Contacts of the helix formed by residues 246 - 258 (chain X) in PDB entry 6JM9
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 246 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105D LYS* 5.4 0.9 - - - -
131X PHE* 3.8 23.8 - - - -
243X PHE 4.8 2.0 + - - -
244X ALA 3.6 2.6 - - - -
245X PHE* 1.4 77.9 - - - +
247X PRO* 1.3 74.7 - - - +
248X GLU* 3.3 3.8 + - - -
249X VAL* 3.7 0.6 + - - -
250X ASP* 3.2 27.5 + - - +
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Residues in contact with PRO 247 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D LYS* 4.3 23.7 - - + -
106D HIS* 4.9 16.2 - - + +
109D SER* 3.7 26.5 - - - +
131X PHE* 5.4 1.3 - - + -
246X GLY* 1.3 85.2 - - - +
248X GLU* 1.4 64.7 + - + +
250X ASP* 3.2 18.6 + - + +
251X HIS* 3.2 26.9 + - + +
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Residues in contact with GLU 248 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246X GLY* 3.3 1.2 - - - -
247X PRO* 1.4 79.1 - - + +
249X VAL* 1.4 65.9 + - + +
251X HIS* 3.2 25.4 + - - +
252X GLN* 3.5 26.5 + - - +
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Residues in contact with VAL 249 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133X PRO* 4.1 20.6 - - + -
224X LEU* 3.7 35.7 - - + -
245X PHE* 3.3 41.5 - - + +
246X GLY* 4.0 2.0 - - - +
248X GLU* 1.4 76.1 - - + +
250X ASP* 1.4 64.2 + - - +
252X GLN* 3.1 21.9 + - + +
253X LEU* 3.2 24.6 + - + +
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Residues in contact with ASP 250 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242X ASN* 3.4 26.3 - - - +
243X PHE 4.6 8.0 + - - +
245X PHE* 4.6 5.0 + - - +
246X GLY 3.2 19.3 + - - +
247X PRO* 3.2 15.5 + - + +
249X VAL* 1.4 74.8 - - - +
251X HIS* 1.4 65.2 + - - +
253X LEU* 3.6 8.0 + - - +
254X LYS* 3.1 45.7 + - - +
270X LYS* 3.4 31.0 + - - +
272X PHE* 5.3 0.7 - - - -
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Residues in contact with HIS 251 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247X PRO* 3.2 17.9 + - + -
248X GLU* 3.3 15.5 - - - +
249X VAL 3.2 0.4 - - - -
250X ASP* 1.4 79.2 - - + +
252X GLN* 1.4 61.0 + - - +
254X LYS* 3.4 24.9 + - + +
255X GLU* 3.2 30.5 + - - +
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Residues in contact with GLN 252 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224X LEU* 4.3 15.8 - - + +
229X ARG* 3.9 3.4 + - - +
248X GLU* 3.5 31.9 + - - +
249X VAL* 3.1 18.0 + - - +
251X HIS* 1.4 77.1 - - + +
253X LEU* 1.4 58.5 + - - +
255X GLU* 3.5 25.3 - - - +
256X ARG* 3.2 47.2 + - - +
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Residues in contact with LEU 253 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162X LEU* 4.5 15.0 - - + -
223X PHE* 4.6 10.1 - - + +
224X LEU* 3.6 23.8 - - + -
240X VAL* 4.5 7.0 - - + -
242X ASN* 3.6 36.6 - - + +
245X PHE* 4.6 4.3 - - + -
249X VAL* 3.2 32.2 + - + +
250X ASP* 3.8 5.8 - - - +
252X GLN* 1.4 70.3 - - - +
254X LYS* 1.4 64.8 + - - +
255X GLU 3.2 0.2 - - - -
256X ARG* 3.0 24.3 + - - +
257X PHE* 2.9 40.2 + - + -
272X PHE* 5.3 0.4 - - + -
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Residues in contact with LYS 254 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250X ASP* 3.1 42.6 + - - +
251X HIS* 3.5 26.7 + - + +
253X LEU* 1.4 79.5 - - - +
255X GLU* 1.4 57.9 + - + +
257X PHE* 3.1 10.3 + - - +
258X ALA* 3.1 22.3 + - - +
270X LYS* 4.2 10.5 - - - +
271X PRO 5.0 0.2 + - - -
272X PHE* 3.8 51.3 - - + +
287X ILE* 3.5 35.7 - - + +
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Residues in contact with GLU 255 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229X ARG* 3.3 23.1 + - - +
251X HIS* 3.2 17.9 + - - +
252X GLN* 3.5 21.1 - - - +
253X LEU 3.2 0.2 - - - -
254X LYS* 1.4 79.4 - - + +
256X ARG* 1.3 56.6 + - - +
257X PHE 3.4 0.2 - - - -
258X ALA* 3.3 20.8 - - - +
259X ASN* 3.5 9.4 + - - +
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Residues in contact with ARG 256 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223X PHE 4.2 7.0 - - - -
224X LEU* 3.6 20.9 - - - +
225X SER* 3.3 42.5 + - - +
226X GLU* 4.8 3.0 + - - -
228X TRP 4.9 0.4 - - - -
229X ARG* 3.6 41.9 - - + +
232X ILE* 3.7 40.9 - - + +
252X GLN* 3.2 57.3 + - - +
253X LEU* 3.0 16.3 + - + +
255X GLU* 1.3 76.2 - - - +
257X PHE* 1.4 62.4 + - + +
258X ALA 3.2 0.7 - - - -
259X ASN* 3.3 24.7 + - - +
260X MET 4.0 0.2 + - - -
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Residues in contact with PHE 257 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162X LEU* 3.7 27.6 - - + -
232X ILE* 4.4 6.3 - - + -
238X ILE* 4.0 12.3 - - + -
240X VAL* 3.8 21.8 - - + -
253X LEU* 2.9 42.2 + - + -
254X LYS* 3.1 10.7 + - + +
256X ARG* 1.4 74.5 - - - +
258X ALA* 1.4 57.7 + - - +
259X ASN 3.3 0.4 - - - -
260X MET* 3.1 46.9 + - - +
266X ILE* 4.2 17.5 - - + -
272X PHE* 3.4 34.8 - + - -
287X ILE* 4.2 10.8 - - + -
290X ILE* 4.2 6.9 - - - +
291X MET* 4.9 4.5 - - + -
317X ILE* 4.4 3.3 - - - +
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Residues in contact with ALA 258 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254X LYS 3.1 8.8 + - - +
255X GLU* 3.3 20.9 - - - +
257X PHE* 1.4 72.5 - - - +
259X ASN* 1.4 65.5 + - - +
260X MET 3.1 8.0 + - - +
287X ILE* 3.7 14.3 - - + +
290X ILE* 3.9 13.6 - - + +
319X ARG* 4.6 5.2 + - - -
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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
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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