Contacts of the helix formed by residues 288 - 302 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285A GLY 5.2 1.1 - - - +
286A VAL 4.4 3.1 - - - +
287A TYR* 1.3 82.0 - - + +
289A GLU* 1.3 79.5 + - + +
290A ASP 3.2 0.5 + - - -
291A GLU* 3.6 3.8 + - - +
292A SER* 2.9 28.1 + - - +
288B PRO* 5.4 16.8 - - + -
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Residues in contact with GLU 289 (chain A).
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* 4.4 17.9 - - + -
273A GLN* 3.5 22.1 + - - +
287A TYR* 3.6 13.3 - - - +
288A PRO* 1.3 97.9 - - + +
290A ASP* 1.3 68.5 + - - +
292A SER* 3.3 9.9 - - - +
293A ASN* 3.1 41.6 + - - +
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Residues in contact with ASP 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A ARG* 2.8 41.9 + - - -
224A VAL* 3.8 20.3 - - + +
273A GLN* 4.3 3.6 + - - -
284A PHE* 3.7 13.6 - - + -
285A GLY* 2.7 33.6 + - - +
286A VAL 3.6 3.3 + - - -
287A TYR* 3.1 22.4 + - - +
289A GLU* 1.3 78.9 - - - +
291A GLU* 1.3 60.0 + - - +
293A ASN* 5.0 0.5 - - - +
294A LEU* 3.3 26.0 - - - +
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Residues in contact with GLU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A PHE* 4.6 7.2 - - + -
284A PHE* 4.0 13.7 - - + -
285A GLY* 5.9 2.8 - - - -
287A TYR 4.4 0.2 + - - -
288A PRO 3.6 3.2 + - - +
290A ASP* 1.3 78.6 - - - +
292A SER* 1.3 67.3 + - - +
294A LEU* 3.2 7.7 + - - +
295A ARG* 2.9 62.2 + - + +
309A LEU* 3.7 24.9 - - + +
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Residues in contact with SER 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A PRO* 2.9 24.2 + - - -
289A GLU* 3.3 10.0 - - - +
291A GLU* 1.3 80.2 - - - +
293A ASN* 1.3 67.6 + - - +
295A ARG* 4.1 5.5 - - - +
296A ALA* 3.1 25.6 + - - +
289B GLU* 6.2 0.3 - - - +
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Residues in contact with ASN 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A ASN* 5.5 2.6 - - - +
253A TYR* 3.3 23.6 + - - +
268A TYR* 3.6 41.0 - - + -
271A PHE* 3.9 9.2 - - - -
289A GLU* 3.1 40.1 + - - +
290A ASP 5.0 0.7 - - - +
292A SER* 1.3 83.8 + - - +
294A LEU* 1.3 65.8 + - + +
296A ALA* 3.7 5.7 + - - +
297A PHE 3.6 6.4 + - - -
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Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A VAL* 4.8 5.4 - - + +
225A VAL* 4.2 2.7 - - - -
226A GLY* 3.6 28.5 - - - +
228A PHE* 3.9 24.0 - - + -
253A TYR* 4.8 0.2 - - + -
266A LEU* 3.5 34.4 - - + +
267A GLY* 4.0 1.3 - - - -
268A TYR* 3.9 27.4 - - + +
284A PHE* 4.2 8.7 - - + -
290A ASP 3.3 21.3 - - - +
291A GLU 3.2 5.6 + - - +
292A SER 3.1 0.6 - - - -
293A ASN* 1.3 77.6 - - + +
295A ARG* 1.3 65.9 + - - +
297A PHE* 3.0 15.2 + - - +
298A LEU* 3.0 16.9 + - - +
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Residues in contact with ARG 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A PHE* 3.6 19.9 - - + -
291A GLU* 2.9 46.4 + - - +
292A SER* 4.3 5.2 - - - +
294A LEU* 1.3 75.9 - - - +
296A ALA* 1.3 57.7 + - - +
298A LEU* 3.9 2.4 - - - +
299A GLU* 2.8 39.5 + - - +
306A ASN* 2.7 58.2 + - - +
307A GLY 2.8 30.1 + - - -
