Contacts of the strand formed by residues 38 - 47 (chain F) in PDB entry 3BXB
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 THR 38 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225E PRO* 5.9 3.1 - - + -
32F GLY* 3.5 0.4 - - - -
33F LYS* 3.0 48.6 + - - +
36F GLU* 3.9 14.5 + - + +
37F GLY* 1.3 78.0 - - - +
39F GLN* 1.3 65.2 + - - +
69F PHE* 3.7 3.0 - - - -
214F HIS* 4.2 15.9 - - + +
215F GLU 3.4 3.8 - - - -
216F VAL* 3.8 28.0 - - + -
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Residues in contact with GLN 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F MET* 3.5 22.9 - - + +
31F GLU 3.7 6.3 - - - +
32F GLY* 4.0 0.9 - - - -
37F GLY 5.1 0.4 + - - +
38F THR* 1.3 78.1 - - - +
40F THR* 1.3 61.2 + - - +
63F NRQ 3.7 16.9 - - + +
66F SER* 2.6 46.5 + - - -
69F PHE* 3.5 23.2 + - + +
70F ILE* 6.2 0.2 - - - +
214F HIS* 3.0 20.1 + - - -
215F GLU* 3.0 58.0 + - + +
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Residues in contact with THR 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227E LYS* 4.6 7.4 + - - +
11F MET* 3.6 4.2 - - - +
30F GLY* 3.1 3.7 - - - -
31F GLU* 3.0 45.0 + - - +
39F GLN* 1.3 71.6 - - - +
41F MET* 1.3 70.2 + - - +
42F ARG* 4.1 20.9 - - + +
63F NRQ 3.9 2.2 - - - -
202F ILE* 6.0 2.0 - - + -
212F GLU* 5.0 8.5 - - + +
213F GLN 3.3 13.7 - - - +
214F HIS* 3.3 21.4 + - + +
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Residues in contact with MET 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F MET* 3.5 34.5 - - + +
12F LYS 4.9 0.2 - - - -
13F LEU* 3.8 19.5 - - + +
28F SER* 2.8 24.9 - - - +
29F GLU 3.4 8.3 - - - +
30F GLY* 4.4 0.4 - - - -
39F GLN* 5.1 0.4 - - - +
40F THR* 1.3 76.6 - - - +
42F ARG* 1.3 62.5 + - - +
43F ILE* 4.1 11.0 - - + -
62F PHE* 3.4 27.8 - - - +
63F NRQ 3.6 20.8 - - + +
117F TYR* 3.5 26.2 - - + -
211F VAL 3.9 0.5 - - - +
212F GLU* 3.3 2.9 - - - -
213F GLN* 2.8 33.1 + - + +
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Residues in contact with ARG 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F THR 4.2 0.2 - - - +
28F SER* 3.3 3.7 - - - -
29F GLU* 2.7 45.2 + - + +
30F GLY* 4.1 12.2 - - - +
31F GLU* 2.6 41.2 + - - -
40F THR* 4.1 15.7 + - + +
41F MET* 1.3 74.2 - - - +
43F ILE* 1.3 61.5 + - - +
44F LYS* 4.0 3.1 + - - +
210F TYR* 3.6 29.2 - - + +
211F VAL 3.6 3.4 - - - -
212F GLU* 3.7 22.3 + - + +
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Residues in contact with ILE 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F CYS* 4.3 3.8 - - + -
27F THR 3.7 8.1 - - - +
28F SER* 3.5 19.7 - - - +
41F MET* 4.4 6.5 - - + -
42F ARG* 1.3 73.7 - - - +
44F LYS* 1.3 71.1 + - - +
45F VAL* 5.4 0.2 - - + -
55F PHE* 3.8 28.7 - - + -
62F PHE* 3.6 47.3 - - + -
209F THR 4.4 0.2 - - - -
210F TYR* 3.2 10.0 - - - -
211F VAL* 2.6 47.5 + - + +
213F GLN* 4.1 25.6 - - + +
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Residues in contact with LYS 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F CYS* 3.2 5.0 - - - +
27F THR* 3.0 46.4 + - - +
42F ARG 5.0 3.1 - - - +
43F ILE* 1.3 77.6 - - - +
45F VAL* 1.3 62.3 + - - +
46F VAL* 3.7 11.3 + - + -
209F THR 3.4 7.2 - - - +
210F TYR* 4.0 24.0 - - + -
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Residues in contact with VAL 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F LYS 3.5 7.2 - - - +
26F CYS* 4.1 15.9 - - - -
43F ILE* 5.4 0.2 - - + -
44F LYS* 1.3 73.1 - - - +
46F VAL* 1.3 62.0 + - - +
47F GLU 3.4 24.2 - - - +
49F GLY* 3.9 20.4 - - - +
51F LEU* 4.0 19.5 - - + -
55F PHE* 4.2 12.6 - - + -
208F GLU 3.6 24.2 - - - +
209F THR* 2.9 29.5 + - + +
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Residues in contact with VAL 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F LYS* 2.7 45.7 + - + +
26F CYS* 4.3 1.6 - - - +
27F THR* 4.0 29.2 - - + +
44F LYS* 3.7 12.7 + - + +
45F VAL* 1.3 80.3 - - - +
47F GLU* 1.3 65.8 + - + +
49F GLY 5.5 0.2 - - - -
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Residues in contact with GLU 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F HIS* 3.2 19.8 + - - +
24F PHE* 3.2 5.8 - - - -
25F LYS* 3.0 66.7 + - + +
45F VAL* 3.4 9.4 - - - +
46F VAL* 1.3 83.4 - - + +
48F GLY* 1.3 59.2 + - - +
49F GLY 3.1 9.8 + - - -
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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