Contacts of the helix formed by residues 45 - 57 (chain G) 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 PHE 45 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A C 5.9 0.9 - - - +
64A A 3.3 61.2 - + + +
44G ASP* 1.3 80.1 + - - +
46G LYS* 1.3 63.5 + - - +
47G ALA 3.2 2.3 + - - -
48G GLN* 3.5 14.0 + - - +
49G LEU* 3.5 14.5 + - + +
80G ARG* 3.4 30.9 - - + +
83G ASN* 3.3 36.3 - - + -
84G ILE* 3.7 27.6 - - + -
87G GLN* 3.3 22.2 - - - -
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Residues in contact with LYS 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A A 4.8 6.3 - - - +
65A U 3.3 42.8 + - - +
66A G 3.5 46.7 + - - +
67A U 3.4 36.4 + - - -
44G ASP* 3.1 12.0 + - - +
45G PHE* 1.3 82.4 - - + +
47G ALA* 1.3 62.1 + - - +
49G LEU* 4.0 0.8 + - - -
50G ALA* 3.5 20.8 + - - +
67I LYS* 6.0 1.6 - - - +
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Residues in contact with ALA 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A C 4.5 7.6 - - + +
66A G 3.4 38.4 - - + +
43G THR* 6.0 1.8 - - + -
44G ASP* 3.3 28.3 + - + +
45G PHE 3.2 0.6 - - - -
46G LYS* 1.3 78.8 - - - +
48G GLN* 1.3 60.1 + - + +
50G ALA* 3.3 3.8 + - - +
51G ARG* 3.0 35.5 + - - +
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Residues in contact with GLN 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A C 6.0 0.7 - - - +
37G ILE* 5.6 2.9 - - + +
39G VAL* 3.3 29.1 - - + +
40G ASN* 2.5 45.8 + - - +
41G MET* 5.2 0.6 - - - +
43G THR* 4.6 6.2 - - + -
44G ASP* 3.2 24.1 + - + +
45G PHE* 3.5 10.9 + - - +
46G LYS 3.4 0.4 - - - -
47G ALA* 1.3 79.1 - - + +
49G LEU* 1.3 61.2 + - - +
51G ARG* 3.4 16.6 + - - +
52G CYS* 3.2 27.2 + - - -
80G ARG* 4.5 10.3 + - - +
84G ILE* 4.5 13.7 - - + +
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Residues in contact with LEU 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A A 4.6 8.3 - - + +
65A U 3.3 37.9 + - + +
45G PHE* 3.5 14.1 + - + +
46G LYS* 4.6 2.7 - - - +
47G ALA 3.4 0.4 - - - -
48G GLN* 1.3 75.1 - - - +
50G ALA* 1.3 60.3 + - - +
52G CYS* 3.3 12.7 + - + +
53G GLN* 3.1 25.8 + - + +
84G ILE* 3.4 40.7 - - + +
87G GLN* 3.4 33.2 - - + +
88G LEU* 4.5 16.1 - - + +
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Residues in contact with ALA 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A U 3.7 21.0 + - - +
66A G 3.6 36.6 - - + +
46G LYS 3.5 17.8 + - - +
47G ALA 3.3 6.1 + - - +
49G LEU* 1.3 78.6 - - - +
51G ARG* 1.3 61.2 + - - +
53G GLN* 3.4 2.7 + - - +
54G LYS* 3.2 24.9 + - - +
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Residues in contact with ARG 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A C 4.0 54.8 + - + +
31A C 2.8 36.1 + - - -
66A G 5.3 3.8 - - + -
37G ILE* 4.4 18.0 - - + +
38G TYR 5.8 1.6 + - - -
47G ALA* 3.0 25.2 + - - +
48G GLN* 3.7 14.3 - - - +
49G LEU 3.3 0.2 - - - -
50G ALA* 1.3 76.4 - - - +
52G CYS* 1.3 63.3 + - - +
