Contacts of the helix formed by residues 33 - 43 (chain G) in PDB entry 5ANC
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 ASN 33 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A LYS* 4.5 28.9 + - - +
11G PHE* 5.7 1.8 - - - -
31G PHE* 4.4 6.1 - - - +
32G ILE* 1.3 106.3 - - - +
34G THR* 1.3 62.9 + - - +
35G LYS* 3.8 38.8 - - + +
36G VAL* 3.5 13.1 + - + +
37G GLU* 3.4 18.0 + - - +
3388N G 4.8 2.7 - - - -
3421N G 3.9 4.6 + - - +
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Residues in contact with THR 34 (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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33G ASN* 1.3 70.6 - - - +
35G LYS* 1.3 56.2 + - - +
36G VAL 3.2 0.2 - - - -
37G GLU* 3.2 21.9 + - - +
38G SER* 2.7 40.3 + - - +
3388N G 3.1 32.7 + - - +
3389N G 4.2 24.3 + - - +
3420N U 6.0 0.9 - - - -
3421N G 3.5 20.0 + - - +
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Residues in contact with LYS 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A PHE* 4.1 10.3 - - - -
11G PHE* 5.9 3.6 - - - -
33G ASN* 3.8 26.9 - - + +
34G THR* 1.3 77.2 - - - +
36G VAL* 1.3 63.9 + - + +
38G SER* 3.2 9.6 + - - -
39G LEU* 2.9 40.5 + - + +
49G ILE* 3.7 25.4 - - + -
51G TRP* 3.2 37.6 - - - +
52G SER* 5.0 10.8 - - - +
3420N U 3.1 28.4 + - - +
3421N G 3.0 27.3 + - - +
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Residues in contact with VAL 36 (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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6G CYS* 4.9 1.3 - - + -
8G TYR* 4.2 14.4 - - + +
9G SER* 3.6 30.7 - - - +
11G PHE* 5.0 8.7 - - + -
31G PHE* 3.6 24.5 - - + -
32G ILE* 4.2 8.1 - - + -
33G ASN* 3.5 33.2 + - + +
34G THR 3.2 0.6 - - - -
35G LYS* 1.3 81.0 - - + +
37G GLU* 1.3 58.2 + - - +
39G LEU* 3.2 13.2 + - + +
40G PHE* 2.9 27.5 + - - +
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Residues in contact with GLU 37 (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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94E TYR* 3.1 32.1 - - - -
19G MET* 4.8 15.3 - - - +
20G LYS 5.1 0.2 - - - +
31G PHE* 4.2 27.9 - - + -
33G ASN 3.4 9.6 + - - +
34G THR* 3.2 24.5 + - - +
36G VAL* 1.3 78.7 - - - +
38G SER* 1.3 57.5 + - - +
40G PHE* 3.2 8.2 + - - +
41G PHE* 2.9 62.4 + - + -
3388N G 5.1 1.3 + - - +
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Residues in contact with SER 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G THR* 2.7 25.8 + - - +
35G LYS* 3.2 5.9 + - - -
37G GLU* 1.3 75.1 - - - +
39G LEU* 1.3 59.0 + - - +
41G PHE* 3.2 10.7 + - - +
42G ARG* 2.9 36.0 + - - +
3419N C 4.6 0.2 - - - -
3420N U 2.6 46.2 + - - -
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Residues in contact with LEU 39 (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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8G TYR* 3.8 18.8 - - + -
35G LYS* 2.9 34.2 + - + +
36G VAL* 3.2 13.2 + - + +
38G SER* 1.3 75.9 - - - +
40G PHE* 1.3 51.9 + - - +
42G ARG* 3.2 23.7 + - - +
43G LYS* 2.6 32.6 + - - -
44G ILE* 3.4 36.7 + - + +
46G PRO* 4.0 29.2 - - + -
47G ARG 4.7 1.8 - - - +
48G ASP 6.1 0.4 - - - +
49G ILE* 4.8 11.4 - - + -
52G SER* 5.5 2.5 - - - +
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Residues in contact with PHE 40 (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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7G ASN 5.9 0.4 - - - -
8G TYR* 4.0 33.1 - + + -
21G PHE* 3.8 24.0 - + - -
23G ARG* 4.4 19.1 - - - -
29G PHE* 3.5 41.1 - + - -
31G PHE* 3.5 21.3 - + + -
36G VAL 2.9 12.4 + - - +
37G GLU* 3.3 9.0 - - - +
39G LEU* 1.3 75.7 - - - +
41G PHE* 1.3 77.0 + + - +
43G LYS* 3.3 30.1 + - + +
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Residues in contact with PHE 41 (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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94E TYR* 3.2 29.4 - + - -
21G PHE* 3.6 20.6 - + - -
23G ARG* 3.4 30.7 - - - -
37G GLU* 2.9 44.6 + - + +
38G SER* 3.2 8.0 + - - +
40G PHE* 1.3 87.8 - + - +
42G ARG* 1.3 58.3 + - - +
43G LYS* 4.5 10.3 + - - +
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Residues in contact with ARG 42 (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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38G SER* 2.9 19.5 + - - +
39G LEU* 3.5 24.8 - - - +
41G PHE* 1.3 78.9 - - - +
43G LYS* 1.3 69.4 + - - +
44G ILE* 3.5 37.4 - - + +
48G ASP* 3.9 21.2 + - - +
49G ILE* 6.0 2.4 - - - +
3419N C 3.4 27.0 + - - -
3420N U 2.7 28.4 + - - -
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Residues in contact with LYS 43 (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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8G TYR* 3.3 14.7 + - - -
23G ARG* 3.8 23.5 - - - +
39G LEU 2.6 15.1 + - - -
40G PHE* 3.3 23.8 + - + +
41G PHE* 4.5 8.5 + - - +
42G ARG* 1.3 78.4 - - - +
44G ILE* 1.3 59.0 + - - +
47G ARG* 5.5 0.2 + - - -
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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