Contacts of the strand formed by residues 40 - 48 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B ALA* 3.7 16.8 - - + -
33B LEU 3.2 20.4 - - - +
34B VAL* 3.7 8.6 - - + +
38B GLU* 1.3 97.2 - - + +
41B PHE* 1.3 66.2 + - - +
42B CYS 3.0 31.4 - - - +
43B SER* 5.1 1.3 - - - +
73B LEU* 4.1 23.9 - - + +
141B TRP* 4.3 24.7 - - + -
151B MET* 4.3 15.9 - - + +
193B GLY* 3.7 19.7 - - - +
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Residues in contact with PHE 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LEU* 3.0 45.0 + - + -
34B VAL 3.7 7.6 - - - -
35B MET* 3.4 40.6 - - + -
38B GLU* 4.2 1.8 - - - +
40B LEU* 1.3 79.9 - - - +
42B CYS* 1.3 97.9 + - + +
58B CYS* 3.7 18.4 - - + -
60B GLN* 3.8 24.9 - - + -
63B TYR* 4.6 6.1 - + + -
193B GLY* 4.3 13.2 - - - -
195B SER* 4.9 1.7 - - - -
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Residues in contact with CYS 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LEU* 3.0 27.6 + - + -
40B LEU* 3.0 18.0 - - - +
41B PHE* 1.3 118.4 - - + +
43B SER* 1.3 63.1 + - - +
57B HIS* 5.0 2.7 - - - -
58B CYS* 2.1 49.4 - - + -
193B GLY 4.4 4.7 - - - -
195B SER* 3.7 13.5 - - - -
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Residues in contact with SER 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B GLN* 3.5 18.7 + - - -
31B ALA 3.0 13.8 + - - -
33B LEU* 3.9 9.6 - - - +
40B LEU* 5.1 0.2 - - - +
42B CYS* 1.3 78.0 + - - +
44B GLY* 1.3 60.6 + - - +
54B SER* 2.9 19.9 + - - -
140B GLY* 4.5 5.7 - - - -
141B TRP* 3.9 13.7 - - - -
193B GLY 4.5 6.1 + - - -
194B ASP 4.6 1.3 + - - -
195B SER 3.0 6.2 + - - +
196B GLY* 3.3 9.3 - - - +
197B GLY* 3.7 23.9 - - - -
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Residues in contact with GLY 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B TRP 3.6 0.5 - - - +
30B GLN* 3.8 2.1 - - - -
31B ALA* 2.7 39.3 + - - -
33B LEU* 4.1 0.9 - - - +
43B SER* 1.3 78.1 - - - +
45B VAL* 1.3 69.8 + - - +
52B VAL* 3.9 6.7 - - - -
53B LEU 3.0 12.8 - - - -
54B SER* 4.1 1.6 - - - -
196B GLY 3.6 4.3 - - - -
198B PRO* 4.8 2.1 - - - +
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Residues in contact with VAL 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B TRP* 3.4 10.5 - - + +
44B GLY* 1.3 80.9 - - - +
46B LEU* 1.3 60.1 + - - +
47B VAL* 3.0 9.3 + - + -
52B VAL* 4.0 3.1 - - - +
53B LEU* 2.5 42.1 + - + +
121B ILE* 3.4 31.4 - - + -
196B GLY 4.2 5.2 - - - +
198B PRO* 3.5 35.9 - - + -
209B LEU* 3.6 27.1 - - + -
212B LEU* 4.2 6.1 - - + -
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Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B PRO 5.0 0.7 - - - +
29B TRP* 2.9 21.0 + - - +
31B ALA* 4.8 0.6 - - - +
44B GLY 4.1 0.2 - - - -
45B VAL* 1.3 67.7 - - - +
47B VAL* 1.3 58.6 + - - +
48B HIS 2.8 26.9 - - - +
49B PRO* 4.2 2.9 - - + +
51B TRP 3.4 9.6 - - - +
52B VAL* 4.0 16.4 - - + +
67B LEU* 4.4 14.6 - - + -
108B LEU* 4.1 13.9 - - + -
112B VAL* 4.1 13.7 - - + -
114B GLU* 5.7 2.5 - - + -
118B ILE* 4.0 27.6 - - + +
119B ARG 4.3 9.6 - - - +
120B SER* 3.2 15.5 - - - +
121B ILE* 3.0 25.8 + - - +
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Residues in contact with VAL 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B VAL* 3.0 13.2 + - + +
46B LEU* 1.3 75.3 - - - +
48B HIS* 1.3 66.1 + - + +
51B TRP* 3.2 15.5 + - + +
53B LEU* 3.7 28.3 - - + +
105B LEU* 4.2 13.9 - - + -
120B SER* 4.0 6.6 + - - -
121B ILE 3.6 14.9 - - - +
123B ILE* 3.7 29.6 - - + -
209B LEU* 3.8 17.3 - - + -
238B ILE* 5.2 1.3 - - + -
242B VAL* 5.0 4.3 - - + -
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Residues in contact with HIS 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LEU* 2.8 28.9 + - - +
47B VAL* 1.3 84.3 - - + +
49B PRO* 1.3 97.8 - - + +
50B GLN* 2.8 25.0 + - + -
51B TRP* 3.1 34.8 + + + +
120B SER* 3.8 6.4 - - - -
242B VAL* 3.7 23.3 + - + +
243B 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