Contacts of the helix formed by residues 251 - 266 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D LYS* 4.5 0.2 - - - -
41D ASN* 4.4 2.2 - - - -
250D VAL* 1.3 73.5 - - - +
252D SER* 1.3 57.6 + - - +
254D ASP* 3.3 16.5 + - - +
255D SER* 2.9 30.0 + - - -
284D ASN* 3.4 7.0 + - - +
290D THR* 4.1 12.8 - - - -
291D GLY* 4.6 4.0 - - - -
1312D ANP 2.7 26.2 + - - -
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Residues in contact with SER 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D PRO 2.9 16.4 + - - -
251D GLY* 1.3 75.6 - - - +
253D GLY* 1.3 59.1 + - - +
255D SER* 3.4 0.7 + - - -
256D THR* 2.9 31.0 + - - -
281D GLY* 2.6 24.1 + - - -
284D ASN* 3.1 19.5 + - - +
285D ALA* 3.4 11.8 + - - +
1312D ANP 3.4 32.7 + - - -
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Residues in contact with GLY 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D ASP* 4.5 2.7 - - - -
183D LYS* 3.9 6.9 - - - +
252D SER* 1.3 72.1 - - - +
254D ASP* 1.3 57.1 + - - -
256D THR* 3.3 4.9 + - - -
257D VAL* 3.0 33.8 + - - +
1312D ANP 2.7 53.0 + - - -
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Residues in contact with ASP 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D LYS* 2.8 59.0 + - - +
41D ASN* 3.0 37.2 + - + -
42D VAL* 3.6 16.4 - - + +
45D VAL* 6.3 0.2 - - + -
134D SER* 5.1 0.5 + - - -
163D ASP* 3.8 13.7 - - - +
251D GLY* 3.3 7.8 + - - +
253D GLY* 1.3 77.3 - - - +
255D SER* 1.3 56.4 + - - +
257D VAL* 3.2 5.7 + - - +
258D ALA* 3.0 25.3 + - - +
1312D ANP 2.9 8.5 + - - -
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Residues in contact with SER 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D VAL* 3.6 28.9 - - - +
251D GLY 2.9 16.8 + - - -
252D SER 3.5 8.3 - - - -
253D GLY 3.3 0.2 - - - -
254D ASP* 1.3 73.3 - - - +
256D THR* 1.3 63.0 + - - +
258D ALA* 3.3 4.7 + - - +
259D GLY 3.0 17.5 + - - -
280D LEU* 3.4 37.3 + - - +
284D ASN* 3.3 19.3 + - - +
291D GLY* 4.2 0.2 - - - -
293D VAL* 4.4 1.1 - - - +
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Residues in contact with THR 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D LYS* 3.9 18.8 - - + -
220D ILE* 5.1 6.1 - - + -
222D SER* 5.2 2.9 - - - -
252D SER 2.9 17.9 + - - -
253D GLY* 3.3 11.9 + - - -
255D SER* 1.3 73.9 - - - +
257D VAL* 1.3 59.0 + - - +
259D GLY* 3.0 3.6 + - - -
260D ILE* 2.8 34.7 + - + +
277D ALA* 3.1 38.0 + - + +
278D ASN* 4.6 4.0 - - - +
281D GLY* 3.7 1.4 - - - +
1312D ANP 3.3 22.1 - - - +
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Residues in contact with VAL 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D VAL* 3.9 23.3 - - + -
132D ALA* 4.3 7.2 - - + -
133D ILE 5.8 0.2 - - - +
134D SER* 4.6 4.9 - - - +
161D ILE* 4.0 20.2 - - + +
163D ASP* 3.6 29.8 - - + +
183D LYS* 4.0 20.9 - - + -
253D GLY 3.0 18.6 + - - +
254D ASP 3.2 8.5 + - - +
256D THR* 1.3 75.5 - - - +
258D ALA* 1.3 53.7 + - - +
260D ILE* 3.4 7.8 + - + +
261D THR* 2.7 41.1 + - - +
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Residues in contact with ALA 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D VAL* 3.7 29.1 - - + +
45D VAL* 3.7 21.8 - - + -
46D LEU* 3.2 24.0 - - + +
254D ASP 3.0 12.0 + - - +
255D SER 3.3 8.7 + - - +
257D VAL* 1.3 76.2 - - - +
259D GLY* 1.3 57.7 - - - +
261D THR* 3.5 1.2 + - - -
262D SER* 3.0 25.6 + - - -
280D LEU* 4.3 2.7 - - + -
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Residues in contact with GLY 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D SER 3.0 8.0 + - - -
