Contacts of the helix formed by residues 246 - 260 (chain A) in PDB entry 2JG7
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 SER 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A PHE* 3.8 0.2 - - - -
245A GLY* 1.3 74.5 - - - +
247A THR* 1.3 61.2 + - - +
248A HIS* 3.8 7.1 + - - +
249A VAL* 3.1 22.2 + - - +
250A GLY* 2.8 27.2 + - - -
268A LEU* 3.9 0.6 - - - +
398A GLU* 5.7 0.2 - - - -
1510A NAD 2.7 55.3 + - - -
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Residues in contact with THR 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A GLY 3.7 1.4 + - - -
246A SER* 1.3 73.4 - - - +
248A HIS* 1.3 61.3 + - - +
251A LYS* 3.2 22.9 + - - +
268A LEU* 3.8 9.2 - - - -
269A GLY* 3.8 23.3 - - - +
398A GLU* 4.8 8.3 - - + +
424A GLN* 5.3 13.2 - - + +
472A HIS* 3.4 43.2 + - + +
261B PHE* 4.1 8.1 - - - -
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Residues in contact with HIS 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A SER* 3.2 6.9 - - - +
247A THR* 1.3 80.6 - - - +
249A VAL* 1.3 79.3 + - + +
251A LYS* 3.6 11.3 + - - +
252A MET* 3.7 29.7 + - + +
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Residues in contact with VAL 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A PHE* 3.4 20.2 - - + -
246A SER* 3.1 19.4 + - - +
248A HIS* 1.3 86.3 - - + +
250A GLY* 1.3 66.9 + - - +
252A MET* 3.1 20.4 + - + +
253A VAL* 3.1 11.6 + - + +
1510A NAD 3.3 64.6 - - + +
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Residues in contact with GLY 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A PHE* 3.7 19.8 - - - -
246A SER 2.8 17.8 + - - -
247A THR 4.0 0.7 - - - -
248A HIS 3.4 0.4 - - - -
249A VAL* 1.3 77.1 - - - +
251A LYS* 1.3 50.1 + - - +
253A VAL* 3.3 4.8 + - - +
254A ALA* 2.7 37.0 + - - +
266A LEU* 4.4 3.1 - - - +
268A LEU* 3.7 18.6 - - - -
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Residues in contact with LYS 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A THR 3.2 17.1 + - - +
248A HIS* 3.7 8.1 - - - +
249A VAL 3.2 0.6 - - - -
250A GLY* 1.3 74.3 - - - +
252A MET* 1.3 65.5 + - - +
254A ALA* 3.3 4.4 + - + +
255A MET* 2.9 39.2 + - + +
258B GLN 5.3 3.1 - - - +
259B GLU* 3.0 53.7 + - - +
261B PHE* 3.7 26.6 - - + -
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Residues in contact with MET 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A THR* 5.7 0.2 - - - +
248A HIS* 3.7 34.2 + - + +
249A VAL* 3.1 14.0 + - - +
251A LYS* 1.3 78.4 - - + +
253A VAL* 1.3 63.2 + - + +
255A MET* 3.4 6.5 + - - +
256A MET* 3.1 40.1 + - + +
1510A NAD 3.5 26.9 - - - +
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Residues in contact with VAL 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ILE* 5.3 0.2 - - + -
229A GLY 5.0 0.4 - - - +
233A ALA* 4.2 9.2 - - + -
241A LEU* 3.5 31.6 - - + -
243A PHE* 4.0 29.8 - - + -
249A VAL* 3.1 10.2 + - + +
250A GLY 3.6 8.1 - - - +
252A MET* 1.3 77.0 - - - +
254A ALA* 1.3 66.4 + - - +
256A MET* 3.1 10.3 + - + +
257A VAL* 2.9 25.3 + - + +
264A LYS* 6.4 0.2 - - + -
266A LEU* 5.0 3.8 - - + -