54G LYS* 4.7 3.1 - - - +
55G LEU* 3.3 26.3 + - - +
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Residues in contact with CYS 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G ILE* 3.7 32.5 - - + -
39G VAL* 5.8 0.7 - - - -
48G GLN* 3.2 22.1 + - - -
49G LEU* 3.3 19.2 + - + +
51G ARG* 1.3 76.1 - - - +
53G GLN* 1.3 62.3 + - - +
55G LEU* 4.3 0.4 - - - -
56G LEU* 3.3 25.5 + - - +
69G ILE* 4.4 12.1 - - + +
71G ILE* 5.0 4.0 - - - -
84G ILE* 4.2 27.6 - - - +
88G LEU* 4.7 11.3 - - + +
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Residues in contact with GLN 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A U 2.6 42.8 + - + +
120E ARG* 5.2 11.4 - - - +
49G LEU* 3.1 15.9 + - - +
50G ALA 3.4 5.4 + - - +
51G ARG 3.3 0.6 - - - -
52G CYS* 1.3 77.0 - - - +
54G LYS* 1.3 64.3 + - - +
56G LEU* 3.6 6.6 + - - +
57G ASP* 3.0 54.5 + - - +
88G LEU* 4.2 18.2 - - + +
91G GLY* 4.6 1.8 + - - -
92G SER* 4.5 20.0 + - - +
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Residues in contact with LYS 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A G 6.2 1.2 - - - -
28A G 4.6 13.7 + - - -
66A G 6.0 1.8 + - - +
50G ALA 3.2 14.2 + - - +
51G ARG* 4.7 3.4 - - - +
53G GLN* 1.3 77.7 - - - +
55G LEU* 1.3 63.1 + - - +
57G ASP* 3.4 4.7 + - - +
58G GLY* 3.3 20.8 + - - -
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Residues in contact with LEU 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G ASN* 3.6 54.2 + - + +
36G ASP 4.6 4.0 - - - +
37G ILE* 3.8 32.8 - - + -
51G ARG 3.3 16.7 + - - +
52G CYS 4.6 1.3 - - - +
53G GLN 3.4 0.4 - - - -
54G LYS* 1.3 78.7 - - - +
56G LEU* 1.3 60.0 + - - +
58G GLY* 3.8 8.7 + - - +
62G GLY* 5.3 10.4 - - - -
63G GLN* 4.9 13.0 - - + +
66G CYS* 4.5 4.5 - - - +
69G ILE* 4.7 5.9 - - + +
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Residues in contact with LEU 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G CYS 3.3 16.9 + - - +
53G GLN* 4.0 8.3 - - - +
54G LYS 3.3 0.4 - - - -
55G LEU* 1.3 80.2 - - - +
57G ASP* 1.3 63.1 + - - +
58G GLY 3.4 0.2 - - - -
66G CYS* 3.3 8.0 - - - +
67G SER 5.5 0.2 - - - +
68G GLU* 5.3 4.9 - - - +
69G ILE* 4.2 32.2 - - + +
88G LEU* 4.1 32.8 - - + -
92G SER* 4.3 16.6 - - - +
96G LEU* 4.3 13.9 - - + -
134G VAL* 5.5 5.4 - - + -
135G PHE 5.6 2.5 - - - +
136G ARG* 3.0 43.6 + - + +
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Residues in contact with ASP 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E GLN* 3.4 27.7 - - + +
119E ARG* 2.9 33.1 + - - +
120E ARG* 4.9 15.4 + - - +
123E LEU* 5.7 4.7 - - - +
53G GLN* 3.0 39.3 + - - +
54G LYS* 3.4 5.8 + - - +
55G LEU 3.4 0.2 - - - -
56G LEU* 1.3 84.4 - - - +
58G GLY* 1.3 59.3 + - - +
59G GLY 3.3 1.2 + - - -
66G CYS* 4.8 0.2 - - - -
92G SER* 5.6 1.6 + - - -
136G ARG* 5.5 0.3 + - - -
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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