Contacts of the helix formed by residues 288 - 302 (chain B) in PDB entry 2GB0
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 PRO 288 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A PRO* 5.4 17.0 - - + -
285B GLY 5.1 1.3 - - - +
286B VAL 4.3 3.4 - - - +
287B TYR* 1.3 82.3 - - + +
289B GLU* 1.3 80.5 + - + +
290B ASP 3.2 0.3 + - - -
291B GLU* 3.6 3.6 + - - +
292B SER* 2.9 26.8 + - - +
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Residues in contact with GLU 289 (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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271B PHE* 4.4 17.0 - - + -
273B GLN* 3.5 22.0 + - - +
287B TYR* 3.6 14.0 - - - +
288B PRO* 1.3 98.4 - - + +
290B ASP* 1.3 68.0 + - - +
292B SER* 3.3 10.1 - - - +
293B ASN* 3.0 43.8 + - - +
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Residues in contact with ASP 290 (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 ARG* 2.8 41.3 + - - -
224B VAL* 3.8 20.0 - - - +
273B GLN* 4.3 4.0 + - - -
284B PHE* 3.7 14.6 - - + -
285B GLY* 2.7 33.8 + - - +
286B VAL 3.5 3.1 + - - -
287B TYR* 3.0 20.2 + - - +
289B GLU* 1.3 79.0 - - - +
291B GLU* 1.3 59.6 + - - +
294B LEU* 3.3 27.4 - - - +
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Residues in contact with GLU 291 (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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228B PHE* 4.7 6.1 - - + -
284B PHE* 4.0 14.1 - - + -
285B GLY* 5.5 3.3 - - - -
287B TYR 4.4 0.2 + - - -
288B PRO 3.6 4.4 + - - +
289B GLU 3.3 0.2 - - - -
290B ASP* 1.3 78.2 - - + +
292B SER* 1.3 66.7 + - - +
294B LEU* 3.2 7.1 + - - +
295B ARG* 3.0 61.4 + - + +
309B LEU* 3.8 26.0 - - + +
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Residues in contact with SER 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A GLU* 6.2 0.3 - - - +
288B PRO* 2.9 24.5 + - - +
289B GLU* 3.3 9.5 - - - +
291B GLU* 1.3 79.3 - - - +
293B ASN* 1.3 67.8 + - - +
295B ARG* 3.5 5.8 + - - +
296B ALA* 3.0 25.3 + - - +
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Residues in contact with ASN 293 (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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250B ASN* 5.5 2.8 - - - +
253B TYR* 3.3 23.1 + - - +
268B TYR* 3.6 42.3 - - + -
271B PHE* 3.9 9.9 - - - -
289B GLU* 3.0 38.2 + - - +
290B ASP 5.0 0.9 - - - +
292B SER* 1.3 84.4 + - - +
294B LEU* 1.3 65.0 + - + +
296B ALA* 3.7 5.6 + - - +
297B PHE 3.6 7.1 + - - -
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Residues in contact with LEU 294 (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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224B VAL* 4.8 5.8 - - + +
225B VAL* 4.3 2.0 - - - -
226B GLY* 3.6 28.5 - - - +
228B PHE* 3.8 25.1 - - + -
253B TYR* 4.9 0.4 - - + -
266B LEU* 3.4 34.8 - - + +
267B GLY* 4.0 2.2 - - - -
268B TYR* 3.9 28.3 - - + +
284B PHE* 4.2 9.6 - - + -
290B ASP 3.3 20.9 - - - +
291B GLU* 3.2 5.6 + - - +
292B SER 3.2 0.4 - - - -
293B ASN* 1.3 78.9 - - + +
295B ARG* 1.3 66.4 + - - +
297B PHE 3.0 11.3 + - - -
298B LEU* 3.0 16.9 + - - +
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Residues in contact with ARG 295 (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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228B PHE* 3.7 20.3 - - + -
291B GLU* 3.0 46.9 + - - +
292B SER* 4.2 4.7 - - - +
294B LEU* 1.3 77.6 - - - +
296B ALA* 1.3 57.4 + - - +
298B LEU* 4.3 1.6 - - - +
299B GLU* 2.8 39.0 + - - +
306B ASN* 2.6 58.3 + - - +
307B GLY 2.8 30.7 + - - -