1510A NAD 3.6 34.3 - - + +
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Residues in contact with ALA 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A GLY 2.7 21.4 + - - +
251A LYS* 3.5 8.3 - - + +
253A VAL* 1.3 73.8 - - - +
255A MET* 1.3 53.2 + - - +
257A VAL* 3.1 3.7 + - - +
258A GLN* 2.8 35.7 + - - +
264A LYS* 4.0 11.8 - - + +
266A LEU* 3.7 19.0 - - + +
258B GLN* 3.4 30.3 - - + +
261B PHE* 5.0 0.7 - - + -
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Residues in contact with MET 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A LYS* 2.9 31.4 + - + +
252A MET* 3.7 6.5 - - - +
254A ALA* 1.3 76.2 - - - +
256A MET* 1.3 58.0 + - + +
258A GLN* 4.4 2.9 - - - -
259A GLU* 3.0 28.1 + - - +
255B MET* 3.4 47.1 - - + +
258B GLN* 3.8 10.3 - - + -
259B GLU* 3.5 44.0 - - + -
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Residues in contact with MET 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A THR* 3.7 37.7 - - + +
233A ALA* 3.9 20.8 - - + +
234A LYS* 3.7 28.1 - - + +
252A MET* 3.1 44.9 + - + +
253A VAL* 3.1 19.0 + - + +
255A MET* 1.3 76.7 - - + +
257A VAL* 1.3 63.7 + - - +
259A GLU* 3.3 18.1 - - - +
260A ARG* 3.6 11.3 - - - +
1510A NAD 4.7 2.2 - - - +
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Residues in contact with VAL 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ALA* 3.4 19.3 - - - +
241A LEU* 3.8 27.8 - - + -
253A VAL* 2.9 21.7 + - + +
254A ALA 3.7 3.8 - - - +
256A MET* 1.3 72.6 - - - +
258A GLN* 1.3 65.2 + - - +
260A ARG* 3.2 17.7 + - - +
262A GLY* 3.0 52.7 + - - +
263A ARG 3.7 12.6 - - - +
264A LYS* 3.9 17.9 - - + +
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Residues in contact with GLN 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A ALA 2.8 20.3 + - - +
255A MET 3.8 1.1 - - - +
257A VAL* 1.3 72.1 - - - +
259A GLU* 1.3 64.3 + - - +
261A PHE* 3.0 35.8 + - - +
262A GLY 5.1 1.3 + - - +
264A LYS* 3.0 24.2 + - - +
251B LYS* 5.3 1.8 - - - +
254B ALA* 3.3 27.5 - - + +
255B MET* 3.7 21.3 - - + +
258B GLN* 4.0 21.5 - - + -
264B LYS* 3.0 27.7 - - - -
266B LEU* 4.2 5.7 - - - +
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Residues in contact with GLU 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A MET 3.0 13.4 + - - +
256A MET* 3.3 15.9 - - - +
258A GLN* 1.3 77.0 - - - +
260A ARG* 1.3 60.6 + - - +
261A PHE* 3.7 3.5 + - - -
251B LYS* 3.1 44.7 + - - +
255B MET* 3.5 24.4 - - + -
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Residues in contact with ARG 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A MET 3.5 8.7 + - - -
233A ALA* 2.8 24.6 + - - +
234A LYS* 3.4 22.3 - - - +
235A ASP 2.9 23.6 + - - -
236A GLU* 3.8 34.3 + - + +
238A VAL* 3.0 32.1 + - - +
241A LEU* 4.7 3.0 - - - +
256A MET 3.6 8.1 - - - +
257A VAL* 3.3 26.2 - - - +
258A GLN 3.1 0.4 - - - -
259A GLU* 1.3 81.0 - - - +
261A PHE* 1.3 71.5 - - - +
262A GLY* 3.2 21.2 + - - -
263A ARG 5.3 0.4 + - - -
472B HIS* 4.6 6.9 - - - -
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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