Contacts of the helix formed by residues 45 - 59 (chain F) in PDB entry 6AHU
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 LYS 45 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A G 3.4 23.1 - - - +
52A C 3.3 47.1 + - - +
53A A 2.6 30.5 + - - -
37F HIS 5.0 0.4 - - - +
38F MET* 4.7 2.0 - - - -
42F GLU* 2.9 47.4 + - + +
43F GLY 3.2 1.0 - - - -
44F SER* 1.3 77.6 + - - +
46F ILE* 1.3 57.3 + - - +
48F ASN* 3.4 11.9 - - + +
49F LEU* 2.6 55.9 + - + +
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Residues in contact with ILE 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A C 5.7 12.1 - - - -
38A U 4.2 18.4 - - - +
39A G 4.3 21.5 - - + +
38F MET* 4.2 16.6 - - + -
42F GLU 4.1 7.4 - - - +
43F GLY 3.5 15.5 - - - +
44F SER 3.2 0.4 - - - -
45F LYS* 1.3 77.6 - - - +
47F ARG* 1.3 59.8 + - - +
49F LEU* 5.0 2.2 - - - -
50F MET* 3.3 36.4 + - + +
76F LYS* 3.9 26.9 - - + +
79F THR* 5.6 6.3 - - - +
80F CYS* 5.8 10.1 - - + -
83F ILE* 5.2 11.2 - - + -
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Residues in contact with ARG 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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38A U 3.2 31.4 + - + +
39A G 3.0 28.0 + - - +
40A A 2.6 34.6 + - - -
50A G 5.3 0.2 + - - -
44F SER* 3.3 17.1 + - - +
45F LYS 3.2 0.2 - - - -
46F ILE* 1.3 77.8 - - - +
48F ASN* 1.3 62.2 + - - +
50F MET* 4.4 1.1 - - - -
51F ALA* 3.6 18.6 + - - +
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Residues in contact with ASN 48 (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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50A G 3.2 67.7 + - + +
52A C 4.1 4.8 - - - -
44F SER* 2.8 29.3 + - - -
45F LYS* 2.9 20.0 + - + +
47F ARG* 1.3 81.7 - - - +
49F LEU* 1.3 65.8 + - - +
50F MET 3.3 0.2 - - - -
51F ALA* 3.3 11.6 + - - +
52F PHE* 3.2 24.0 - - - -
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Residues in contact with LEU 49 (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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51A U 5.2 7.4 - - - +
52A C 4.1 18.6 - - - +
36F VAL* 3.7 37.0 - - + +
37F HIS 3.5 26.0 - - - +
38F MET* 3.8 21.1 - - + -
45F LYS* 2.6 35.3 + - + +
46F ILE* 4.7 1.1 - - - +
48F ASN* 1.3 72.8 - - - +
50F MET* 1.3 59.3 + - - +
52F PHE* 3.3 11.4 + - + +
53F ALA* 2.9 27.7 + - - +
80F CYS* 4.5 11.9 - - - -
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Residues in contact with MET 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A U 3.9 20.2 - - + +
46F ILE* 3.3 27.6 + - + +
47F ARG 5.1 0.7 - - - +
49F LEU* 1.3 74.1 - - - +
51F ALA* 1.3 60.6 + - - +
53F ALA* 3.7 15.0 - - + -
54F THR* 2.8 38.6 + - - +
67F PHE* 5.9 0.4 - - - -
80F CYS* 3.3 36.8 - - - +
83F ILE* 3.8 24.2 - - + +
84F LEU* 3.5 38.4 - - + +
87F ARG* 5.9 2.5 - - + -
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Residues in contact with ALA 51 (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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50A G 4.3 14.8 - - - +
47F ARG 3.6 16.0 + - - +
48F ASN 3.3 12.6 + - - +
49F LEU 3.2 0.8 - - - -
50F MET* 1.3 79.5 - - - +
52F PHE* 1.3 59.2 + - + +
54F THR* 4.2 3.5 - - - -
55F ALA* 3.3 22.9 + - - +
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Residues in contact with PHE 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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49A U 5.7 3.4 - - + -
50A G 3.6 33.4 - - - -
51A U 3.2 30.3 - - - -
36F VAL* 6.5 0.7 - - + -
48F ASN 3.2 24.1 + - - -
49F LEU* 3.3 13.2 + - + +
51F ALA* 1.3 77.7 - - + +
53F ALA* 1.3 56.5 + - - +
54F THR 3.3 0.4 - - - -
55F ALA* 3.5 9.7 - - + +
56F SER* 2.7 34.7 + - - -
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Residues in contact with ALA 53 (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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36F VAL* 5.8 6.7 - - + +
49F LEU 2.9 17.5 + - - +
50F MET* 3.6 18.1 + - - -
51F ALA 3.5 0.2 - - - -
52F PHE* 1.3 76.6 - - - +
54F THR* 1.3 61.1 + - - +
56F SER* 3.6 13.0 + - - -
57F MET* 3.7 8.7 + - - +
65F ILE* 5.9 2.2 - - + -
67F PHE* 5.6 4.5 - - + -
80F CYS* 6.1 0.4 - - - -
84F LEU* 3.4 43.2 - - + +
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Residues in contact with THR 54 (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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50F MET* 2.8 26.5 + - - +
51F ALA* 4.2 3.8 - - - -
53F ALA* 1.3 76.1 - - - +
55F ALA* 1.3 61.8 + - - +
57F MET* 3.3 33.4 + - + +
58F ALA* 3.7 5.7 + - - +
84F LEU* 4.8 3.9 - - - +
87F ARG* 4.8 26.0 + - + +
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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 ALA 3.3 18.1 + - - +
52F PHE* 3.2 16.4 + - + +
54F THR* 1.3 75.6 - - - +
56F SER* 1.3 54.0 + - - +
58F ALA* 2.9 9.4 + - - +
59F GLN* 2.6 49.1 + - + +
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Residues in contact with SER 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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34F GLY* 6.1 0.2 - - - -
52F PHE 2.7 20.2 + - - -
53F ALA* 3.8 9.4 - - - -
54F THR 3.3 0.6 - - - -
55F ALA* 1.3 70.1 - - - +
57F MET* 1.3 62.7 + - - +
59F GLN* 3.2 20.7 - - - +
61F ALA* 4.9 14.3 - - - +
62F THR 5.4 1.4 + - - -
65F ILE* 3.4 28.3 - - - +
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Residues in contact with MET 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 ALA 3.7 6.6 + - - +
54F THR* 3.3 25.9 + - + +
55F ALA 3.2 0.8 - - - -
56F SER* 1.3 77.6 - - - +
58F ALA* 1.3 61.8 + - + +
59F GLN 4.3 2.1 - - - +
84F LEU* 5.8 1.6 - - + -
87F ARG* 4.1 25.4 - - + +
88F LEU* 3.8 38.6 - - + +
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Residues in contact with ALA 58 (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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54F THR 3.7 4.7 + - - +
55F ALA* 2.9 12.1 + - - +
57F MET* 1.3 81.3 - - + +
59F GLN* 1.3 69.2 + - + +
60F PRO* 3.7 3.8 - - - +
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Residues in contact with GLN 59 (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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55F ALA* 2.6 34.1 + - + +
56F SER* 3.2 19.4 - - - +
57F MET 4.3 2.3 - - - +
58F ALA* 1.3 77.6 - - - +
60F PRO* 1.3 75.6 - - + +
61F ALA* 3.1 11.5 + - + +
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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