Contacts of the strand formed by residues 37 - 44 (chain D) 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 LEU 37 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D LEU* 4.0 14.6 - - + -
36D GLN* 1.3 75.8 + - - +
38D ILE* 1.3 60.6 + - - +
39D GLN 4.9 0.2 - - - +
40D LEU* 3.7 21.5 - - + -
52D THR* 2.8 26.2 - - + +
53D ASN 2.7 24.7 - - - +
54D VAL* 3.1 31.0 - - + -
164D ARG* 2.6 21.0 + - - +
166D ASP* 4.5 21.8 - - - +
168D SER* 4.5 2.8 + - - -
169D THR* 3.0 24.1 + - - +
205D PHE* 4.5 10.5 - - + -
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Residues in contact with ILE 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D GLN* 2.8 32.4 + - + +
37D LEU* 1.3 72.1 - - - +
39D GLN* 1.3 77.6 + - + +
53D ASN* 3.4 6.3 + - - -
55D ARG* 3.7 35.0 - - - +
169D THR* 2.6 31.8 - - + +
197E GLN* 5.1 8.3 - - - +
199E THR* 3.1 47.6 - - + +
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Residues in contact with GLN 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LEU* 3.8 1.6 - - - +
38D ILE* 1.3 98.2 - - + +
40D LEU* 1.3 58.7 + - - +
41D ILE* 3.8 12.7 - - + +
52D THR* 2.4 28.2 + - - -
53D ASN* 3.0 20.9 + - + +
55D ARG* 4.9 9.2 - - - +
123D ILE* 5.8 3.5 - - + +
169D THR* 3.8 4.2 + - - +
92E GLU* 4.2 21.8 + - - +
93E ASN* 4.6 16.5 + - - +
96E ASP* 5.4 3.8 - - - +
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Residues in contact with LEU 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LEU* 3.7 23.6 - - + -
39D GLN* 1.3 76.8 - - - +
41D ILE* 1.3 60.8 + - - +
42D ASN 3.5 2.0 - - - -
43D VAL* 3.5 16.2 - - + -
50D VAL* 3.2 27.1 - - + -
51D GLU 4.4 0.4 - - - +
52D THR* 2.7 45.1 - - + +
169D THR 5.4 4.7 + - - +
170D PHE* 6.2 1.8 - - - -
171D MET* 2.9 47.7 - - + +
176D TRP* 5.0 8.1 - - + -
205D PHE* 6.3 0.4 - - + -
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Residues in contact with ILE 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D GLN* 4.9 12.5 - - + +
40D LEU* 1.3 76.1 - - - +
42D ASN* 1.3 71.3 + - + +
51D GLU* 2.6 43.3 + - + +
52D THR* 4.2 4.9 - - - -
53D ASN 5.6 0.2 - - - +
123D ILE* 4.5 14.1 - - + -
171D MET* 4.5 4.6 - - - +
46E GLU* 3.8 15.9 - - - +
48E ALA* 5.8 1.6 - - + -
96E ASP* 2.8 41.1 - - - +
126E THR* 3.2 31.9 - - + +
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Residues in contact with ASN 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D LEU 3.5 1.5 - - - -
41D ILE* 1.3 82.1 + - + +
43D VAL* 1.3 75.6 + - - +
44D ASP* 5.7 1.6 - - - +
49D ILE* 4.7 1.7 - - - +
51D GLU* 2.7 47.1 + - + +
171D MET* 5.3 1.3 - - - -
46E GLU* 2.7 44.5 + - - +
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Residues in contact with VAL 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D LEU* 3.5 15.0 - - + -
42D ASN* 1.3 93.9 + - - +
44D ASP* 1.3 75.0 + - - +
45D GLU* 4.1 2.8 + - - +
48D GLN 4.9 0.9 - - - -
49D ILE* 2.3 30.7 - - - +
50D VAL* 3.1 44.6 - - + -
130D ILE* 6.2 2.0 - - + -
171D MET* 5.5 2.8 - - + +
176D TRP* 4.7 18.4 - - + -
209D ARG* 4.4 17.9 + - - +
46E GLU* 5.4 1.3 + - - +
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Residues in contact with ASP 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ASN* 5.7 1.3 - - - +
43D VAL* 1.3 77.2 - - - +
45D GLU* 1.3 54.9 + - - +
46D VAL* 3.0 22.5 - - - +
47D ASN* 2.6 52.3 + - + +
48D GLN* 2.6 32.6 + - - -
49D ILE* 2.9 21.0 + - + +
270D ALA 4.6 0.3 - - - +
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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