Contacts of the strand formed by residues 40 - 44 (chain C) in PDB entry 2BP1
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 ALA 40 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C ARG 3.2 6.4 + - - +
39C VAL* 1.3 75.8 - - - +
41C SER* 1.3 64.9 + - - +
42C VAL* 5.5 0.9 - - + -
69C HIS* 5.7 1.3 - - - -
71C GLU* 5.8 3.4 - - - +
301C TYR* 3.5 6.2 - - - -
311C GLY 5.1 3.4 - - - +
312C ASP 3.1 16.3 + - - +
313C ALA* 3.3 11.6 - - + -
314C VAL 2.9 22.9 + - - -
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Residues in contact with SER 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ALA* 1.3 73.6 - - - +
42C VAL* 1.3 65.4 + - - +
64C PHE* 3.3 19.2 - - - -
69C HIS* 3.7 39.9 + - - +
70C THR 4.9 0.5 + - - -
71C GLU* 4.4 5.0 + - - +
301C TYR* 2.4 33.7 + - - -
314C VAL 3.3 4.3 - - - -
316C LEU* 4.3 10.5 - - - -
331C THR* 4.1 6.9 - - - +
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Residues in contact with VAL 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ALA* 5.5 0.9 - - + -
41C SER* 1.3 79.0 - - - +
43C LEU* 1.3 62.1 + - - +
64C PHE* 3.8 3.4 - - - -
71C GLU* 3.5 32.3 - - + +
72C LEU 4.2 1.1 - - - -
73C ASP* 3.8 30.5 - - + +
104C ALA* 6.5 0.2 - - + -
224C TYR* 4.0 21.5 - - + -
313C ALA* 3.8 23.6 - - + -
314C VAL 2.8 10.0 + - - +
315C ILE* 3.4 13.3 - - + -
316C LEU* 2.9 30.7 + - - +
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Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C VAL* 1.3 71.6 - - - +
44C GLY* 1.3 66.2 + - - +
45C THR* 3.7 3.0 - - + +
48C MET* 4.1 20.6 - - + -
60C ALA 4.4 1.6 - - - -
61C VAL* 4.0 25.8 - - + +
64C PHE* 3.5 22.8 - - + -
71C GLU 3.0 8.7 + - - -
72C LEU* 3.6 29.0 - - + -
73C ASP 2.8 31.4 + - - +
315C ILE* 4.1 1.6 - - - -
316C LEU* 4.8 3.6 - - + +
318C MET* 4.2 11.0 - - + -
324C LEU* 3.6 37.5 - - + -
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Residues in contact with GLY 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C VAL 3.6 1.8 + - - -
43C LEU* 1.3 73.2 - - - +
45C THR* 1.3 58.2 + - - +
47C GLU* 5.3 0.7 + - - +
73C ASP 3.9 0.2 - - - -
315C ILE* 3.6 6.8 - - - +
316C LEU 2.9 20.5 + - - +
317C GLY* 5.1 0.5 - - - -
318C MET* 3.7 28.8 + - - +
1361C NDP 2.9 31.5 + - - -
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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