256D THR 3.0 7.5 + - - -
258D ALA* 1.3 72.6 - - - +
260D ILE* 1.3 59.1 + - - +
262D SER* 3.3 1.7 + - - -
263D ALA* 2.9 26.8 + - - +
276D LYS* 3.5 23.2 - - - +
277D ALA* 4.1 9.2 - - - -
280D LEU* 3.5 20.3 - - - +
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Residues in contact with ILE 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D ILE* 3.9 12.3 - - + -
181D VAL* 3.9 33.0 - - + -
183D LYS* 3.8 31.9 - - + -
220D ILE* 3.8 25.8 - - + -
256D THR* 2.8 29.5 + - + +
257D VAL* 3.7 9.6 - - + +
259D GLY* 1.3 70.5 - - - +
261D THR* 1.3 58.1 + - - +
263D ALA* 3.1 8.1 + - - +
264D ILE* 2.8 31.9 + - + +
273D LEU* 4.3 9.4 - - + +
277D ALA* 3.8 14.7 - - + +
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Residues in contact with THR 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D ILE* 3.5 38.1 - - + -
46D LEU* 4.9 2.2 - - - -
130D ALA* 4.1 6.9 - - + +
132D ALA* 3.8 16.9 - - + +
161D ILE* 3.7 39.3 - - + +
257D VAL 2.7 22.2 + - - -
258D ALA* 3.9 5.4 - - - -
260D ILE* 1.3 72.0 - - - +
262D SER* 1.3 60.1 + - - +
264D ILE* 3.3 1.9 + - - +
265D LEU* 2.9 30.0 + - - +
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Residues in contact with SER 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D ILE* 4.2 9.7 - - - +
46D LEU* 4.3 1.6 - - - -
49D VAL* 4.6 5.0 - - - +
51D GLU* 2.5 37.7 + - - +
258D ALA 3.0 18.4 + - - -
259D GLY* 3.5 5.4 - - - -
261D THR* 1.3 77.0 - - - +
263D ALA* 1.3 61.4 + - - +
265D LEU* 3.4 1.4 + - - +
266D ASN* 2.8 30.4 + - - -
268D GLU* 4.4 0.2 - - - -
276D LYS* 2.8 27.5 + - - -
280D LEU* 5.9 0.9 - - - -
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Residues in contact with ALA 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259D GLY 2.9 13.6 + - - +
260D ILE 3.4 8.3 - - - +
262D SER* 1.3 78.3 + - - +
264D ILE* 1.3 61.0 + - - +
266D ASN 3.5 0.5 + - - -
267D HIS* 3.1 3.6 + - - -
268D GLU* 2.9 49.0 + - + +
273D LEU* 3.5 42.8 - - + +
276D LYS* 4.3 2.0 - - + +
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Residues in contact with ILE 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D ALA* 4.7 3.6 - - + -
159D PRO* 3.8 33.7 - - + -
161D ILE* 4.3 15.9 - - + -
180D THR* 4.8 7.9 - - + -
181D VAL* 4.2 15.7 - - + -
217D GLU* 5.9 1.6 - - - +
218D TRP* 4.3 11.0 - - + +
260D ILE* 2.8 29.6 + - + +
261D THR 3.7 4.7 - - - +
263D ALA* 1.3 73.6 - - - +
265D LEU* 1.3 64.4 + - - +
267D HIS* 3.1 24.6 + - - +
273D LEU* 3.8 20.9 - - + -
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Residues in contact with LEU 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0D HIS* 3.7 36.6 + - + +
1D MSE 4.0 22.2 - - - +
2D ILE* 3.9 24.2 - - + -
51D GLU* 3.7 19.3 - - - +
52D PRO* 4.4 6.7 - - + -
129D GLU* 3.8 40.5 - - + +
130D ALA* 4.5 4.2 - - + +
261D THR 2.9 16.4 + - - +
262D SER 3.6 4.5 - - - +
264D ILE* 1.3 77.9 - - - +
266D ASN* 1.3 58.4 + - - +
267D HIS* 3.3 14.9 + - - -
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Residues in contact with ASN 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0D HIS* 3.7 21.5 + - - -
51D GLU* 2.9 28.3 + - - +
262D SER* 2.8 26.9 + - - +
264D ILE 3.2 0.4 - - - -
265D LEU* 1.3 76.7 - - - +
267D HIS* 1.3 74.3 + - - +
268D GLU* 3.2 23.0 + - + +
276D LYS* 4.4 1.0 - - - +
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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