Contacts of the strand formed by residues 40 - 48 (chain P) in PDB entry 2BDI
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 40 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32P ALA* 3.8 16.6 - - + -
33P LEU 3.1 20.2 - - - +
34P VAL* 3.7 7.7 - - + +
38P GLU* 1.3 96.0 - - + +
41P PHE* 1.3 63.1 + - - +
42P CYS 3.1 33.2 - - - +
43P SER* 5.1 1.3 - - - +
73P LEU* 4.1 24.8 - - + +
141P TRP* 4.3 25.1 - - + -
151P MET* 4.3 14.8 - - + +
193P GLY* 3.7 22.3 - - - +
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Residues in contact with PHE 41 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33P LEU* 3.0 39.5 + - + -
34P VAL 3.7 7.6 - - - -
35P MET* 3.4 39.3 - - + -
38P GLU* 4.2 1.1 - - - +
40P LEU* 1.3 78.9 - - - +
42P CYS* 1.3 92.1 + - + +
58P CYS* 3.3 22.7 - - - -
60P GLN* 3.8 25.4 - - + -
63P TYR* 4.6 5.6 - + + -
193P GLY* 4.3 15.1 - - - -
195P SER* 4.9 1.9 - - - -
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Residues in contact with CYS 42 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33P LEU* 2.8 32.3 + - + -
40P LEU* 3.1 17.2 - - - +
41P PHE* 1.3 115.9 - - + +
43P SER* 1.3 65.0 + - - +
57P HIS* 5.0 2.2 - - - -
58P CYS* 2.1 49.6 - - - -
193P GLY 4.4 4.5 - - - -
195P SER* 3.7 12.3 - - - -
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Residues in contact with SER 43 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30P GLN* 3.5 18.4 + - - -
31P ALA 3.0 11.7 - - - -
33P LEU* 3.9 6.6 - - - +
40P LEU* 5.1 0.2 - - - +
42P CYS* 1.3 79.3 + - - +
44P GLY* 1.3 60.2 + - - +
54P SER* 3.0 19.4 + - - -
140P GLY* 4.5 6.1 - - - -
141P TRP* 3.8 15.2 - - - -
193P GLY 4.5 6.8 + - - -
194P ASP 4.7 1.4 + - - -
195P SER 3.0 6.1 + - - -
196P GLY* 3.2 10.6 - - - +
197P GLY* 3.7 23.6 - - - -
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Residues in contact with GLY 44 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29P TRP 3.6 0.5 - - - +
30P GLN* 3.8 2.1 - - - -
31P ALA* 2.7 39.0 + - - +
33P LEU* 4.0 1.1 - - - +
43P SER* 1.3 77.4 - - - +
45P VAL* 1.3 69.1 + - - +
52P VAL* 3.9 6.5 - - - -
53P LEU 2.9 13.7 - - - -
54P SER* 4.1 1.8 - - - -
196P GLY 3.6 4.3 - - - -
198P PRO* 4.9 2.1 - - - +
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Residues in contact with VAL 45 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29P TRP* 3.4 10.3 - - + +
44P GLY* 1.3 80.0 - - - +
46P LEU* 1.3 60.5 + - - +
47P VAL* 3.0 8.0 + - + -
52P VAL* 4.0 3.3 - - - +
53P LEU* 2.5 43.6 + - + +
121P ILE* 3.4 30.5 - - + -
196P GLY 4.3 0.2 - - - +
198P PRO* 3.5 35.4 - - + -
209P LEU* 3.6 27.6 - - + -
212P LEU* 4.2 11.4 - - + -
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Residues in contact with LEU 46 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28P PRO 5.0 0.4 - - - +
29P TRP* 2.9 20.6 + - - +
31P ALA* 4.8 1.0 - - - +
44P GLY 4.1 0.2 - - - -
45P VAL* 1.3 68.2 - - - +
47P VAL* 1.3 61.7 + - - +
48P HIS 2.9 28.0 - - - +
49P PRO* 4.3 2.5 - - + +
51P TRP 3.4 9.6 - - - +
52P VAL* 3.9 17.1 - - + +
67P LEU* 4.3 14.4 - - + -
108P LEU* 4.1 13.7 - - + -
112P VAL* 4.1 14.1 - - + -
114P GLU* 5.8 2.7 - - + -
118P ILE* 4.0 27.4 - - + +
119P ARG* 4.3 11.7 - - - +
120P SER* 3.2 12.7 - - - +
121P ILE* 3.0 25.1 + - - +
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Residues in contact with VAL 47 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45P VAL* 3.0 15.7 + - + +
46P LEU* 1.3 74.8 - - - +
48P HIS* 1.3 62.5 + - + +
51P TRP* 3.2 15.2 + - + +
53P LEU* 3.7 22.9 - - + +
105P LEU* 4.3 14.1 - - + -
120P SER* 4.1 6.5 + - - -
121P ILE 3.7 14.1 - - - +
123P ILE* 3.7 32.1 - - + -
209P LEU* 3.8 17.5 - - + -
238P ILE* 5.2 1.3 - - + -
242P VAL* 5.1 4.9 - - + -
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Residues in contact with HIS 48 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46P LEU* 2.9 28.1 + - - +
47P VAL* 1.3 84.3 - - + +
49P PRO* 1.3 94.7 - - + +
50P GLN* 2.7 25.7 + - + -
51P TRP* 3.2 33.7 + + + +
120P SER* 3.8 7.2 - - - -
242P VAL* 3.7 22.7 + - + +
243P GLN* 5.5 5.7 + - - -
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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