308B GLU* 4.1 1.4 - - - +
309B LEU* 3.5 17.0 - - - +
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Residues in contact with ALA 296 (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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271A PHE* 5.9 8.1 - - + -
250B ASN* 6.0 2.5 - - - +
253B TYR* 5.1 3.6 - - - +
292B SER 3.0 18.6 + - - +
293B ASN* 3.8 10.8 - - - +
294B LEU 3.2 0.2 - - - -
295B ARG* 1.3 76.9 - - - +
297B PHE* 1.3 62.8 + - - +
299B GLU* 3.6 23.5 - - - +
300B GLU* 3.8 10.9 - - - +
301B TYR* 5.4 0.2 - - - -
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Residues in contact with PHE 297 (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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92B PHE* 4.7 1.6 - + - -
244B PHE* 4.1 8.1 - + - -
246B VAL* 3.7 31.9 - - + -
248B VAL* 4.1 4.3 - - + -
253B TYR* 3.6 47.5 + + + -
266B LEU* 3.6 28.3 - - + -
293B ASN 3.6 1.6 + - - -
294B LEU 3.0 8.1 + - - +
296B ALA* 1.3 79.6 - - - +
298B LEU* 1.3 66.1 + - + +
300B GLU 3.2 1.7 + - - -
301B TYR* 2.9 68.2 + + + +
302B MET* 4.0 25.8 - - + -
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Residues in contact with LEU 298 (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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228B PHE* 3.7 32.3 - - + -
264B LEU* 3.8 22.7 - - + -
266B LEU* 3.7 13.2 - - + -
294B LEU 3.0 20.7 + - - +
295B ARG 3.2 3.1 + - - +
297B PHE* 1.3 79.1 - - + +
299B GLU* 1.3 65.7 + - - +
302B MET* 2.9 51.0 + - + +
303B PRO* 2.9 1.9 - - - -
305B ALA* 3.4 23.6 - - + +
306B ASN* 3.9 25.1 - - + +
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Residues in contact with GLU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ARG* 2.8 26.8 + - - +
296B ALA* 3.6 17.8 - - - +
298B LEU* 1.3 74.2 - - - +
300B GLU* 1.3 62.7 + - + +
303B PRO* 3.8 19.4 - - - +
306B ASN* 3.7 17.3 + - - +
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Residues in contact with GLU 300 (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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274A LYS* 3.6 25.6 + - - -
131B THR* 2.9 20.9 + - - +
133B PRO* 5.1 8.8 - - - +
296B ALA 3.8 14.8 - - - +
297B PHE 3.2 3.7 + - - +
298B LEU 3.1 0.6 - - - -
299B GLU* 1.3 84.6 - - + +
301B TYR* 1.3 89.6 - - + +
302B MET 3.9 0.2 - - - -
303B PRO* 4.6 0.4 - - - -
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Residues in contact with TYR 301 (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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92B PHE* 4.6 7.9 - + + -
130B ILE* 3.3 3.3 - - - +
131B THR* 2.7 41.3 + - - -
132B VAL* 4.1 12.1 - - + -
133B PRO* 4.0 12.8 - - + +
136B TYR* 3.1 31.5 + + - -
248B VAL* 3.3 31.7 - - + +
249B PRO* 3.8 5.9 - - - +
296B ALA 5.4 0.2 - - - -
297B PHE* 2.9 56.4 + + + +
300B GLU* 1.3 95.1 + - + +
302B MET* 1.3 68.3 + - + +
303B PRO* 3.4 6.1 - - - -
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Residues in contact with MET 302 (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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92B PHE* 4.6 11.0 - - + -
129B GLY 3.2 14.1 - - - +
130B ILE* 4.2 14.1 - - + -
235B TYR* 3.4 12.3 - - + -
241B PHE* 3.9 19.3 - - + -
244B PHE* 3.6 54.5 - - + -
264B LEU* 4.0 7.9 - - - -
297B PHE* 4.0 15.5 + - + -
298B LEU* 2.9 26.4 + - + +
301B TYR* 1.3 85.6 - - + +
303B PRO* 1.3 61.5 - - - +
304B GLY 3.3 2.5 - - - -
305B ALA* 3.0 25.0 + - + +
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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