Contacts of the helix formed by residues 251 - 266 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41C ASN* 4.2 10.3 - - - -
250C VAL* 1.3 73.3 - - - +
252C SER* 1.3 57.1 + - - -
253C GLY 3.3 2.5 - - - -
254C ASP* 3.3 14.9 + - - +
255C SER* 2.9 30.7 + - - -
284C ASN* 3.3 6.9 - - - -
290C THR* 4.2 2.9 - - - -
291C GLY* 4.6 3.0 - - - -
1312C TA6 4.1 0.9 - - - -
1313C ANP 2.6 25.5 + - - -
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Residues in contact with SER 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C PRO* 3.1 19.1 + - - +
251C GLY* 1.3 77.2 - - - +
253C GLY* 1.3 56.5 + - - +
255C SER* 3.2 3.8 + - - -
256C THR* 2.8 31.0 + - - -
281C GLY* 2.8 20.3 + - - -
284C ASN* 2.9 23.0 + - - +
285C ALA* 3.5 8.5 + - - +
1313C ANP 3.4 33.2 - - - -
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Residues in contact with GLY 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C ASP* 4.5 1.3 - - - -
183C LYS* 3.7 13.7 - - - -
252C SER* 1.3 76.5 - - - +
254C ASP* 1.3 56.8 + - - +
256C THR* 3.2 5.4 + - - -
257C VAL* 2.9 32.0 + - - +
1313C ANP 2.8 44.4 + - - -
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Residues in contact with ASP 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LYS* 3.3 39.1 - - - +
41C ASN* 2.9 38.0 + - + -
42C VAL* 3.5 19.0 - - + +
134C SER* 4.9 0.7 - - - -
163C ASP* 3.9 7.6 - - - +
251C GLY* 3.5 4.4 - - - +
253C GLY* 1.3 73.5 - - - +
255C SER* 1.3 58.9 + - - +
257C VAL* 3.1 3.9 + - - -
258C ALA* 3.0 26.0 + - - +
1312C TA6 2.7 23.0 + - - -
1313C ANP 3.1 9.2 + - - -
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Residues in contact with SER 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C VAL* 3.6 29.8 - - - +
251C GLY 2.9 16.9 + - - -
252C SER 3.4 8.7 - - - -
254C ASP* 1.3 75.2 - - - +
256C THR* 1.3 62.2 + - - +
258C ALA* 3.3 3.5 + - - +
259C GLY 3.1 17.5 + - - -
280C LEU* 3.5 37.8 - - - +
284C ASN* 3.3 19.1 + - - +
291C GLY* 4.3 1.2 - - - -
293C VAL* 4.4 0.6 - - - +
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Residues in contact with THR 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C LYS* 4.3 13.9 - - + -
220C ILE* 5.2 4.9 - - + -
222C SER* 5.3 2.9 - - - -
252C SER 2.8 15.5 + - - -
253C GLY* 3.2 15.2 + - - +
255C SER* 1.3 75.5 - - - +
257C VAL* 1.3 54.5 + - - +
259C GLY* 3.2 2.9 + - - -
260C ILE* 2.9 40.4 + - + +
277C ALA* 3.2 38.4 + - + +
278C ASN* 5.4 3.6 - - - +
281C GLY* 3.6 1.6 - - - +
1313C ANP 3.3 23.8 - - - +
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Residues in contact with VAL 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C VAL* 3.8 22.4 - - + -
132C ALA* 4.6 4.0 - - + -
134C SER* 4.0 9.4 - - - +
161C ILE* 3.9 20.6 - - + +
163C ASP* 3.6 26.0 - - + +
183C LYS* 3.9 23.8 - - + -
253C GLY 2.9 18.3 + - - +
254C ASP* 3.1 8.3 + - - +
256C THR* 1.3 72.1 - - - +
258C ALA* 1.3 56.5 + - - +
260C ILE* 3.8 8.3 - - + +
261C THR* 2.6 42.1 + - - +
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Residues in contact with ALA 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C VAL* 3.6 30.0 - - - +
45C VAL* 3.8 20.4 - - + -
46C LEU* 3.5 19.9 - - + +
49C VAL* 5.7 0.2 - - + -
254C ASP 3.0 11.1 + - - +
255C SER 3.5 8.7 - - - +
256C THR 3.3 0.2 - - - -
257C VAL* 1.3 75.5 - - - +
259C GLY* 1.3 58.7 + - - +
261C THR* 3.9 1.1 - - - -
262C SER* 2.9 32.3 + - - -
280C LEU* 4.4 2.9 - - + -
