Contacts of the strand formed by residues 333 - 340 (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 HIS 333 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A ILE* 3.5 40.5 - - + +
179A SER 5.0 5.3 + - - -
180A PRO* 5.6 2.4 - - + +
212A LEU* 5.3 1.9 + - + -
213A ASN* 6.1 0.8 - - - +
330A HIS* 3.1 51.1 + + + +
332A GLU* 1.3 100.9 + - + +
334A SER* 1.3 61.6 + - - +
335A ASN* 3.0 19.8 + - - +
336A VAL* 3.1 21.1 + - + +
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Residues in contact with SER 334 (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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196A LYS* 4.8 5.1 - - - +
329A LEU* 3.7 39.2 - - - +
330A HIS 4.2 0.9 + - - -
332A GLU 4.2 0.6 - - - -
333A HIS* 1.3 71.7 - - - +
335A ASN* 1.3 58.2 + - - +
336A VAL 3.2 4.5 + - - -
337A VAL* 5.4 0.3 - - - +
360A LEU 5.0 3.1 - - - +
361A ALA* 6.1 0.2 - - - -
364A GLY* 5.2 3.3 - - - -
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Residues in contact with ASN 335 (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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178A ILE* 3.7 7.3 - - - +
179A SER 2.9 24.5 + - - +
180A PRO* 3.8 11.5 + - - +
181A ASP 4.2 0.8 - - - -
182A SER 3.6 21.6 + - - +
183A VAL* 3.8 7.9 - - - +
195A ASP 3.6 16.4 + - - +
196A LYS* 3.5 21.8 - - + +
197A LEU 3.0 25.4 + - - +
333A HIS* 3.4 20.6 + - - +
334A SER* 1.3 80.0 + - - +
336A VAL* 1.3 58.5 + - - +
337A VAL* 5.2 1.8 - - - -
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Residues in contact with VAL 336 (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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178A ILE* 3.8 35.0 - - + -
183A VAL* 4.2 3.8 - - + -
197A LEU* 3.4 9.9 - - + +
199A VAL* 4.3 12.6 - - + -
212A LEU* 4.8 3.4 - - + -
329A LEU* 3.4 6.5 - - - +
330A HIS* 2.8 46.4 + - + -
333A HIS* 3.1 7.2 + - + +
334A SER 3.2 0.6 - - - -
335A ASN* 1.3 95.3 - - - +
337A VAL* 1.3 65.2 + - - +
338A ILE* 3.8 24.2 - - + -
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Residues in contact with VAL 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LYS* 6.1 0.2 - - + -
197A LEU 2.8 17.7 + - - +
198A ILE* 3.5 8.2 - - + +
199A VAL* 2.8 27.5 + - - +
328A ASP 3.6 9.9 - - - +
329A LEU* 4.0 11.7 - - + -
334A SER 5.4 0.7 - - - +
335A ASN 5.2 2.0 - - - -
336A VAL* 1.3 78.6 - - - +
338A ILE* 1.3 67.8 + - - +
357A LEU* 3.6 31.9 - - + +
360A LEU* 3.8 18.4 - - + -
361A ALA* 3.7 35.4 - - + +
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Residues in contact with ILE 338 (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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199A VAL* 3.8 17.3 - - + +
205A ASN* 5.7 0.4 - - - +
209A LEU* 4.4 17.0 - - + -
212A LEU* 4.3 11.9 - - + -
214A LEU* 4.4 11.2 - - + -
326A ILE* 3.4 13.0 - - + +
327A ILE* 3.3 7.8 - - - +
328A ASP 2.8 37.3 + - - +
330A HIS* 4.4 13.9 - - + -
336A VAL* 3.8 17.3 - - + -
337A VAL* 1.3 84.7 - - - +
339A ALA* 1.3 63.8 + - - +
340A ALA* 4.1 20.0 - - + -
375A ILE* 4.3 21.3 - - + -
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Residues in contact with ALA 339 (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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14A MET* 4.6 1.8 - - + -
199A VAL 3.0 18.9 + - - +
200A SER* 3.6 14.2 - - - -
202A GLY 5.1 0.5 + - - -
205A ASN* 3.2 12.8 - - - +
326A ILE 3.2 5.4 - - - -
327A ILE* 4.7 1.3 - - + +
337A VAL 4.3 0.2 + - - -
338A ILE* 1.3 73.8 - - - +
340A ALA* 1.3 59.4 + - - +
342A PHE* 3.7 22.8 - - + -
353A VAL* 4.9 1.1 - - + -
357A LEU* 3.9 33.2 - - + -
400A FAD 5.2 0.9 + - - -
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Residues in contact with ALA 340 (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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202A GLY* 6.3 0.2 - - - -
205A ASN* 3.2 30.3 - - + +
209A LEU* 4.3 7.6 - - + -
218A LEU* 4.4 2.2 - - + -
325A PHE* 3.9 0.3 - - - -
326A ILE* 2.8 46.5 + - + +
338A ILE* 4.1 15.2 - - + -
339A ALA* 1.3 74.4 - - - +
341A GLY* 1.3 64.5 + - - +
342A PHE* 3.5 13.9 + - - -
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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