Contacts of the strand formed by residues 37 - 48 (chain B) in PDB entry 4BNR
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 PHE 37 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B THR* 4.2 0.2 - - - -
37B GLY* 1.3 87.9 + - - +
38B SER* 1.3 76.2 + - - +
39B PHE* 4.9 6.1 - - + -
49I GLU* 3.5 38.4 + - - +
52I MET* 3.7 32.1 - - + +
53I ARG* 3.9 22.9 - - - +
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Residues in contact with SER 38 (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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34B GLN* 2.8 28.8 + - - -
35B GLU 3.2 14.1 - - - -
36B THR* 4.3 4.5 - - - -
37B PHE* 1.3 87.3 + - - +
39B PHE* 1.3 62.9 + - - +
40B HIS 4.3 0.2 - - - -
65B GLN* 3.7 16.3 + - - -
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Residues in contact with PHE 39 (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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34B GLN* 3.2 4.8 - - - -
35B GLU* 2.8 45.6 + - + +
37B PHE* 4.4 21.1 - - + -
38B SER* 1.3 76.5 - - - +
40B HIS* 1.3 78.5 + - - +
41B PHE* 3.5 8.5 + + + -
28I GLY 5.3 0.9 - - - -
29I LEU* 3.7 18.6 - - + -
52I MET* 4.3 14.1 - - + -
17J ARG* 3.3 45.1 - - + -
19J ILE* 3.6 29.6 - - + -
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Residues in contact with HIS 40 (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 SER* 2.6 30.8 + - - +
33B PHE 3.7 5.4 - - - -
34B GLN* 4.0 7.3 - - + +
39B PHE* 1.3 91.1 - - - +
41B PHE* 1.3 62.3 + - - +
42B CYS 2.9 26.2 + - - -
43B GLY* 4.1 2.7 - - - -
73B MET* 3.9 19.6 - - + +
140B GLY* 5.9 0.2 - - - -
141B TRP* 3.8 41.3 - + + +
151B THR* 6.0 2.9 - - + -
193B GLY* 2.8 30.0 + - - -
17J ARG* 4.2 6.2 + - + +
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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 PHE* 3.2 54.4 + + - -
34B GLN 3.5 17.7 - - - -
35B GLU* 3.6 18.8 - - + -
39B PHE* 3.8 7.6 - + + -
40B HIS* 1.3 79.5 - - - +
42B CYS* 1.3 75.1 + - + +
58B CYS 3.5 23.6 - - - -
60B ASP* 5.8 0.4 - - - -
64B LEU* 3.8 14.8 - - + -
193B GLY* 4.0 2.7 - - - -
16J ALA* 3.5 1.2 - - - -
17J ARG* 2.8 48.4 + - - +
18J ILE* 4.4 15.5 - - + -
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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 PHE* 2.9 28.9 + - + +
40B HIS* 2.9 16.1 + - - -
41B PHE* 1.3 103.4 - - + +
43B GLY* 1.3 65.3 + - - +
58B CYS* 2.0 49.6 - - + -
193B GLY 4.0 4.7 - - - -
195B SER* 3.3 7.0 - - - +
16J ALA* 3.5 18.2 - - - -
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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* 4.2 4.7 - - - -
31B LEU 3.4 11.7 - - - -
33B PHE* 4.0 3.0 - - - +
40B HIS* 4.3 4.0 - - - -
42B CYS* 1.3 76.5 - - - +
44B ALA* 1.3 62.0 + - - +
54B THR* 2.8 21.1 + - - -
140B GLY* 6.3 1.1 - - - -
193B GLY 3.9 5.6 + - - -
194B ASP* 4.2 2.0 + - - -
195B SER 2.7 12.4 + - - +
196B GLY 3.3 10.1 - - - -
197B GLY* 3.9 9.2 - - - -
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Residues in contact with ALA 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 TYR 3.8 0.2 - - - +
30B GLN* 3.8 5.7 + - - -
31B LEU* 2.8 50.9 + - + +
33B PHE* 4.6 6.5 - - + -
43B GLY* 1.3 75.7 - - - +
45B SER* 1.3 61.4 + - - +
52B ALA* 4.4 6.3 - - + -
53B ILE 3.3 15.7 - - - +
54B THR* 3.9 9.0 - - - -
66B ILE* 5.0 1.1 - - + -
106B LEU* 4.5 8.3 - - + -
196B GLY 3.3 7.5 + - - -
197B GLY* 3.9 2.1 - - - -
198B PRO* 4.2 0.7 - - - +
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Residues in contact with SER 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 TYR* 3.3 7.0 - - - -
31B LEU* 3.9 4.0 - - - -
44B ALA* 1.3 74.6 - - - +
46B ILE* 1.3 62.5 + - - +
47B TYR 3.4 0.2 + - - -
52B ALA* 3.2 5.2 - - - -
53B ILE* 2.8 41.9 + - - +
121B ILE* 4.1 19.1 - - - -
196B GLY 4.6 0.5 + - - -
197B GLY 4.3 1.0 - - - -
198B PRO* 3.2 35.0 - - - +
209B LEU* 3.7 14.9 - - - +
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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 3.6 22.9 - - - +
29B TYR* 2.9 14.4 + - - +
31B LEU* 3.5 33.4 - - + -
45B SER* 1.3 70.7 - - - +
47B TYR* 1.3 59.9 + - - +
48B ASN 3.5 19.5 - - - +
51B TYR 4.2 2.9 - - - -
53B ILE* 5.5 0.4 - - - -
68B ALA* 4.2 0.2 - - + -
112B LEU* 3.9 11.2 - - + -
114B PHE* 3.9 8.7 - - + -
118B VAL* 3.6 26.5 - - + -
119B ALA 3.8 10.1 - - - +
120B PRO* 3.4 19.9 - - + +
121B ILE* 3.0 34.4 + - - +
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Residues in contact with TYR 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 SER 3.4 2.0 + - - -
46B ILE* 1.3 72.8 - - - +
48B ASN* 1.3 82.4 + - + +
51B TYR* 3.0 17.4 + - + +
53B ILE* 3.8 23.6 - - + -
105B LEU* 5.6 0.7 - - + -
120B PRO* 3.3 16.0 - - - +
121B ILE 4.7 7.1 - - - +
123B LEU* 3.5 33.7 - - + -
239B ILE* 3.9 17.5 - - + -
240B LYS* 3.7 24.3 - - - +
243B ALA* 3.4 34.3 - - + -
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Residues in contact with ASN 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* 3.5 10.6 - - - +
47B TYR* 1.3 103.1 - - + +
49B GLU* 1.3 80.4 + - - +
50B ASN* 2.8 29.6 + - - +
51B TYR* 2.9 38.0 + - - +
112B LEU* 4.1 2.9 - - - +
114B PHE* 3.6 12.1 - - + -
120B PRO* 4.6 1.3 - - - -
243B ALA 4.4 6.3 + - - -
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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