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Residues in contact with GLY 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C SER 3.1 12.0 + - - -
256C THR 3.2 5.1 + - - -
258C ALA* 1.3 75.8 - - - +
260C ILE* 1.3 61.3 + - - +
262C SER* 3.5 0.4 + - - -
263C ALA* 3.0 21.0 + - - +
273C LEU 5.0 0.2 - - - -
276C LYS* 3.5 21.6 - - - +
277C ALA* 4.1 8.5 - - - -
280C LEU* 3.5 21.8 - - - +
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Residues in contact with ILE 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C ILE* 4.5 6.5 - - + -
181C VAL* 3.9 34.3 - - + -
183C LYS* 3.6 33.4 - - + -
220C ILE* 3.7 22.4 - - + -
256C THR* 2.9 30.9 + - + +
257C VAL* 3.8 8.7 - - + +
258C ALA 3.4 0.2 - - - -
259C GLY* 1.3 71.4 - - - +
261C THR* 1.3 58.9 + - - +
263C ALA* 3.1 7.8 + - - +
264C ILE* 2.8 33.4 + - + +
273C LEU* 4.3 15.7 - - + -
277C ALA* 3.7 13.2 - - + +
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Residues in contact with THR 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C ILE* 3.8 37.2 - - + -
46C LEU* 4.9 2.7 - - - -
130C ALA* 4.3 6.0 - - + +
132C ALA* 3.9 15.5 - - + +
161C ILE* 3.8 34.2 - - + +
257C VAL 2.6 23.5 + - - -
258C ALA* 3.9 5.1 - - - -
260C ILE* 1.3 72.9 - - - +
262C SER* 1.3 61.6 + - - +
264C ILE* 3.4 7.2 + - - +
265C LEU* 2.9 29.3 + - - +
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Residues in contact with SER 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ILE* 4.6 1.6 - - - -
46C LEU* 4.3 2.3 - - - +
49C VAL* 4.2 7.8 - - - +
51C GLU* 2.6 39.9 + - - +
258C ALA 2.9 19.0 + - - -
259C GLY* 3.6 4.5 - - - -
261C THR* 1.3 76.2 - - - +
263C ALA* 1.3 61.5 + - - +
265C LEU* 3.2 4.0 + - - -
266C ASN* 2.8 30.6 + - - +
268C GLU* 4.4 0.4 - - - -
276C LYS* 3.0 24.3 + - - +
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Residues in contact with ALA 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C GLY 3.0 14.2 + - - +
260C ILE 3.4 7.9 - - - +
262C SER* 1.3 75.7 + - - +
264C ILE* 1.3 57.3 + - - +
266C ASN 3.3 1.2 + - - -
267C HIS 3.0 8.8 + - - -
268C GLU* 3.0 54.9 + - + +
273C LEU* 3.5 35.4 - - + -
276C LYS* 4.3 2.6 - - + +
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Residues in contact with ILE 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C ALA* 4.9 3.1 - - + -
159C PRO* 4.2 28.3 - - + -
161C ILE* 4.4 18.2 - - + -
180C THR* 5.0 7.0 - - + -
181C VAL* 4.1 17.7 - - + -
217C GLU* 5.9 0.9 - - - +
218C TRP* 4.4 10.8 - - + +
260C ILE* 2.8 32.8 + - + +
261C THR* 3.6 8.1 - - - +
263C ALA* 1.3 69.9 - - - +
265C LEU* 1.3 66.9 + - - +
266C ASN 3.2 0.5 + - - -
267C HIS* 3.2 21.6 + - - +
273C LEU* 4.1 17.0 - - + -
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Residues in contact with LEU 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0C HIS* 4.0 26.9 - - + +
1C MSE 4.5 1.1 - - - +
2C ILE* 3.8 30.3 - - + -
51C GLU* 3.6 24.0 - - - +
52C PRO* 4.6 4.9 - - + -
129C GLU* 3.9 35.6 - - + +
130C ALA* 4.9 7.6 - - + +
261C THR 2.9 20.7 + - - +
262C SER 3.5 4.9 - - - +
264C ILE* 1.3 74.8 - - - +
266C ASN* 1.3 67.5 + - - +
267C HIS* 3.4 15.1 + - - -
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Residues in contact with ASN 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C GLU* 2.8 37.0 + - - +
262C SER* 2.8 23.4 + - - +
265C LEU* 1.3 86.0 - - - +
267C HIS* 1.3 74.7 + - - +
268C GLU* 3.2 21.6 + - + +
276C LYS* 5.1 0.6 - - - +
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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