Contacts of the helix formed by residues 248 - 266 (chain D) in PDB entry 2GL7
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 VAL 248 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208D VAL* 3.9 45.1 - - + +
211D ALA* 5.7 2.2 - - + -
212D ARG* 5.6 0.4 - - + -
246D SER* 3.1 16.3 + - - +
247D PRO* 1.3 87.6 - - + +
249D ASP* 1.3 61.0 + - - +
250D SER* 3.6 20.2 - - - +
251D VAL* 3.4 16.2 + - + -
252D LEU* 3.1 23.4 + - - +
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Residues in contact with ASP 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D SER 5.6 0.3 - - - +
247D PRO 3.8 6.8 + - - +
248D VAL* 1.3 71.3 - - - +
250D SER* 1.3 68.2 + - - +
251D VAL 3.1 1.6 - - - -
252D LEU* 3.0 18.8 + - - +
253D PHE* 2.9 54.5 + - + -
288D LYS* 5.0 5.4 + - - +
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Residues in contact with SER 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212D ARG* 3.2 32.8 - - - +
248D VAL* 3.6 13.4 - - - +
249D ASP* 1.3 78.9 - - - +
251D VAL* 1.3 63.2 + - - +
253D PHE* 4.0 9.9 - - - +
254D TYR* 3.1 36.5 + - - -
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Residues in contact with VAL 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D ALA* 3.8 38.8 - - + +
212D ARG* 3.8 7.6 - - - +
215D ALA* 4.6 9.3 - - + +
243D MET* 4.1 26.9 - - + -
246D SER* 3.5 28.9 - - - +
248D VAL* 3.4 21.0 + - + +
249D ASP 3.1 0.6 - - - -
250D SER* 1.3 74.0 + - - +
252D LEU* 1.3 65.9 + - - +
254D TYR* 3.5 7.6 + - - +
255D ALA* 3.0 23.4 + - - +
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Residues in contact with LEU 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D MET 4.3 6.7 - - - +
244D LEU* 3.8 33.4 - - + +
246D SER* 4.3 9.8 - - - +
248D VAL 3.1 13.2 + - - +
249D ASP* 3.0 21.9 + - - +
251D VAL* 1.3 77.4 - - - +
253D PHE* 1.3 65.4 + - + +
255D ALA* 3.4 2.8 + - - +
256D ILE* 3.1 24.1 + - - +
285D LEU* 4.0 9.9 - - + -
288D LYS* 4.1 24.0 - - + +
293D PHE* 3.7 37.0 - - + -
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Residues in contact with PHE 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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249D ASP* 2.9 50.5 + - + +
250D SER* 4.0 7.9 - - - +
252D LEU* 1.3 80.5 - - + +
254D TYR* 1.3 64.6 + - + +
256D ILE* 4.6 2.9 - - - -
257D THR* 2.9 33.7 + - - +
290D ASN* 4.2 18.2 - - + -
293D PHE* 3.8 34.5 - + + -
48E LEU* 3.6 52.7 - - + +
49E VAL* 4.5 7.4 - - + -
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Residues in contact with TYR 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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176D HIS* 4.4 12.2 + - - -
212D ARG* 3.6 37.3 + - + -
215D ALA* 4.0 18.2 - - + +
216D GLY* 3.6 26.1 - - - -
219D HIS* 3.8 26.2 - + + -
240D LEU* 5.5 0.7 - - - -
250D SER* 3.1 29.5 + - - +
251D VAL* 3.8 4.7 - - - +
253D PHE* 1.3 75.8 - - - +
255D ALA* 1.3 59.9 + - - +
257D THR* 3.2 2.8 + - - -
258D THR* 2.6 33.6 + - - -
49E VAL* 3.9 34.8 + - + -
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Residues in contact with ALA 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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215D ALA* 5.3 2.0 - - + +
240D LEU* 3.9 35.0 - - + +
243D MET* 4.0 15.7 - - + +
244D LEU* 4.0 9.0 - - + -
251D VAL* 3.0 18.9 + - + +
252D LEU 3.6 5.2 - - - +
253D PHE 3.2 0.2 - - - -
254D TYR* 1.3 77.5 - - - +
256D ILE* 1.3 57.5 + - - +
258D THR* 3.9 1.4 - - - -
259D LEU* 3.1 35.2 + - - +
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Residues in contact with ILE 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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244D LEU* 3.7 20.9 - - + -
252D LEU 3.1 13.0 + - - +
253D PHE* 4.0 8.5 - - - +
255D ALA* 1.3 75.2 - - - +
257D THR* 1.3 66.9 + - + +
259D LEU* 3.9 3.8 - - + +
260D HIS* 3.0 24.6 + - - +
282D MET* 5.0 8.1 - - + -
285D LEU* 5.2 1.3 - - + -
293D PHE* 3.9 26.9 - - + -
296D ILE* 3.8 18.6 - - + +
297D THR* 3.7 32.1 - - + +
300D CYS* 3.5 25.8 - - + -
48E LEU* 5.0 0.2 - - + -
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Residues in contact with THR 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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219D HIS* 3.0 30.0 + - - -
253D PHE 2.9 19.7 + - - +
254D TYR* 3.2 3.1 + - - -
256D ILE* 1.3 73.5 - - + +
258D THR* 1.3 61.0 + - - +
260D HIS* 3.4 8.2 + - - +
261D ASN* 3.1 34.0 + - - +
296D ILE* 4.1 25.8 - - + -
45E LYS* 4.2 20.5 - - + +
48E LEU* 4.1 7.2 - - + -
49E VAL* 3.8 13.8 - - + +
