Contacts of the strand formed by residues 40 - 48 (chain B) in PDB entry 2BQ6
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 GLY 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 LEU* 3.5 29.5 - - - +
33B LEU 3.1 8.7 - - - -
34B ILE* 3.9 2.6 - - - +
38B ASN 4.3 0.4 + - - -
39B GLU* 1.3 74.2 - - - +
41B PHE* 1.3 59.2 + - - -
42B CYS 3.7 0.9 - - - -
67B ARG* 5.7 0.8 - - - +
141B PHE* 5.2 1.4 - - - +
151B GLN* 2.8 26.4 + - - +
193B GLY 5.7 0.2 - - - -
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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* 2.9 57.5 + - + -
34B ILE 3.5 2.5 - - - -
35B ASN* 3.4 29.8 - - + +
39B GLU 3.5 8.1 - - - +
40B GLY* 1.3 74.2 - - - -
42B CYS* 1.3 72.3 + - + +
58B CYS 3.8 19.3 - - - -
61B GLN* 3.5 41.6 - - + +
64B PHE* 3.5 30.5 - + + -
151B GLN* 4.1 4.5 + - - +
192B GLN* 4.7 5.0 + - - +
193B GLY* 3.3 23.1 + - - -
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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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32B LEU* 2.9 24.9 - - - +
33B LEU* 3.1 28.4 + - + -
41B PHE* 1.3 97.5 - - + +
43B GLY* 1.3 60.7 + - - +
58B CYS* 2.0 50.9 - - - -
61B GLN* 4.2 9.4 - - - -
192B GLN* 5.6 0.2 - - - -
193B GLY 3.6 9.9 - - - -
195B SER* 3.4 11.7 - - - +
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Residues in contact with GLY 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* 4.3 5.8 - - - -
31B ALA 3.4 10.1 - - - -
32B LEU* 5.0 0.7 - - - -
33B LEU* 3.8 8.2 - - - +
42B CYS* 1.3 76.3 - - - +
44B GLY* 1.3 58.3 + - - -
54B THR* 3.3 12.8 + - - -
140B GLY* 6.1 0.9 - - - -
193B GLY 3.7 4.2 + - - -
194B ASP* 4.2 2.7 - - - -
195B SER 2.6 15.6 + - - +
196B GLY* 2.8 17.6 - - - +
197B GLY* 3.8 8.7 - - - -
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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 3.5 1.0 - - - +
30B GLN* 4.1 0.2 + - - -
31B ALA* 2.7 40.5 + - - -
33B LEU* 5.2 1.6 - - - -
43B GLY* 1.3 75.4 - - - -
45B THR* 1.3 61.9 + - - -
52B ILE* 4.3 5.6 - - - -
53B LEU 3.4 7.4 - - - -
54B THR* 4.7 0.2 - - - -
196B GLY 3.2 9.1 + - - -
197B GLY* 3.7 2.2 - - - -
198B PRO* 3.4 14.0 - - - +
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Residues in contact with THR 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* 3.3 7.6 - - + +
31B ALA* 3.9 0.4 - - - +
44B GLY* 1.3 75.1 - - - -
46B ILE* 1.3 68.2 + - - +
47B LEU* 3.3 1.2 + - + -
52B ILE* 3.3 7.0 - - - +
53B LEU* 2.8 48.9 + - - +
121B ALA* 4.1 18.6 - - + -
196B GLY 4.3 0.3 + - - -
197B GLY 3.9 3.5 + - - -
198B PRO* 3.0 38.0 - - + +
200B VAL* 5.1 0.2 - - + -
209B VAL* 3.8 24.1 - - + +
211B GLY 5.1 0.3 + - - -
212B ILE* 5.8 0.2 - - - +
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Residues in contact with ILE 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 3.1 27.6 - - - +
29B TRP 2.9 12.4 + - - +
30B GLN 3.8 11.4 - - - +
45B THR* 1.3 71.6 - - - +
47B LEU* 1.3 60.7 + - - +
48B SER 4.1 7.6 - - - +
52B ILE* 3.6 15.9 - - + -
68B VAL* 4.2 15.3 - - + -
112B ILE* 4.1 20.6 - - + -
114B PHE* 4.3 7.6 - - + -
118B VAL* 4.2 11.4 - - + -
119B ALA 3.3 19.3 - - - +
120B PRO* 3.2 18.5 - - + +
121B ALA* 2.9 31.4 + - - +
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Residues in contact with LEU 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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44A CYS* 5.4 0.9 - - - +
45B THR* 3.3 1.5 + - - +
46B ILE* 1.3 75.7 - - - +
48B SER* 1.3 63.1 + - - +
51B TYR* 2.8 17.6 + - + +
53B LEU* 3.8 41.1 - - + +
105B VAL* 4.6 7.4 - - + -
120B PRO* 3.5 13.4 - - - +
121B ALA 3.9 8.8 - - - +
123B LEU* 4.0 31.4 - - + +
209B VAL* 4.4 11.7 - - + -
238B ILE* 3.7 28.0 - - + -
242B MET* 3.8 25.5 - - + +
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Residues in contact with SER 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 ILE* 3.6 4.5 - - - +
47B LEU* 1.3 79.4 - - - +
49B GLU* 1.3 62.6 + - - +
50B PHE* 4.2 2.2 + - - +
51B TYR* 2.6 37.6 + - - +
112B ILE* 4.1 5.0 - - - +
114B PHE* 4.3 4.0 - - - -
120B PRO* 4.3 7.9 - - - -
242B MET* 3.0 26.8 - - - +
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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