Contacts of the helix formed by residues 35 - 43 (chain C) in PDB entry 2B2V
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 35 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32C ALA* 3.3 11.6 + - + +
34C THR* 1.3 81.1 + - - +
36C ILE* 1.3 65.9 + - - +
37C TYR* 3.3 43.7 - - + +
38C ALA* 2.9 33.1 + - - +
39C VAL* 2.9 20.6 + - - +
70C ILE 4.0 1.8 - - - +
71C HIS 4.1 9.4 - - - +
72C ASN 3.9 8.0 + - - -
73C THR* 3.8 19.7 - - + -
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Residues in contact with ILE 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ASN* 2.6 60.3 - - + +
34C THR 3.6 1.0 + - - -
35C THR* 1.3 73.6 - - - +
37C TYR* 1.3 56.4 + - - +
39C VAL* 3.4 6.8 + - + +
40C GLU* 2.9 59.1 + - + +
69C HIS 5.1 1.8 - - - +
70C ILE* 3.5 39.4 + - + +
72C ASN 4.9 0.6 + - - -
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Residues in contact with TYR 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ALA 5.5 0.2 - - - -
35C THR* 3.3 33.4 - - + +
36C ILE* 1.3 80.1 - - + +
38C ALA* 1.3 63.3 + - + +
40C GLU* 4.3 6.6 - - - +
41C ALA* 2.8 30.1 + - - +
70C ILE* 3.5 39.9 - - + -
71C HIS* 2.9 34.5 + + - +
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Residues in contact with ALA 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ALA 3.2 18.4 - - - +
33C THR* 3.9 13.5 - - - -
35C THR* 2.9 24.7 + - - +
37C TYR* 1.3 79.1 - - + +
39C VAL* 1.3 57.4 + - - +
41C ALA* 4.2 2.0 - - - -
42C ASP* 2.6 48.7 + - - +
43C GLY 3.7 2.4 + - - +
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Residues in contact with VAL 39 (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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138A ALA* 6.1 4.5 - - + -
139A HIS* 4.1 4.8 + - - +
33C THR 3.9 13.5 - - - +
34C THR* 4.1 11.2 - - - +
35C THR 2.9 19.8 + - - +
36C ILE* 3.7 8.1 - - + +
38C ALA* 1.3 73.0 - - - +
40C GLU* 1.3 70.5 + - + +
43C GLY* 2.7 36.7 + - - +
44C ASP* 3.7 36.8 - - + +
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Residues in contact with GLU 40 (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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139A HIS* 3.8 11.1 - - - -
182A TYR* 4.8 5.8 + - - -
183A PHE* 6.1 0.2 - - - -
186A LYS 4.6 18.6 - - - +
107B ASN 4.1 12.3 - - - +
36C ILE* 2.9 43.3 + - + +
37C TYR* 4.3 4.8 - - - +
39C VAL* 1.3 82.2 - - + +
41C ALA* 1.3 63.4 + - - +
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Residues in contact with ALA 41 (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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139A HIS* 4.0 8.1 + - - -
183A PHE* 5.7 1.4 - - - -
37C TYR 2.8 23.9 + - - +
38C ALA* 3.6 3.6 - - - +
39C VAL 3.1 0.2 - - - -
40C GLU* 1.3 80.9 - - - +
42C ASP* 1.3 75.9 + - - +
43C GLY 3.6 0.4 + - - -
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Residues in contact with ASP 42 (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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139A HIS* 3.8 6.0 + - - -
140A SER 3.9 1.7 - - - +
141A ASN* 3.0 34.0 + - - +
33C THR* 5.6 5.2 - - - +
38C ALA* 2.6 32.5 + - - +
41C ALA* 1.3 86.5 - - - +
43C GLY* 1.3 58.5 + - - +
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Residues in contact with GLY 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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139A HIS* 3.3 23.8 + - - -
140A SER 3.5 2.9 - - - -
141A ASN* 3.4 15.1 + - - +
33C THR 4.5 0.9 - - - +
38C ALA 3.7 1.6 - - - +
39C VAL* 2.7 35.3 + - - -
42C ASP* 1.3 74.6 - - - +
44C ASP* 1.3 63.4 + - - -
45C PRO* 3.5 4.7 - - - +
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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