Contacts of the strand formed by residues 219 - 228 (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 GLN 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A LEU* 1.3 74.0 + - - +
220A PRO* 1.3 91.2 - - - +
221A TYR* 3.2 41.4 - - + +
274A LYS* 3.7 34.3 - - + +
275A ILE 3.7 6.9 - - - +
318A THR* 4.3 1.1 - - - -
319A LYS* 2.9 36.3 + - + +
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Residues in contact with PRO 220 (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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203A ALA* 4.0 16.6 - - + +
206A SER* 3.2 26.2 - - - +
218A LEU 3.6 9.0 - - - +
219A GLN* 1.3 112.6 - - - +
221A TYR* 1.3 59.9 + - - +
274A LYS* 3.7 1.4 - - - -
275A ILE* 3.2 41.8 + - + +
277A PRO* 4.1 9.6 - - + -
316A MET* 5.0 0.9 - - - -
317A TYR 3.1 10.3 - - - +
318A THR* 4.2 4.7 - - + +
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Residues in contact with TYR 221 (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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219A GLN* 3.2 48.6 - - + +
220A PRO* 1.3 73.4 - - - +
222A ARG* 1.3 60.4 + - - +
223A GLN* 3.4 19.8 + - + +
272A GLY* 3.6 26.2 - - - -
273A GLN 3.2 7.2 - - - +
274A LYS* 3.7 31.1 - - + -
275A ILE* 3.9 4.3 - - - -
316A MET* 3.3 9.5 - - - +
317A TYR* 2.8 31.7 + - + +
319A LYS* 3.4 45.7 + - + +
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Residues in contact with ARG 222 (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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221A TYR* 1.3 68.4 - - - +
223A GLN* 1.3 60.6 + - - +
224A VAL* 3.5 16.4 + - + +
272A GLY* 3.2 22.7 - - - -
273A GLN* 2.7 46.0 + - - +
275A ILE* 3.7 16.7 - - + +
280A ILE* 3.9 13.2 - - + -
281A ASN 2.9 22.8 + - - +
283A GLU 3.0 22.0 + - - -
286A VAL* 3.8 1.4 - - - +
287A TYR* 3.1 34.3 - - - -
290A ASP* 2.8 43.6 + - - -
314A VAL* 3.7 18.5 - - + +
315A CYS 3.8 3.6 - - - -
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Residues in contact with GLN 223 (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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221A TYR* 3.4 21.1 - - - +
222A ARG* 1.3 77.0 - - - +
224A VAL* 1.3 65.3 + - - +
254A TYR* 5.1 1.3 + - - +
268A TYR 3.2 17.0 + - - -
269A HIS 4.0 2.2 + - - +
271A PHE 3.0 23.8 + - - +
272A GLY* 3.3 18.9 + - - -
313A ALA 4.2 0.2 - - - +
314A VAL* 3.9 0.2 - - - -
315A CYS* 2.8 37.9 + - - +
317A TYR* 3.5 56.6 + - + +
319A LYS* 4.9 2.1 + - - -
400A FAD 3.8 12.6 - - + +
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Residues in contact with VAL 224 (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* 3.5 41.0 + - + +
223A GLN* 1.3 78.4 - - - +
225A VAL* 1.3 70.0 + - - +
254A TYR* 4.3 1.9 + - - -
267A GLY* 3.9 10.6 - - - -
268A TYR 4.4 6.1 + - - +
273A GLN* 5.4 0.2 - - - +
284A PHE* 3.7 22.0 - - + -
290A ASP* 3.8 27.4 - - - +
294A LEU* 4.8 5.6 - - + +
313A ALA 3.3 9.6 - - - +
314A VAL* 3.9 14.1 - - + -
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Residues in contact with VAL 225 (chain A).
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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46A GLY* 4.9 4.0 - - - -
224A VAL* 1.3 80.5 - - - +
226A GLY* 1.3 59.5 + - - +
227A PHE* 4.8 5.8 - - + -
254A TYR* 3.3 24.2 - - + +
265A LYS* 3.9 33.4 - - + +
266A LEU 3.3 13.5 - - - +
267A GLY* 4.0 2.7 - - - -
284A PHE* 3.4 8.6 - - - -
294A LEU* 4.2 0.9 - - - -
312A GLY* 3.4 4.0 - - - -
313A ALA* 3.1 50.6 + - + +
315A CYS* 6.2 0.4 - - + -
400A FAD 3.7 16.4 - - + -
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Residues in contact with GLY 226 (chain A).
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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225A VAL* 1.3 75.0 - - - +
227A PHE* 1.3 63.6 + - - -
228A PHE* 3.5 20.1 - - - -
265A LYS* 3.3 3.9 - - - +
266A LEU 3.0 32.9 + - - -
284A PHE* 4.4 2.0 - - - -
294A LEU* 3.6 7.7 - - - +
309A LEU* 4.1 6.5 - - - -
311A ARG 3.4 8.3 - - - -
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Residues in contact with PHE 227 (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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46A GLY* 3.8 13.9 - - - -
47A ASP* 4.7 4.3 - - + -
48A THR* 5.3 1.8 - - + -
225A VAL* 4.8 8.5 - - + -
226A GLY* 1.3 77.5 - - - -
228A PHE* 1.3 56.0 - - - +
262A CYS* 3.7 40.6 - - + +
263A GLY 4.0 10.1 - - - -
264A LEU 3.4 4.7 - - - -
265A LYS* 3.6 35.2 - - + -
309A LEU* 3.5 4.4 - - - +
310A LYS* 2.7 33.9 + - + -
311A ARG* 2.8 72.8 + - + +
312A GLY* 4.7 0.9 - - - -
313A ALA* 5.4 2.5 - - + -
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Residues in contact with PHE 228 (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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226A GLY* 3.5 24.2 - - - -
227A PHE* 1.3 75.3 - - - +
229A GLU* 1.3 57.7 + - - +
230A SER* 2.8 22.6 + - - +
263A GLY* 3.1 13.5 - - - -
264A LEU* 2.9 15.6 + - + +
266A LEU* 4.7 5.8 - - + -
291A GLU* 4.6 6.3 - - + -
294A LEU* 3.9 32.8 - - + -
295A ARG* 3.6 34.8 - - + -
298A LEU* 3.7 21.5 - - + -
305A ALA 3.5 17.7 - - - +
307A GLY 3.7 18.2 - - - +
308A GLU 3.5 2.0 - - - +
309A LEU* 3.9 21.5 - - + -
310A LYS* 3.8 4.9 - - - -
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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