Contacts of the strand formed by residues 38 - 47 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32E GLY* 3.2 1.5 - - - -
33E LYS* 2.7 51.4 + - - +
36E GLU* 4.1 15.0 + - + +
37E GLY* 1.3 83.4 - - - +
39E GLN* 1.3 65.5 + - - +
69E PHE* 3.3 4.4 - - - -
214E HIS* 4.2 14.1 - - + +
215E GLU 3.5 3.1 - - - -
216E VAL* 4.0 21.5 - - + -
225F PRO* 6.1 1.1 - - + -
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Residues in contact with GLN 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E MET* 3.2 24.0 - - + +
31E GLU 3.6 6.1 - - - -
32E GLY* 4.0 0.9 - - - -
37E GLY 5.2 0.2 - - - +
38E THR* 1.3 77.8 - - - +
40E THR* 1.3 61.0 + - - +
41E MET* 4.6 1.4 - - - +
63E NRQ 3.6 19.6 - - + +
66E SER* 2.7 50.9 + - - -
69E PHE* 3.5 19.1 + - + +
214E HIS* 2.9 21.2 + - - -
215E GLU* 2.9 49.4 + - + +
217E ALA* 6.2 0.4 - - - +
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Residues in contact with THR 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E MET* 4.1 1.7 - - - +
30E GLY* 3.1 22.3 - - - -
31E GLU* 3.1 17.6 + - - +
39E GLN* 1.3 70.6 - - - +
41E MET* 1.3 70.8 + - - +
42E ARG* 3.6 25.6 - - - +
202E ILE* 5.7 1.6 - - + +
212E GLU* 4.0 28.2 + - + +
213E GLN 3.3 5.6 - - - +
214E HIS* 3.3 22.0 + - - +
227F LYS* 4.9 6.4 + - - +
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Residues in contact with MET 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E MET* 3.7 33.7 - - + +
13E LEU* 4.4 9.4 - - + -
28E SER* 3.3 26.7 - - - +
29E GLU* 3.6 5.2 - - - -
30E GLY 4.2 8.7 - - - +
39E GLN* 4.6 4.7 - - - +
40E THR* 1.3 76.7 - - - +
42E ARG* 1.3 63.2 + - - +
43E ILE* 4.3 14.7 - - + +
62E PHE* 3.1 36.8 - - + +
63E NRQ 3.5 22.4 - - + -
117E TYR* 4.7 2.7 - - + -
211E VAL 3.5 2.3 - - - +
212E GLU* 3.4 2.6 - - - -
213E GLN* 2.8 41.3 + - + +
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Residues in contact with ARG 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E SER* 3.0 18.0 - - - -
29E GLU* 2.8 32.9 + - + +
30E GLY* 4.1 8.5 - - - +
31E GLU* 2.9 42.6 + - - -
40E THR* 3.6 18.2 - - - +
41E MET* 1.3 74.1 - - - +
43E ILE* 1.3 59.3 + - - +
44E LYS* 6.1 1.1 - - - +
210E TYR* 3.3 31.0 - - + +
211E VAL 3.7 3.6 - - - -
212E GLU* 4.0 20.6 - - + +
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Residues in contact with ILE 43 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26E CYS* 4.1 4.3 - - + -
27E THR 3.7 8.3 - - - +
28E SER* 3.5 16.6 - - - -
41E MET* 4.3 6.5 - - + +
42E ARG* 1.3 74.8 - - - +
44E LYS* 1.3 71.4 + - - +
55E PHE* 3.9 18.4 - - + -
62E PHE* 3.7 54.7 - - + -
209E THR 4.6 0.2 - - - -
210E TYR* 2.9 22.8 - - - -
211E VAL* 2.8 31.7 + - + +
213E GLN* 3.9 27.6 - - + +
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Residues in contact with LYS 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E CYS* 3.1 23.9 - - - +
27E THR* 3.0 20.4 + - - +
29E GLU* 6.1 0.9 - - - -
42E ARG* 4.3 1.1 + - - +
43E ILE* 1.3 80.6 - - - +
45E VAL* 1.3 63.6 + - - +
46E VAL* 3.5 18.6 + - + +
209E THR 3.4 6.5 - - - +
210E TYR* 3.9 25.7 - - + -
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Residues in contact with VAL 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E PHE* 5.1 0.2 - - + -
25E LYS 3.6 6.3 - - - +
26E CYS* 4.1 16.4 - - - -
43E ILE* 4.7 0.4 - - - +
44E LYS* 1.3 75.1 - - - +
46E VAL* 1.3 63.5 + - - +
47E GLU 3.4 20.6 - - - +
49E GLY* 3.7 23.6 - - - +
51E LEU* 4.1 23.1 - - + -
55E PHE* 4.3 7.2 - - + -
208E GLU 3.7 22.9 - - - +
209E THR* 2.8 30.4 + - + +
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Residues in contact with VAL 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E LYS* 2.7 36.2 + - + +
27E THR* 3.9 34.8 - - + +
44E LYS* 3.5 18.6 + - + +
45E VAL* 1.3 80.2 - - - +
47E GLU* 1.3 65.1 + - + +
48E GLY 4.3 0.5 + - - -
49E GLY 5.4 0.8 + - - -
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Residues in contact with GLU 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E HIS* 3.9 17.4 + - + -
24E PHE* 3.3 4.5 - - - -
25E LYS* 3.0 67.0 + - + +
45E VAL* 3.4 5.9 - - - +
46E VAL* 1.3 84.0 - - + +
48E GLY* 1.3 64.7 + - - +
49E GLY 3.3 4.3 + - - -
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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