - - +
259B GLY* 1.3 56.5 + - - +
261B THR* 3.4 1.0 + - - -
262B SER* 3.0 26.3 + - - -
280B LEU* 4.4 2.2 - - + -
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Residues in contact with GLY 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B SER 3.0 12.1 + - - -
256B THR 3.1 4.0 + - - -
258B ALA* 1.3 72.6 - - - +
260B ILE* 1.3 65.5 + - - +
262B SER* 3.4 1.7 + - - -
263B ALA* 3.0 20.1 + - - +
276B LYS* 3.5 22.2 - - - +
277B ALA* 4.2 8.7 - - - -
280B LEU* 3.5 21.9 - - - +
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Residues in contact with ILE 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ILE* 4.1 11.0 - - + -
181B VAL* 3.9 35.9 - - + -
183B LYS* 4.3 17.3 - - + -
220B ILE* 3.7 28.7 - - + -
256B THR* 2.8 40.5 + - + +
257B VAL* 3.7 9.2 - - + +
259B GLY* 1.3 71.8 - - - +
261B THR* 1.3 58.3 + - - +
263B ALA* 3.2 7.5 + - - +
264B ILE* 2.9 31.1 + - + +
273B LEU* 4.3 10.5 - - + +
277B ALA* 3.8 14.3 - - + +
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Residues in contact with THR 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ILE* 3.6 38.1 - - + -
46B LEU* 4.7 3.4 - - - -
130B ALA* 4.0 7.2 - - + -
132B ALA* 3.7 16.9 - - + +
161B ILE* 3.7 37.8 - - + +
257B VAL 2.9 17.6 + - - -
258B ALA* 3.9 5.1 - - - -
260B ILE* 1.3 74.6 - - - +
262B SER* 1.3 60.9 + - - +
264B ILE* 3.3 1.3 + - - +
265B LEU* 2.9 30.1 + - - +
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Residues in contact with SER 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ILE* 4.2 6.6 - - - +
46B LEU* 4.2 2.0 - - - -
49B VAL* 4.2 6.5 - - - +
51B GLU* 2.4 41.5 + - - -
258B ALA 3.0 17.9 + - - -
259B GLY* 3.5 5.8 - - - -
261B THR* 1.3 75.8 - - - +
263B ALA* 1.3 62.2 + - - +
265B LEU* 3.4 0.9 + - - +
266B ASN* 3.0 30.7 + - - -
268B GLU* 4.5 0.2 - - - -
276B LYS* 2.9 25.4 + - - +
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Residues in contact with ALA 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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259B GLY 3.0 16.6 + - - +
260B ILE 3.2 4.5 + - - +
262B SER* 1.3 75.1 + - - +
264B ILE* 1.3 59.4 + - - +
266B ASN 3.5 0.7 + - - -
267B HIS* 3.0 7.6 + - - -
268B GLU* 2.9 57.0 + - + +
273B LEU* 3.6 34.1 - - + -
276B LYS* 4.6 1.6 - - + -
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Residues in contact with ILE 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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130B ALA* 4.9 3.4 - - + -
159B PRO* 3.8 34.1 - - + -
161B ILE* 4.4 12.3 - - + -
180B THR* 5.1 5.6 - - + -
181B VAL* 4.4 11.9 - - + -
217B GLU* 5.8 1.8 - - - +
218B TRP* 4.3 19.7 - - + +
260B ILE* 2.9 29.8 + - + +
261B THR 3.9 2.9 - - - +
263B ALA* 1.3 72.3 - - - +
265B LEU* 1.3 69.5 + - - +
267B HIS* 3.2 24.3 + - + +
273B LEU* 3.8 20.9 - - + -
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Residues in contact with LEU 265 (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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0B HIS* 3.6 38.5 - - + +
1B MSE 4.0 15.0 - - - +
2B ILE* 3.9 25.4 - - + -
51B GLU* 3.6 23.1 - - - +
52B PRO* 4.2 16.4 - - + +
129B GLU* 3.8 34.7 - - + +
130B ALA* 4.7 4.4 - - + +
261B THR 2.9 17.4 + - - +
262B SER 3.5 4.5 - - - +
264B ILE* 1.3 78.6 - - - +
266B ASN* 1.3 60.2 + - - +
267B HIS* 3.6 13.3 + - - -
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Residues in contact with ASN 266 (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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0B HIS* 4.4 11.4 + - - -
51B GLU* 3.1 31.3 + - - +
262B SER* 3.0 24.6 + - - +
264B ILE 3.2 0.2 - - - -
265B LEU* 1.3 80.4 - - - +
267B HIS* 1.3 71.0 + - - +
268B GLU* 3.3 21.8 + - + +
276B LYS* 5.0 0.2 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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