Contacts of the strand formed by residues 237 - 240 (chain A) in PDB entry 1B54
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 GLU 237 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ILE* 3.7 1.7 - - - +
43A LEU* 3.5 37.4 - - + +
45A LEU* 3.4 19.1 - - + +
89A HIS* 4.3 2.9 - - - -
112A GLU* 2.7 31.4 - - - +
140A ASN* 4.3 3.1 - - - +
218A LYS* 4.1 12.1 + - - +
219A LEU 3.1 8.2 + - - +
220A SER* 3.3 16.5 + - - +
221A MET 3.0 17.7 + - - +
235A THR* 2.9 17.2 + - - -
236A ALA* 1.3 83.7 - - - +
238A VAL* 1.3 72.5 + - - +
239A ARG* 3.4 5.2 + - - +
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Residues in contact with VAL 238 (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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26A VAL* 4.4 16.4 - - + -
42A ILE* 4.3 6.7 - - + -
43A LEU 3.0 12.6 + - - +
44A LEU* 3.8 9.1 - - - -
45A LEU* 2.9 27.9 + - - +
221A MET 3.7 14.6 - - - +
222A GLY 3.4 6.7 - - - +
227A PHE* 3.6 35.0 - - + +
231A ILE* 4.1 4.9 - - + -
235A THR* 3.9 15.3 - - + -
237A GLU* 1.3 74.2 - - - +
239A ARG* 1.3 61.6 - - - +
240A ILE* 4.0 13.6 + - + -
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Residues in contact with ARG 239 (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 LEU* 3.6 17.0 - - + -
47A VAL* 3.7 12.1 - - + -
91A ILE* 4.0 8.7 - - - -
112A GLU* 3.9 6.1 - - - -
181A MET* 3.8 11.8 - - - +
182A THR 3.0 23.0 + - - -
183A ILE* 4.2 0.4 - - - +
220A SER* 3.0 42.1 + - - +
221A MET* 3.7 6.1 - - - +
222A GLY 2.8 9.8 + - - +
223A MET* 3.2 39.0 - - - +
237A GLU* 3.4 26.7 - - - +
238A VAL* 1.3 72.8 - - - +
240A ILE* 1.3 60.5 + - - +
258A PLP 2.8 55.9 + - + +
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Residues in contact with ILE 240 (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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22A VAL* 4.0 16.4 - - + -
26A VAL* 4.8 0.9 - - + -
44A LEU* 4.1 15.7 - - + +
45A LEU 3.1 9.3 + - - +
46A VAL* 4.6 0.3 - - - +
47A VAL* 3.1 18.7 + - - +
223A MET* 3.9 16.4 - - - -
224A SER* 3.6 15.0 - - - +
227A PHE* 3.4 41.7 - - + -
238A VAL* 4.0 7.8 - - + -
239A ARG* 1.3 78.8 - - - +
241A GLY* 1.3 62.1 + - - +
243A ASP* 3.6 22.4 - - + +
244A ILE* 3.4 26.3 - - + +
258A PLP 3.4 1.6 - - - -
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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