308A GLU* 4.1 2.0 - - - +
309A LEU 3.4 16.8 - - - +
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Residues in contact with ALA 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A ASN* 5.9 2.2 - - - +
253A TYR* 5.1 3.1 - - - +
292A SER 3.1 18.2 + - - +
293A ASN* 3.8 11.0 - - - +
294A LEU 3.2 0.2 - - - -
295A ARG* 1.3 77.2 - - - +
297A PHE* 1.3 62.3 + - - +
299A GLU* 3.6 23.2 - - - +
300A GLU* 3.8 11.1 - - - +
271B PHE* 5.9 7.9 - - + -
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Residues in contact with PHE 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PHE* 4.6 2.2 - + - -
244A PHE* 4.1 7.4 - + - -
246A VAL* 3.7 31.9 - - + -
248A VAL* 4.1 3.8 - - + -
253A TYR* 3.5 47.1 + + + -
266A LEU* 3.6 27.4 - - + -
293A ASN 3.6 1.2 + - - -
294A LEU 3.0 8.7 + - - +
296A ALA* 1.3 79.3 - - - +
298A LEU* 1.3 66.2 + - + +
300A GLU 3.2 1.9 + - - -
301A TYR* 2.9 67.3 + + + -
302A MET* 4.0 26.7 - - + -
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Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A PHE* 3.7 33.0 - - + -
264A LEU* 3.8 25.1 - - + -
266A LEU* 3.7 14.4 - - + -
294A LEU 3.0 18.6 + - - +
295A ARG 3.9 2.5 - - - +
297A PHE* 1.3 84.9 - - + +
299A GLU* 1.3 64.2 + - - +
302A MET* 2.9 48.2 + - + +
303A PRO* 3.0 1.2 - - - -
305A ALA* 3.4 21.1 - - + +
306A ASN* 3.9 25.1 - - + +
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Residues in contact with GLU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A ARG* 2.8 27.9 + - - +
296A ALA* 3.6 17.4 - - - +
298A LEU* 1.3 73.7 - - - +
300A GLU* 1.3 63.6 + - + +
303A PRO* 3.8 18.9 - - - +
306A ASN* 3.7 18.2 + - - +
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Residues in contact with GLU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A THR* 2.9 23.1 + - - +
133A PRO* 4.9 10.2 - - - +
296A ALA 3.8 14.6 - - - +
297A PHE 3.2 3.0 + - - +
298A LEU 3.1 0.8 - - - -
299A GLU* 1.3 83.8 - - + +
301A TYR* 1.3 90.0 + - + +
302A MET 3.9 0.2 - - - -
303A PRO* 4.6 0.2 - - - -
274B LYS* 3.3 29.4 + - - -
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Residues in contact with TYR 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PHE* 4.5 8.5 - + + -
130A ILE* 3.3 3.8 - - - +
131A THR* 2.7 40.0 + - - -
132A VAL* 4.0 11.7 - - + -
133A PRO* 4.0 11.9 - - + +
136A TYR* 2.9 36.2 + + - -
248A VAL* 3.4 27.7 - - + +
249A PRO* 3.8 5.5 - - - +
296A ALA 5.5 0.2 - - - -
297A PHE* 2.9 53.1 + + + +
300A GLU* 1.3 98.9 - - + +
302A MET* 1.3 65.7 - - + +
303A PRO* 3.4 6.1 - - - -
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Residues in contact with MET 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PHE* 4.5 11.7 - - + -
129A GLY 3.2 13.9 - - - +
130A ILE* 4.2 15.3 - - + -
235A TYR* 3.4 10.3 - - + -
241A PHE* 4.0 14.8 - - + -
244A PHE* 3.5 54.5 - - + -
264A LEU* 4.0 12.6 - - - -
297A PHE* 4.0 16.3 + - + -
298A LEU* 2.9 25.5 + - + +
301A TYR* 1.3 83.1 - - + +
303A PRO* 1.3 61.8 - - - +
304A GLY 3.2 2.7 - - - -
305A ALA* 3.0 25.8 + - + +
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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