Contacts of the helix formed by residues 290 - 306 (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 ASN 290 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253D PHE* 4.2 15.2 - - + -
288D LYS* 4.7 1.8 - - + +
289D THR* 1.3 76.8 + - - +
291D VAL* 1.3 56.6 + - - +
292D LYS* 3.2 13.4 + - - +
293D PHE* 3.0 33.9 + - + +
294D LEU* 3.0 27.8 + - - +
48E LEU* 3.6 14.8 - - - +
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Residues in contact with VAL 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D THR 3.2 3.5 + - - +
290D ASN* 1.3 70.2 + - - +
292D LYS* 1.3 75.0 + - + +
294D LEU* 3.2 9.1 + - - +
295D ALA* 3.0 23.2 + - - +
331D TYR* 3.5 36.8 - - + -
333D TYR* 3.8 37.4 - - + -
336D LEU* 4.0 11.7 - - + +
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Residues in contact with LYS 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D ASN* 3.2 9.3 + - - +
291D VAL* 1.3 81.5 - - + +
293D PHE* 1.3 64.2 + - - +
295D ALA* 3.1 12.7 + - - +
296D ILE* 3.2 19.1 + - - +
333D TYR* 4.1 21.7 + - + +
43E ASP 5.3 0.2 + - - -
44E VAL* 3.6 29.8 - - + +
47E SER* 2.8 34.2 + - - +
48E LEU* 4.3 14.1 - - + +
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Residues in contact with PHE 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D LEU* 3.7 29.6 - - + -
253D PHE* 3.8 28.0 - + + -
256D ILE* 3.9 20.6 - - + -
285D LEU* 3.7 44.4 - - + -
288D LYS* 3.7 24.2 - - + -
290D ASN* 3.0 27.9 + - + +
292D LYS* 1.3 76.5 - - - +
294D LEU* 1.3 64.7 + - + +
296D ILE* 3.4 4.1 + - - +
297D THR* 2.8 46.9 + - - -
48E LEU* 4.0 12.3 - - + +
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Residues in contact with LEU 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D LEU 3.7 23.1 - - - +
286D LEU* 3.9 23.3 - - + +
288D LYS 3.3 27.4 - - - +
289D THR* 4.6 0.7 - - - -
290D ASN 3.0 19.0 + - - +
291D VAL* 3.6 9.9 - - - +
292D LYS 3.2 0.4 - - - -
293D PHE* 1.3 82.2 - - + +
295D ALA* 1.3 57.6 + - - +
297D THR* 3.8 2.1 - - - -
298D THR* 2.8 34.3 + - - +
327D ILE* 4.2 9.6 - - + -
331D TYR* 3.8 28.9 - - + +
336D LEU* 3.6 19.1 - - + -
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Residues in contact with ALA 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D VAL 3.0 12.8 + - - +
292D LYS* 3.1 10.9 + - - +
294D LEU* 1.3 74.3 - - - +
296D ILE* 1.3 65.4 + - - +
298D THR* 3.2 7.0 + - - -
299D ASP* 3.2 23.7 + - - +
333D TYR* 4.6 6.5 - - + -
335D LYS* 4.6 1.1 - - + +
336D LEU* 3.7 18.1 - - + +
339D THR* 3.6 16.5 + - + +
41E LEU* 4.2 18.2 - - + +
44E VAL* 4.7 2.5 - - + -
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Residues in contact with ILE 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D ILE* 3.8 32.1 - - + +
257D THR* 4.1 7.2 - - + -
260D HIS* 3.8 20.8 + - + +
292D LYS 3.2 16.7 + - - +
293D PHE* 3.8 4.7 - - - +
295D ALA* 1.3 78.8 - - - +
297D THR* 1.3 56.9 + - - +
299D ASP* 3.3 5.2 + - - +
300D CYS* 3.0 27.0 + - - -
41E LEU* 5.0 7.6 - - + -
44E VAL* 4.0 14.6 - - + -
45E LYS* 3.9 28.5 - - + -
48E LEU* 3.6 28.7 - - + -
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Residues in contact with THR 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D ILE* 3.7 15.8 - - + +
282D MET* 3.7 40.6 - - + +
285D LEU* 4.6 9.4 - - + -
286D LEU* 4.3 11.2 - - + -
293D PHE* 2.8 43.2 + - - -
294D LEU* 3.8 7.0 - - - -
295D ALA 3.3 0.2 - - - -
296D ILE* 1.3 74.9 - - - +
298D THR* 1.3 64.3 + - - +
300D CYS* 3.3 4.2 + - - +
301D LEU* 3.2 22.7 + - + +
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Residues in contact with THR 298 (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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286D LEU* 3.6 23.1 - - + -
294D LEU 2.8 25.2 + - - +
295D ALA* 3.2 3.1 + - - -
297D THR* 1.3 74.6 - - - +
299D ASP* 1.3 55.5 + - - +
301D LEU* 3.3 9.7 + - - +
302D GLN 3.0 22.0 + - - -
324D LEU* 4.2 13.7 - - + -
327D ILE* 4.3 5.4 - - + -
336D LEU* 4.1 0.2 - - - +
339D THR* 2.8 26.7 + - - -
340D THR* 3.5 21.6 + - - +
343D VAL* 3.1 22.3 - - - +
