Contacts of the helix formed by residues 36 - 46 (chain E) in PDB entry 1XFB
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 SER 36 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34E ASP 3.2 4.9 + - - -
35E GLU* 1.3 74.8 - - - +
37E VAL* 1.3 60.2 + - - +
38E GLY* 2.9 6.3 + - - -
39E SER* 2.6 32.0 + - - -
40E MET* 2.8 27.5 + - - +
80E PHE* 3.5 19.3 - - - -
108E LYS* 4.2 15.7 + - - +
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Residues in contact with VAL 37 (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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35E GLU 3.6 1.0 + - - -
36E SER* 1.3 73.2 - - - +
38E GLY* 1.3 63.6 + - - +
40E MET* 3.7 7.7 - - - +
41E ALA* 3.3 3.6 + - - +
51E ASN* 3.0 24.0 + - - +
56E ARG* 3.2 42.6 - - - +
80E PHE* 3.8 21.5 - - + -
82E GLU* 5.2 0.9 - - - +
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Residues in contact with GLY 38 (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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36E SER* 2.9 6.8 + - - -
37E VAL* 1.3 81.2 - - - +
39E SER* 1.3 59.3 + - - -
40E MET 3.0 0.9 - - - -
41E ALA* 2.8 29.3 + - - +
42E LYS* 3.6 5.6 + - - +
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Residues in contact with SER 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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35E GLU* 3.8 10.2 - - - +
36E SER* 2.6 38.2 + - - -
38E GLY* 1.3 73.2 - - - +
40E MET* 1.3 61.3 + - - +
42E LYS* 3.2 21.1 + - - +
43E ARG* 3.2 22.7 + - - +
108E LYS* 5.3 0.9 + - - -
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Residues in contact with MET 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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35E GLU* 3.4 23.6 - - + +
36E SER 2.8 18.7 + - - +
37E VAL* 3.7 6.3 - - - +
39E SER* 1.3 77.2 + - - +
41E ALA* 1.3 65.1 + - - +
43E ARG* 3.5 35.0 - - + -
44E LEU* 3.0 41.1 + - + +
51E ASN* 3.9 1.3 - - - +
56E ARG* 3.5 35.7 - - + -
59E TYR* 4.6 20.2 - - + -
60E ARG* 3.5 21.5 - - - +
311E LEU* 4.9 1.6 - - + -
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Residues in contact with ALA 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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37E VAL 3.3 3.1 + - - +
38E GLY* 2.8 13.5 + - - +
40E MET* 1.3 80.5 - - - +
42E LYS* 1.3 56.8 - - + +
44E LEU* 3.8 1.2 - - - +
45E SER* 2.9 31.7 + - - -
51E ASN* 3.0 35.6 - - + +
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Residues in contact with LYS 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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38E GLY 3.6 6.2 + - - +
39E SER* 3.2 13.1 + - - +
41E ALA* 1.3 79.7 - - + +
43E ARG* 1.3 63.6 + - + +
45E SER* 2.8 24.6 + - - -
46E GLN* 3.3 15.9 - - - +
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Residues in contact with ARG 43 (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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35E GLU* 2.6 40.9 + - - +
39E SER* 3.2 16.0 + - - +
40E MET* 3.5 26.7 - - + -
42E LYS* 1.3 77.0 - - + +
44E LEU* 1.3 64.2 + - - +
46E GLN* 3.4 23.9 + - - +
47E ILE* 3.9 7.3 + - - +
303E GLY* 4.9 2.2 - - - -
304E ARG* 2.8 68.1 - - - +
307E GLN* 4.2 7.7 + - - +
311E LEU* 4.0 22.8 - - + +
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Residues in contact with LEU 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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40E MET* 3.0 26.0 + - + +
41E ALA* 3.9 3.4 - - - +
43E ARG* 1.3 73.4 - - - +
45E SER* 1.3 61.1 + - - +
47E ILE* 3.0 23.1 + - + +
48E GLY 2.4 22.0 - - - +
49E VAL* 3.6 38.6 - - + +
50E GLU 4.0 0.9 - - - +
51E ASN* 3.5 33.4 - - - +
55E ASN* 4.4 7.0 - - + -
56E ARG* 4.1 16.4 - - + -
59E TYR* 4.9 5.2 - - + -
311E LEU* 4.4 8.7 - - + -
314E TRP* 3.8 20.4 - - + -
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Residues in contact with SER 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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41E ALA 2.9 18.0 + - - -
42E LYS* 2.8 17.7 + - - -
44E LEU* 1.3 77.2 - - - +
46E GLN* 1.3 65.3 + - - +
47E ILE 3.0 0.2 - - - -
48E GLY* 3.0 20.4 + - - +
49E VAL 4.2 1.5 + - - -
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Residues in contact with GLN 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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42E LYS* 3.3 13.0 + - - +
43E ARG* 3.6 16.6 + - - +
44E LEU 3.2 0.8 - - - -
45E SER* 1.3 83.4 + - - +
47E ILE* 1.3 62.8 + - + +
48E GLY 3.5 0.2 - - - -
304E ARG* 2.6 34.8 + - - +
315E ARG* 4.5 7.3 + - - -
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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