Contacts of the strand formed by residues 333 - 340 (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 HIS 333 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B ILE* 3.5 39.9 - - + +
179B SER 5.2 3.6 + - - -
180B PRO* 6.0 0.8 - - - +
212B LEU* 5.3 2.1 + - + -
213B ASN* 6.1 1.0 - - - +
330B HIS* 3.2 47.0 + + + +
332B GLU* 1.3 101.7 + - + +
334B SER* 1.3 62.9 + - - +
335B ASN* 3.0 19.1 + - - +
336B VAL* 3.1 25.0 + - + +
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Residues in contact with SER 334 (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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196B LYS* 4.7 5.6 - - - +
329B LEU* 3.7 37.4 - - - +
330B HIS 4.3 0.6 + - - -
332B GLU 4.2 0.4 - - - -
333B HIS* 1.3 72.1 - - - +
335B ASN* 1.3 59.4 + - - +
336B VAL 3.3 2.9 + - - -
337B VAL* 5.4 0.7 - - - +
360B LEU 5.0 2.9 - - - +
364B GLY* 5.2 3.0 - - - -
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Residues in contact with ASN 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ILE* 3.6 6.6 - - - +
179B SER 3.0 25.1 + - - +
180B PRO* 4.0 10.5 + - - +
181B ASP 4.4 0.4 - - - -
182B SER 3.7 11.3 + - - +
183B VAL* 3.7 18.0 - - - +
195B ASP 3.5 15.7 + - - +
196B LYS* 3.4 22.1 - - + +
197B LEU 2.9 25.6 + - - -
333B HIS* 3.4 20.4 + - - +
334B SER* 1.3 80.2 + - - +
336B VAL* 1.3 57.6 + - - +
337B VAL* 4.3 2.5 - - - -
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Residues in contact with VAL 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ILE* 3.8 29.6 - - + -
183B VAL* 4.4 0.7 - - + -
197B LEU* 3.3 24.0 - - + +
199B VAL* 4.2 4.0 - - + -
212B LEU* 4.8 4.0 - - + -
329B LEU* 3.3 6.4 - - - +
330B HIS* 2.8 45.8 + - + -
333B HIS* 3.1 12.6 + - + +
334B SER 3.3 0.6 - - - -
335B ASN* 1.3 96.1 - - - +
337B VAL* 1.3 63.9 + - - +
338B ILE* 3.8 23.8 - - + -
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Residues in contact with VAL 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LYS* 6.0 0.2 - - + -
197B LEU 2.7 17.0 + - - +
198B ILE* 3.4 8.4 - - + +
199B VAL* 2.8 32.4 + - - +
328B ASP 3.7 5.6 - - - +
329B LEU* 4.0 11.2 - - + +
334B SER 5.4 0.2 - - - +
335B ASN 5.2 2.5 - - - -
336B VAL* 1.3 79.9 - - - +
338B ILE* 1.3 64.0 + - - +
357B LEU* 3.6 31.0 - - + +
360B LEU* 3.8 23.6 - - + +
361B ALA* 3.8 36.6 - - + +
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Residues in contact with ILE 338 (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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199B VAL* 3.7 18.4 - - + +
205B ASN* 5.7 0.4 - - - +
209B LEU* 4.4 20.2 - - + -
212B LEU* 4.3 11.2 - - + -
214B LEU* 4.5 7.9 - - + -
326B ILE* 3.4 13.3 - - + +
327B ILE* 3.3 7.8 + - - +
328B ASP 2.8 37.1 + - - +
330B HIS* 4.4 18.2 - - + -
336B VAL* 3.8 18.4 - - + -
337B VAL* 1.3 84.3 - - - +
339B ALA* 1.3 63.5 + - - +
340B ALA* 4.2 19.3 - - + -
357B LEU* 4.8 0.2 - - - -
375B ILE* 4.4 15.3 - - + -
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Residues in contact with ALA 339 (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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14B MET* 4.5 1.6 - - + -
198B ILE* 5.4 0.7 - - + -
199B VAL 2.9 20.4 + - - +
200B SER* 3.6 14.7 - - - -
202B GLY 5.1 0.5 + - - -
205B ASN* 3.2 12.5 - - - +
326B ILE 3.3 5.6 - - - -
327B ILE* 4.7 1.6 - - + +
338B ILE* 1.3 73.4 - - - +
340B ALA* 1.3 58.8 + - - +
342B PHE* 3.7 22.6 - - + -
353B VAL* 4.9 0.9 - - + -
357B LEU* 3.9 32.3 - - + -
400B FAD 5.2 0.9 + - - -
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Residues in contact with ALA 340 (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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202B GLY* 6.2 0.2 - - - -
205B ASN* 3.2 32.3 - - + +
209B LEU* 4.4 5.4 - - + -
218B LEU* 4.4 2.2 - - + -
325B PHE* 4.0 0.2 - - - -
326B ILE* 2.9 48.1 + - + +
338B ILE* 4.1 13.9 - - + -
339B ALA* 1.3 72.3 - - - +
341B GLY* 1.3 64.8 + - - +
342B PHE* 3.5 12.9 + - - -
400B FAD 5.9 0.2 - - - -
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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