Contacts of the strand formed by residues 213 - 216 (chain E) in PDB entry 2BG9
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 ILE 213 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138E TRP* 3.3 56.0 - - + +
139E GLN 4.1 0.4 - - - -
140E ASN* 3.7 21.9 - - + +
186E ARG* 3.2 23.6 + - + +
187E HIS* 3.4 31.2 + - + +
189E PRO* 5.7 2.7 - - + -
211E PHE* 4.1 0.6 - - - +
212E LEU* 1.3 71.2 - - - +
214E ILE* 1.3 59.3 + - - +
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Residues in contact with ILE 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E LEU* 5.6 1.1 - - + -
133E TYR* 2.7 33.3 + - + +
138E TRP* 2.8 32.6 - - - +
173E ASP* 4.8 0.2 - - - +
183E TRP* 3.4 15.0 - - + +
184E THR 2.7 12.3 - - - +
185E ILE* 3.0 34.1 - - + +
186E ARG 4.3 0.2 - - - +
212E LEU* 3.1 24.1 + - + +
213E ILE* 1.3 75.8 - - - +
215E GLN* 1.3 74.1 + - - +
216E ARG* 3.4 22.4 - - + -
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Residues in contact with GLN 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E PHE* 5.2 4.6 - - - +
138E TRP* 2.7 49.2 - - + +
183E TRP* 2.9 5.0 - - - +
184E THR* 2.1 76.5 + - + +
185E ILE* 4.4 0.8 - - - +
186E ARG* 4.3 25.4 + - + +
214E ILE* 1.3 66.5 - - - +
216E ARG* 1.3 79.4 + - - +
217E LYS* 4.5 8.7 - - - +
472E ASN* 5.9 2.4 - - - +
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Residues in contact with ARG 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E LEU* 3.8 25.9 + - - +
44E GLU* 4.9 13.3 - - - +
133E TYR 5.0 9.9 - - - +
134E PHE* 5.9 11.8 - - + -
135E PRO 5.9 0.4 - - - +
138E TRP* 3.7 6.5 - - + -
182E GLU* 2.5 46.0 + - - +
183E TRP* 2.2 64.3 - - + +
184E THR* 4.1 1.2 - - - +
214E ILE* 3.4 10.1 - - + -
215E GLN* 1.3 84.5 - - - +
217E LYS* 1.3 85.5 + - - +
218E PRO* 2.9 8.9 - - - +
279E VAL* 4.8 9.6 - - - +
280E PRO* 4.8 19.2 - - - +
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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