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Residues in contact with ASP 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260D HIS* 3.0 23.4 + - + -
264D LEU* 5.3 1.7 - - - +
295D ALA 3.2 20.9 + - - +
296D ILE 3.7 4.0 - - - +
297D THR 3.2 0.2 - - - -
298D THR* 1.3 75.3 + - - +
300D CYS* 1.3 64.2 + - - +
302D GLN* 3.2 10.9 + - - +
303D ILE* 3.1 29.6 + - - +
338D TRP* 5.9 0.8 - - - -
339D THR* 4.2 13.3 - - + +
342D ARG* 3.3 27.0 + - - -
41E LEU* 3.1 23.8 - - + +
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Residues in contact with CYS 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D ILE* 3.5 22.9 - - + -
259D LEU* 4.8 0.7 - - - -
260D HIS* 3.5 28.5 + - - -
263D LEU* 3.8 21.4 - - + +
282D MET* 3.8 19.3 - - - -
296D ILE 3.0 19.7 + - - -
297D THR 3.5 7.9 - - - +
299D ASP* 1.3 74.5 - - - +
301D LEU* 1.3 63.0 + - - +
303D ILE* 3.2 8.9 + - - +
304D LEU* 3.0 28.2 + - - +
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Residues in contact with LEU 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D LEU* 4.0 22.7 - - + +
282D MET* 3.7 29.2 - - + -
283D VAL* 4.2 20.2 - - + -
286D LEU* 4.0 30.5 - - + -
297D THR 3.2 15.7 + - - +
298D THR* 3.5 13.5 - - - +
299D ASP 3.2 0.2 - - - -
300D CYS* 1.3 76.1 - - - +
302D GLN* 1.3 58.2 + - - +
304D LEU* 3.2 4.8 + - - +
305D ALA* 2.8 35.7 + - - +
315D ILE* 4.3 10.2 - - + +
324D LEU* 5.0 6.7 - - + -
343D VAL* 4.3 13.9 - - + -
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Residues in contact with GLN 302 (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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298D THR 3.0 12.5 + - - +
299D ASP* 3.2 16.8 + - - +
301D LEU* 1.3 76.8 - - - +
303D ILE* 1.3 66.7 + - - +
305D ALA* 4.9 1.8 - - - -
306D TYR* 3.3 27.9 + - - +
339D THR 5.0 0.7 - - - +
342D ARG* 3.1 63.7 - - + +
343D VAL* 3.9 14.0 - - + +
346D VAL* 4.5 7.7 - - + +
27E GLN* 2.8 44.6 + - - +
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Residues in contact with ILE 303 (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* 4.1 16.6 - - + -
263D LEU* 4.0 38.4 - - + +
264D LEU* 4.0 27.6 - - + -
270D LYS* 3.8 29.8 + - + +
274D ARG* 4.5 1.0 + - - -
299D ASP* 3.1 20.5 + - - +
300D CYS* 3.6 7.6 - - - +
302D GLN* 1.3 87.4 - - - +
304D LEU* 1.3 60.4 + - - +
306D TYR* 3.9 10.9 + - - +
27E GLN* 3.5 18.9 + - - +
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Residues in contact with LEU 304 (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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263D LEU* 3.7 26.2 - - + -
270D LYS* 3.6 32.1 - - + +
273D VAL* 3.8 24.7 - - + -
274D ARG* 2.9 31.8 + - + +
279D LEU* 3.6 29.2 - - + -
282D MET* 3.9 18.6 - - + -
300D CYS 3.0 19.6 + - - +
301D LEU 3.7 3.6 - - - +
303D ILE* 1.3 77.0 - - - +
305D ALA* 1.3 61.0 + - - +
306D TYR 3.4 0.2 - - - -
308D ASN* 3.7 1.4 - - - +
311D SER* 3.4 12.7 + - - -
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Residues in contact with ALA 305 (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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301D LEU 2.8 17.9 + - - +
302D GLN* 4.5 1.8 - - - +
304D LEU* 1.3 76.1 - - - +
306D TYR* 1.3 66.2 + - - +
307D GLY 3.2 2.9 + - - -
308D ASN 3.2 11.6 + - - +
311D SER* 4.1 8.7 - - - -
312D LYS* 3.2 22.0 - - + -
315D ILE* 3.8 24.0 - - + -
343D VAL* 5.3 3.6 - - + -
346D VAL* 3.9 15.9 - - + -
347D LEU* 4.9 2.9 - - + -
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Residues in contact with TYR 306 (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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270D LYS* 5.7 2.6 + - - -
274D ARG* 4.8 2.6 + - - -
302D GLN* 3.3 25.9 + - - +
303D ILE 4.2 6.6 - - - +
304D LEU 3.4 2.8 - - - +
305D ALA* 1.3 76.1 - - - +
307D GLY* 1.3 70.4 + - - +
308D ASN* 3.1 6.6 + - - +
346D VAL* 3.9 24.2 - - + +
24E GLU* 4.2 20.6 + - + -
25E GLY 3.1 28.4 + - - -
26E GLU* 3.4 32.0 + - + +
27E GLN* 3.7 25.1 - - + +
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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