Contacts of the helix formed by residues 44 - 57 (chain F) in PDB entry 5B6N
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 44 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E PRO* 4.2 18.8 - - + -
217E TYR* 3.9 1.1 - - - -
40F PRO* 6.0 0.2 - - + -
41F ARG* 3.4 34.4 + - + +
42F ASP 3.6 2.0 - - - -
43F PHE* 1.3 83.2 - - - +
45F PRO* 1.3 67.8 - - - +
46F VAL* 4.3 2.0 + - - -
47F CSD 2.1 37.4 + - - +
48F THR* 2.7 30.0 + - - -
82F TRP* 4.1 0.3 - - - -
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Residues in contact with PRO 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188E MET* 3.5 29.6 - - + -
189E VAL 3.8 16.4 - - - +
190E LEU* 5.2 0.4 - - - -
191E PRO* 4.1 15.3 - - + -
217E TYR* 3.6 36.7 - - + +
218E LEU* 4.2 7.8 - - + +
219E ARG 4.3 0.7 - - - +
44F THR* 1.3 83.8 - - - +
46F VAL* 1.3 68.7 + - + +
47F CSD 3.0 1.8 - - - -
48F THR* 3.1 13.9 + - - +
49F THR* 3.1 22.1 + - - +
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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
----------------------------------------------------------
176E ALA* 3.7 28.7 - - + +
177E THR 3.5 24.5 - - - +
178E PRO* 3.6 11.2 - - + -
179E VAL 4.9 0.2 + - - -
188E MET* 4.3 14.1 - - + -
44F THR* 3.5 1.5 - - - -
45F PRO* 1.3 80.0 - - + +
47F CSD 1.3 61.6 + - - +
49F THR* 2.6 23.3 + - - -
50F GLU* 3.6 10.9 + - - +
132F ARG* 3.5 30.1 - - - +
152F THR 5.4 0.2 - - - +
153F THR 4.9 1.1 - - - +
154F GLY* 4.0 7.9 - - - +
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Residues in contact with CSD 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F HIS* 3.2 12.8 - - + +
40F PRO* 3.1 31.3 - - - +
41F ARG 3.3 15.1 + - - +
44F THR* 2.1 39.5 + - - +
45F PRO 3.0 0.6 - - - -
46F VAL* 1.3 77.6 + - - +
48F THR* 1.3 63.2 + - - +
49F THR 3.3 0.4 - - - -
50F GLU* 3.6 7.8 - - - +
51F LEU* 3.3 19.1 + - - +
82F TRP* 3.2 20.4 - - + -
132F ARG* 2.8 38.7 + - - -
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Residues in contact with THR 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217E TYR* 3.3 9.4 - - - +
218E LEU* 3.7 24.0 - - + -
44F THR 2.7 18.6 + - - -
45F PRO 3.1 8.5 + - - -
47F CSD 1.3 76.6 + - - -
49F THR* 1.3 60.6 + - - +
50F GLU 3.0 4.8 + - - -
52F GLY* 3.3 19.9 + - - -
82F TRP* 3.1 22.5 + - - +
85F ASP 4.3 3.8 - - - +
86F ILE* 3.6 31.0 - - + +
89F TYR* 3.8 13.2 - - + -
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Residues in contact with THR 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178E PRO* 3.8 8.5 - - + +
179E VAL* 3.1 40.8 + - - +
188E MET* 3.8 22.9 - - + -
218E LEU* 5.2 1.1 - - + -
220E TYR* 4.3 1.3 - - - +
45F PRO 3.1 15.7 - - - +
46F VAL 2.6 21.3 + - - -
48F THR* 1.3 76.7 - - - +
50F GLU* 1.3 55.7 + - - +
52F GLY 4.0 1.3 - - - -
53F ARG* 3.3 19.1 + - - +
89F TYR* 3.6 34.1 - - + +
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Residues in contact with GLU 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179E VAL* 3.4 18.2 - - + -
37F PHE* 5.3 0.6 - - + -
39F HIS* 4.8 0.5 - - - +
46F VAL 3.6 9.0 - - - +
47F CSD 3.6 11.6 - - - +
48F THR 3.0 0.8 - - - -
49F THR* 1.3 79.3 + - - +
51F LEU* 1.3 67.4 + - + +
52F GLY 3.1 1.1 - - - -
53F ARG* 3.6 2.1 + - - +
54F ALA* 3.2 25.8 + - - +
132F ARG* 2.6 30.5 + - - -
154F GLY* 3.5 5.0 - - - -
155F ARG* 2.8 57.9 + - - +
157F PHE* 3.8 19.3 - - + -
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Residues in contact with LEU 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F PHE* 3.9 17.7 - - + -
