Contacts of the strand formed by residues 309 - 319 (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 LEU 309 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A GLY* 4.1 5.2 - - - -
227A PHE 3.5 13.2 - - - +
228A PHE* 3.9 21.1 - - + -
284A PHE* 3.5 32.1 - - + -
291A GLU* 3.7 20.0 - - - +
295A ARG* 3.4 17.7 - - - +
308A GLU* 1.3 78.1 - - - +
310A LYS* 1.3 59.7 + - - +
311A ARG* 3.4 29.4 - - - +
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Residues in contact with LYS 310 (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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227A PHE* 2.7 17.4 + - + +
228A PHE 3.8 2.9 - - - -
229A GLU* 2.9 51.2 + - - +
261A GLY 3.5 17.6 + - - -
262A CYS* 3.2 28.3 - - - +
263A GLY* 4.2 0.4 - - - -
308A GLU* 3.7 13.0 - - + +
309A LEU* 1.3 75.4 - - - +
311A ARG* 1.3 61.2 + - + +
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Residues in contact with ARG 311 (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* 4.0 27.1 - - - +
47A ASP* 4.2 18.0 + - - +
150A GLU* 4.5 4.0 + - - -
226A GLY* 3.4 2.4 - - - -
227A PHE* 2.8 71.6 + - + -
262A CYS* 6.2 0.6 - - - +
309A LEU* 3.4 10.7 - - - +
310A LYS* 1.3 84.7 - - + +
312A GLY* 1.3 71.2 + - - +
313A ALA* 5.2 4.4 - - - +
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Residues in contact with GLY 312 (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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225A VAL 3.4 10.8 - - - -
227A PHE* 5.0 1.3 - - - -
284A PHE* 3.8 28.6 - - - +
309A LEU* 5.1 0.6 - - - +
311A ARG* 1.3 86.3 + - - +
313A ALA* 1.3 60.1 + - - +
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Residues in contact with ALA 313 (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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45A HIS* 4.4 13.0 - - + -
46A GLY* 4.3 17.7 - - - -
223A GLN 4.2 0.2 - - - +
224A VAL* 3.3 7.3 - - - +
225A VAL* 3.1 48.9 + - + +
227A PHE* 5.4 0.9 - - + -
284A PHE* 3.9 1.4 - - - -
311A ARG* 5.2 7.6 - - - +
312A GLY* 1.3 75.2 - - - +
314A VAL* 1.3 64.7 + - - +
315A CYS* 5.8 1.3 - - + -
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Residues in contact with VAL 314 (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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40A THR 4.5 1.9 - - - +
45A HIS* 2.7 23.1 + - - -
222A ARG* 3.7 31.4 - - + +
223A GLN 3.9 1.8 - - - -
224A VAL* 3.9 6.1 - - + +
280A ILE* 4.0 9.2 - - + -
281A ASN 3.7 17.9 - - - +
282A ARG* 3.3 43.0 + - + +
283A GLU 3.7 2.5 - - - -
284A PHE* 3.6 22.4 - - - +
313A ALA* 1.3 81.2 - - - +
315A CYS* 1.3 65.0 + - - +
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Residues in contact with CYS 315 (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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42A GLY 4.1 1.3 - - - -
43A SER* 3.7 13.7 - - - -
45A HIS* 3.6 19.3 - - + +
49A ARG* 3.6 15.7 - - - -
222A ARG* 3.8 1.9 - - - -
223A GLN 2.8 32.2 + - - +
225A VAL* 6.2 0.4 - - + -
280A ILE* 5.5 0.4 - - - -
282A ARG* 6.3 0.4 - - - +
313A ALA* 5.3 2.5 - - + -
314A VAL* 1.3 80.1 - - - +
316A MET* 1.3 69.1 + - - +
400A FAD 1.8 61.9 - - + -
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Residues in contact with MET 316 (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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41A ASN 3.3 26.5 - - - +
42A GLY* 3.8 14.8 + - - +
43A SER* 2.7 30.3 + - - +
203A ALA* 3.6 31.9 - - + -
204A TRP* 3.9 14.6 - - + -
220A PRO* 5.0 0.4 - - + -
221A TYR 3.3 9.9 - - - +
275A ILE* 3.8 12.6 - - + -
277A PRO* 3.8 20.2 - - - -
280A ILE* 3.5 25.1 - - + -
282A ARG* 4.0 5.2 - - - +
315A CYS* 1.3 84.2 - - - +
317A TYR* 1.3 68.4 + - - +
400A FAD 3.4 6.1 - - - +
803A CL 4.0 2.3 - - - +
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Residues in contact with TYR 317 (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 3.7 0.4 - - - +
220A PRO* 3.1 4.0 - - - +
221A TYR* 2.8 37.1 + - + +
223A GLN* 3.5 34.4 + - + -
254A TYR* 3.4 23.7 + - - -
269A HIS* 2.7 55.1 + + - -
316A MET* 1.3 76.4 - - - +
318A THR* 1.3 61.9 + - - +
319A LYS* 4.0 22.2 - - + -
343A SER 4.4 2.5 - - - -
344A GLY* 3.4 23.5 + - - +
400A FAD 3.4 39.6 + + - -
803A CL 3.7 4.7 - - - -
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Residues in contact with THR 318 (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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43A SER* 5.1 2.6 + - - -
202A GLY 3.9 8.2 - - - +
203A ALA* 3.0 38.4 + - - +
205A ASN* 5.4 0.2 - - + -
206A SER* 4.6 8.1 - - - -
218A LEU* 4.0 33.2 - - + -
219A GLN 3.5 7.4 - - - +
220A PRO* 4.2 1.9 - - + +
317A TYR* 1.3 76.3 + - - +
319A LYS* 1.3 59.7 + - - +
341A GLY* 3.3 18.6 - - - +
342A PHE 5.1 0.4 - - - -
343A SER* 2.9 23.6 + - - -
803A CL 3.5 10.1 - - - +
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Residues in contact with LYS 319 (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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217A PRO 3.8 0.9 - - - +
218A LEU* 3.3 8.0 - - - -
219A GLN* 2.9 36.1 + - + +
221A TYR* 3.4 47.7 + - + +
223A GLN* 4.9 2.2 + - - -
269A HIS 4.9 5.8 + - - -
270A THR* 4.7 13.5 + - - +
272A GLY 5.9 0.8 - - - +
317A TYR* 4.1 23.0 - - + -
318A THR* 1.3 76.3 - - - +
320A THR* 1.3 70.2 + - - +
323A GLU* 4.0 24.2 + - + +
343A SER* 3.4 21.3 - - - +
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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