Contacts of the helix formed by residues 246 - 258 (chain B) in PDB entry 1XGS
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 GLU 246 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237B TYR* 3.2 22.2 - - + +
241B GLN* 5.0 15.3 + - + +
244B MET 3.3 3.3 + - - -
245B PRO* 1.3 70.9 - - - +
247B GLY* 1.3 57.1 + - - +
249B LEU* 3.5 9.9 - - + +
250B LYS* 2.9 64.5 + - - +
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Residues in contact with GLY 247 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245B PRO* 3.0 3.8 + - - +
246B GLU* 1.3 81.0 - - - +
248B GLN* 1.3 61.3 + - - +
250B LYS* 3.9 7.2 - - - +
251B LEU* 3.3 20.6 + - - +
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Residues in contact with GLN 248 (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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218B GLN* 2.8 42.6 + - - +
244B MET* 4.1 9.2 - - - +
245B PRO* 3.2 36.5 + - + +
247B GLY* 1.3 73.6 - - - +
249B LEU* 1.3 56.5 + - - +
250B LYS 3.3 0.2 - - - -
251B LEU* 3.6 6.6 - - - +
252B ALA* 2.8 35.7 + - - +
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Residues in contact with LEU 249 (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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222B LEU* 4.6 9.4 - - + -
237B TYR* 3.8 29.8 - - + +
240B LEU* 3.7 38.6 - - + +
241B GLN* 3.8 17.5 - - + +
243B ASP* 6.0 0.2 - - + -
244B MET* 3.6 36.3 - - + +
245B PRO 3.1 12.6 + - - +
246B GLU* 3.5 11.4 - - - +
248B GLN* 1.3 75.9 - - - +
250B LYS* 1.3 64.6 + - - +
252B ALA* 3.3 2.7 + - - +
253B LEU* 3.0 38.3 + - + +
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Residues in contact with LYS 250 (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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237B TYR* 3.1 33.2 - - + +
246B GLU* 2.9 48.2 + - - +
247B GLY* 3.9 6.7 - - - +
249B LEU* 1.3 75.0 - - - +
251B LEU* 1.3 61.5 + - - +
253B LEU* 4.7 2.9 - - - -
254B LYS* 2.6 49.4 + - + +
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Residues in contact with LEU 251 (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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216B VAL* 5.9 4.9 - - + -
218B GLN* 5.3 5.2 - - - +
219B ALA* 6.4 0.2 - - + -
247B GLY 3.3 12.7 + - - +
248B GLN* 3.6 11.0 - - - +
249B LEU 3.2 0.4 - - - -
250B LYS* 1.3 79.1 - - - +
252B ALA* 1.3 57.9 + - - +
254B LYS* 3.3 9.6 + - + +
255B THR* 2.8 46.4 + - - +
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Residues in contact with ALA 252 (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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218B GLN* 4.5 9.6 - - - +
219B ALA* 4.1 24.5 - - - +
222B LEU* 3.6 22.2 - - + -
244B MET* 4.8 5.2 - - - -
248B GLN 2.8 21.4 + - - +
249B LEU* 3.3 3.8 + - - +
251B LEU* 1.3 74.7 - - - +
253B LEU* 1.3 62.0 + - - +
255B THR* 3.3 3.8 + - - -
256B LEU* 3.0 29.7 + - - +
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Residues in contact with LEU 253 (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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206B TYR* 4.0 21.0 - - + +
222B LEU* 3.9 19.5 - - + -
226B ILE* 4.4 8.1 - - + -
235B PHE* 4.4 12.3 - - + -
237B TYR* 3.6 35.2 - - + -
240B LEU* 4.4 6.7 - - + -
249B LEU* 3.0 29.1 + - + +
250B LYS* 4.7 1.3 - - - -
252B ALA* 1.3 75.6 - - - +
254B LYS* 1.3 70.6 + - - +
256B LEU* 3.2 4.0 + - - +
257B GLU* 2.8 30.3 + - - +
262B ILE* 3.7 25.3 - - + +
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Residues in contact with LYS 254 (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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206B TYR* 3.5 27.4 + - - -
237B TYR* 5.5 1.4 - - - -
250B LYS* 2.6 57.3 + - + +
251B LEU* 3.5 12.1 - - + +
253B LEU* 1.3 81.2 - - - +
255B THR* 1.3 54.2 + - - +
257B GLU* 3.0 14.1 + - - +
258B LYS* 2.7 48.3 + - + +
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Residues in contact with THR 255 (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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214B VAL* 4.2 10.5 - - + -
216B VAL* 4.1 14.3 - - + +
219B ALA* 4.0 21.8 - - + +
251B LEU* 2.8 36.0 + - - +
252B ALA* 3.6 5.1 - - - -
254B LYS* 1.3 75.6 - - - +
256B LEU* 1.3 57.1 + - - +
258B LYS* 3.5 7.7 + - - +
259B ALA* 3.1 30.6 + - + +
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Residues in contact with LEU 256 (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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214B VAL* 4.5 10.5 - - + -
219B ALA* 3.5 32.1 - - + +
222B LEU* 3.8 24.7 - - + -
223B LEU* 3.8 27.4 - - + +
226B ILE* 4.0 15.0 - - + -
252B ALA 3.0 20.6 + - - +
253B LEU 3.6 4.3 - - - +
255B THR* 1.3 78.0 - - - +
257B GLU* 1.3 57.3 + - - +
259B ALA* 3.7 1.7 + - + -
260B GLY 3.3 1.6 + - - -
261B ALA* 2.7 46.1 + - + +
262B ILE* 3.3 18.8 + - + -
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Residues in contact with GLU 257 (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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203B THR* 5.1 5.1 + - - +
206B TYR* 4.2 11.7 - - + -
253B LEU 2.8 15.9 + - - +
254B LYS* 3.6 15.7 - - - +
256B LEU* 1.3 75.5 - - - +
258B LYS* 1.3 62.5 + - + +
260B GLY* 3.0 18.9 + - - -
262B ILE* 3.4 24.0 - - + +
263B TYR* 4.3 1.4 - - - +
264B GLY* 3.4 31.8 + - - +
266B PRO* 6.1 0.9 - - - +
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Residues in contact with LYS 258 (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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254B LYS* 2.7 30.3 + - + +
255B THR* 3.9 7.2 - - - +
257B GLU* 1.3 74.3 - - + +
259B ALA* 1.3 57.6 + - - +
260B GLY 3.3 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
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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