Contacts of the strand formed by residues 48 - 51 (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 THR 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A GLY 2.8 7.3 + - - -
47A ASP* 1.3 87.2 - - + +
49A ARG* 1.3 86.4 + - - +
146A VAL* 3.7 11.4 - - + -
147A LEU 3.3 2.2 - - - -
148A PHE* 3.6 28.5 - - + -
227A PHE* 5.2 2.1 - - + -
256A PHE* 3.5 22.1 - - + +
259A PHE* 4.1 12.8 - - + -
265A LYS* 2.9 41.2 + - - +
400A FAD 5.0 0.5 + - - -
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Residues in contact with ARG 49 (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 2.7 25.5 + - - -
44A HIS* 3.3 10.0 - - - +
45A HIS 2.8 30.7 + - - +
48A THR* 1.3 93.0 + - - +
50A ILE* 1.3 64.0 + - - +
51A ILE 3.8 0.2 + - - -
146A VAL* 3.4 3.6 - - - -
147A LEU* 2.8 40.0 + - + +
149A SER* 3.5 22.5 + - - -
256A PHE* 3.5 5.8 - - - -
265A LYS* 4.1 6.5 - - - +
315A CYS* 3.6 11.9 - - - -
347A PHE* 3.7 23.7 - - + +
400A FAD 2.9 65.2 + - + +
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Residues in contact with ILE 50 (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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49A ARG* 1.3 74.3 - - - +
51A ILE* 1.3 65.5 + - - +
52A ARG* 3.5 31.2 - - + -
89A VAL* 4.0 10.1 - - + -
145A GLY 3.5 9.2 - - - +
146A VAL* 4.3 0.9 - - + -
147A LEU* 5.2 0.2 - - - -
243A GLY* 3.8 19.5 - - - -
244A PHE 3.9 12.6 - - - +
245A MET* 5.7 5.4 - - + -
254A TYR* 5.1 6.3 - - + -
255A GLY 3.8 21.1 - - - +
256A PHE* 3.6 23.1 - - + -
348A LYS* 3.3 14.3 - - - +
400A FAD 2.7 36.5 + - + +
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Residues in contact with ILE 51 (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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49A ARG 3.8 0.2 + - - -
50A ILE* 1.3 74.9 - - - +
52A ARG* 1.3 67.8 + - - +
53A HIS* 4.1 3.6 - - + +
65A ALA* 4.1 9.9 - - + +
68A SER* 4.6 0.2 - - - -
69A GLN* 3.3 33.0 - - + +
72A TRP* 3.7 24.9 - - + -
84A PHE* 3.6 25.8 - - + -
89A VAL* 3.6 3.8 - - - +
144A SER* 3.2 2.9 - - - -
145A GLY 2.9 43.0 + - - +
147A LEU* 3.9 17.3 - - + -
348A LYS* 3.6 28.9 - - + +
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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