39F HIS* 3.6 36.3 - - + +
47F CSD 3.3 18.3 + - - +
48F THR 4.9 0.2 - - - +
50F GLU* 1.3 81.9 - - + +
52F GLY* 1.3 62.1 + - - +
53F ARG 3.4 0.2 - - - -
54F ALA* 3.9 5.8 - - - -
55F ALA* 3.3 22.9 + - - +
70F ALA* 4.6 1.6 - - + -
82F TRP* 3.6 22.0 - - + -
86F ILE* 3.7 20.0 - - + +
100F PHE* 3.5 25.3 - - + -
102F ILE* 4.0 22.0 - - + -
155F ARG* 5.4 0.2 - - - +
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Residues in contact with GLY 52 (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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48F THR 3.3 18.3 + - - -
50F GLU 3.1 0.6 - - - -
51F LEU* 1.3 80.3 - - - +
53F ARG* 1.3 58.7 + - - +
55F ALA* 3.7 1.7 + - - +
56F LYS* 3.6 14.4 + - - +
86F ILE* 4.2 10.7 - - - +
89F TYR* 4.3 7.6 - - - -
90F ASN* 2.3 38.3 + - - -
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Residues in contact with ARG 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179E VAL* 4.5 9.6 - - + -
180E ASP* 3.7 23.1 + - - +
49F THR 3.3 20.5 + - - +
50F GLU* 4.0 4.0 - - - +
51F LEU 3.4 0.2 - - - -
52F GLY* 1.3 74.8 - - - +
54F ALA* 1.3 66.4 + - - +
55F ALA 3.2 0.2 - - - -
56F LYS* 3.2 42.7 + - - +
57F LEU* 3.1 50.6 + - + +
89F TYR* 5.7 0.2 - - + -
157F PHE* 4.7 15.7 - - + +
158F ASP* 3.9 17.6 + - - -
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Residues in contact with ALA 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F PHE* 4.5 6.7 - - + -
50F GLU 3.2 16.6 + - - +
51F LEU* 4.0 3.4 - - - +
52F GLY 3.4 0.2 - - - -
53F ARG* 1.3 81.1 - - - +
55F ALA* 1.3 56.4 + - - +
57F LEU* 3.0 9.0 + - - +
58F ALA* 2.9 27.2 + - - +
68F LEU* 3.9 11.0 - - + +
100F PHE* 3.7 20.6 - - + -
157F PHE* 3.9 25.4 - - + -
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Residues in contact with ALA 55 (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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51F LEU 3.3 17.0 + - - +
52F GLY* 3.9 6.1 - - - +
53F ARG 3.2 0.8 - - - -
54F ALA* 1.3 75.8 - - - +
56F LYS* 1.3 62.4 + - - +
57F LEU 3.1 1.3 - - - -
58F ALA* 3.7 11.8 + - - +
59F PRO* 3.9 4.7 - - - +
87F ASN* 5.4 4.0 - - - +
90F ASN* 4.7 4.9 - - - +
92F GLU* 5.8 2.9 - - - +
97F LYS 5.2 1.1 - - - +
98F LEU* 4.8 7.6 - - + -
99F PRO* 3.8 34.4 - - + +
100F PHE* 3.6 5.3 - - + -
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Residues in contact with LYS 56 (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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52F GLY 3.6 9.1 + - - +
53F ARG* 3.2 60.5 + - - +
55F ALA* 1.3 79.9 - - - +
57F LEU* 1.3 61.8 + - - +
58F ALA 3.4 0.2 - - - -
59F PRO* 3.6 15.0 - - - +
60F GLU* 5.2 1.0 + - - +
89F TYR* 4.6 10.1 + - - -
90F ASN* 3.9 29.5 - - + +
92F GLU* 6.5 1.3 - - - -
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Residues in contact with LEU 57 (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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53F ARG* 3.1 50.3 + - + +
54F ALA* 3.0 9.5 + - - +
56F LYS* 1.3 81.7 - - - +
58F ALA* 1.3 61.8 + - - +
59F PRO 3.4 1.8 - - - -
60F GLU* 3.3 33.9 + - + +
61F PHE* 2.9 28.3 + - + -
157F PHE* 4.0 31.0 - - + +
158F ASP* 4.7 3.6 - - - +
161F LEU* 4.1 16.4 - - + -
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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
------------------------------------------------------------
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