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Residues in contact with THR 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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215D ALA 4.7 0.9 + - - -
218D LEU* 3.9 12.8 - - + +
219D HIS* 3.2 24.9 + - - +
222D SER* 3.6 26.2 - - - -
231D ILE* 4.6 4.3 - - + -
240D LEU* 3.8 27.3 - - + +
254D TYR 2.6 23.5 + - - -
255D ALA 3.9 3.1 - - - -
257D THR* 1.3 76.5 + - - +
259D LEU* 1.3 63.4 + - - +
261D ASN* 3.3 4.0 + - - +
262D LEU* 3.1 25.9 + - + +
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Residues in contact with LEU 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D ILE* 4.2 14.6 - - + -
240D LEU* 3.9 33.0 - - + +
241D VAL* 4.1 11.4 - - + +
244D LEU* 3.9 34.3 - - + -
255D ALA 3.1 23.2 + - - +
256D ILE* 3.9 5.8 - - - +
258D THR* 1.3 76.2 - - - +
260D HIS* 1.3 57.5 + - - +
262D LEU* 3.2 7.9 + - + +
263D LEU* 3.0 35.6 + - + +
273D VAL* 4.0 23.3 - - + -
282D MET* 4.6 14.6 - - + -
300D CYS* 5.2 0.7 - - - -
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Residues in contact with HIS 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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256D ILE 3.0 18.4 + - - +
257D THR* 3.5 7.6 - - - +
258D THR 3.2 0.2 - - - -
259D LEU* 1.3 74.7 - - - +
261D ASN* 1.3 64.7 + - - +
263D LEU* 3.2 4.4 + - - +
264D LEU* 3.0 40.6 + - + +
296D ILE* 3.8 14.9 + - + +
299D ASP* 3.0 38.4 + - + -
300D CYS* 3.5 25.5 - - - -
303D ILE* 4.1 10.9 - - + +
41E LEU* 4.1 12.9 - - + +
45E LYS* 3.2 29.9 + - + +
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Residues in contact with ASN 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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219D HIS* 4.7 3.6 - - - -
222D SER* 2.9 42.7 + - - +
223D HIS* 3.9 20.0 + - - -
228D LEU* 4.1 4.6 - - + +
257D THR* 3.1 16.9 + - - -
258D THR 3.3 8.0 + - - +
260D HIS* 1.3 74.7 - - - +
262D LEU* 1.3 60.8 + - - +
264D LEU* 3.4 5.7 + - - +
265D HIS* 3.2 36.9 + - + +
45E LYS* 2.6 35.9 + - - +
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Residues in contact with LEU 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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228D LEU* 3.4 41.5 - - + +
231D ILE* 4.1 14.8 - - + -
232D PHE* 5.0 1.8 - - + +
237D ILE* 3.7 29.6 - - + -
240D LEU* 4.0 20.6 - - + -
258D THR* 3.1 22.4 + - + +
259D LEU* 3.5 12.3 - - + +
260D HIS 3.2 0.2 - - - -
261D ASN* 1.3 77.7 - - - +
263D LEU* 1.3 58.7 + - + +
266D GLN* 3.0 40.5 + - + +
269D ALA* 3.2 20.5 - - + +
273D VAL* 6.2 0.2 - - + -
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Residues in contact with LEU 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 LEU 3.0 20.6 + - - +
260D HIS 3.2 4.9 + - - +
262D LEU* 1.3 75.9 - - - +
264D LEU* 1.3 63.0 + - - +
266D GLN 5.0 1.7 + - - +
269D ALA* 4.0 4.5 - - + -
270D LYS* 3.8 32.8 - - + +
273D VAL* 3.9 16.6 - - + -
282D MET* 4.7 6.1 - - + -
300D CYS* 3.8 44.2 - - + +
303D ILE* 4.0 27.5 - - + +
304D LEU* 3.7 32.3 - - + -
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Residues in contact with LEU 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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260D HIS* 3.0 44.8 + - + +
261D ASN* 3.7 5.4 - - - +
262D LEU 3.2 0.4 - - - -
263D LEU* 1.3 79.7 - - - +
265D HIS* 1.3 87.1 + - + +
266D GLN 3.9 0.4 - - - -
299D ASP* 5.3 1.6 - - - +
303D ILE* 4.0 20.6 - - + -
27E GLN* 6.1 0.4 - - - +
28E GLU 5.9 3.1 - - - +
45E LYS* 4.0 11.4 - - - +
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Residues in contact with HIS 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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222D SER 5.6 0.7 - - - -
228D LEU* 4.0 22.6 - - + +
261D ASN* 3.2 28.3 + - + +
264D LEU* 1.3 106.4 + - + +
266D GLN* 1.3 61.3 + - - +
267D GLU 4.2 1.1 + - - -
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Residues in contact with GLN 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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154A PRO* 5.2 3.8 - - - +
225D ARG 4.5 1.6 - - - +
228D LEU* 3.3 12.3 - - + +
229D LEU* 3.3 47.6 + - - +
232D PHE* 4.1 29.5 - - + -
262D LEU* 3.0 30.3 + - + +
263D LEU 5.2 1.6 - - - +
264D LEU 3.9 1.0 - - - -
265D HIS* 1.3 79.4 - - - +
267D GLU* 1.3 91.7 + - - +
268D GLY 3.3 0.3 + - - -
269D ALA* 3.2 20.2 + - + +
270D LYS* 6.0 0.5 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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