Contacts of the helix formed by residues 53 - 61 (chain G) in PDB entry 3B4V
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 53 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23E ILE* 4.2 16.7 + - - +
25E TRP* 3.0 35.8 + - - +
61F THR* 3.8 24.5 + - + +
65F HIS* 4.6 16.6 - - - +
69F ARG* 6.1 0.2 - - - +
51G PRO 3.5 0.2 + - - -
52G GLY* 1.3 68.1 - - - -
54G LYS* 1.3 68.5 + - - +
55G ILE 3.2 3.4 - - - -
56G ASN* 3.0 17.7 + - - +
57G LEU* 3.0 18.7 + - - +
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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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24E GLY 3.2 27.5 + - - +
25E TRP* 4.0 16.6 - - + +
27E ASP* 3.2 31.9 + - - -
28E TRP* 3.4 38.1 - - + +
50G HIS* 3.8 15.9 - - + -
51G PRO* 3.1 24.0 + - + +
53G ASN* 1.3 81.5 + - - +
55G ILE* 1.3 57.0 + - - +
57G LEU* 3.2 8.2 + - + +
58G LEU 3.0 23.6 + - - -
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Residues in contact with ILE 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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11G VAL* 3.9 21.5 - - + -
13G TRP* 3.5 34.0 - - + -
25G VAL* 4.5 4.7 - - + -
28G THR* 4.0 22.0 - - + -
46G SER* 6.5 0.2 - - - -
48G LEU 3.9 22.0 - - - +
49G THR* 5.9 0.2 - - + -
50G HIS* 3.8 27.4 - - - +
52G GLY 3.4 18.7 + - - +
54G LYS* 1.3 77.9 - - - +
56G ASN* 1.3 71.8 + - - +
58G LEU* 3.3 20.5 + - + +
59G GLY 3.2 15.4 + - - -
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Residues in contact with ASN 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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54F SER 5.7 0.6 + - - -
55F SER* 5.0 5.1 + - - +
56F LEU* 4.6 14.6 + - - +
61F THR* 4.5 10.1 + - - +
13G TRP* 5.7 0.2 - - - -
23G SER 5.2 0.5 - - - +
25G VAL* 4.7 19.0 - - - +
52G GLY 3.8 1.2 - - - +
53G ASN* 3.2 28.6 - - + +
55G ILE* 1.3 86.1 - - - +
57G LEU* 1.3 56.5 + - - +
59G GLY* 3.0 5.2 + - - -
60G PHE* 2.9 54.3 + - + -
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Residues in contact with LEU 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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25E TRP* 3.5 57.0 - - + -
28E TRP* 3.5 33.0 - - + -
29E ILE* 4.0 13.5 - - + -
58F PHE* 4.1 15.0 - - + -
53G ASN 3.0 11.4 + - - +
54G LYS* 3.2 13.9 + - + +
56G ASN* 1.3 71.4 - - - +
58G LEU* 1.3 61.3 + - - +
60G PHE* 3.5 7.5 - - + -
61G LEU* 2.8 50.7 + - + +
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Residues in contact with LEU 58 (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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28E TRP* 3.6 27.7 - - + -
96E ASP* 6.1 2.9 - - + -
13G TRP* 4.9 0.7 - - + -
48G LEU* 5.2 7.0 - - + +
50G HIS* 3.9 25.4 - - + +
54G LYS 3.0 12.2 + - - +
55G ILE* 3.4 24.7 - - + +
56G ASN 3.3 0.2 - - - -
57G LEU* 1.3 74.6 - - - +
59G GLY* 1.3 59.9 + - - +
61G LEU* 3.5 1.6 + - - -
62G GLY 3.2 2.9 + - - -
63G LEU* 2.9 69.9 + - + +
64G VAL* 3.6 15.9 - - + +
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Residues in contact with GLY 59 (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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13G TRP* 3.8 16.4 - - - -
22G CYS 3.9 8.0 - - - +
23G SER* 4.1 14.9 - - - -
55G ILE 3.2 4.4 + - - -
56G ASN 3.0 8.6 + - - -
58G LEU* 1.3 75.9 - - - +
60G PHE* 1.3 67.0 + - - +
61G LEU 3.0 1.3 - - - -
62G GLY* 3.0 14.0 + - - -
64G VAL* 3.8 14.5 - - - +
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Residues in contact with PHE 60 (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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25E TRP* 4.3 3.8 - + - -
103E LYS* 5.1 1.4 + - - -
105E ILE* 3.9 21.3 - - + +
55F SER* 5.6 1.8 - - - -
56F LEU 3.3 27.1 - - - -
57F SER* 4.2 2.2 - - - -
58F PHE* 3.6 54.1 - + + -
61F THR* 3.3 23.8 - - + -
23G SER* 4.8 12.1 - - - -
24G LEU* 6.6 0.2 - - + -
56G ASN* 2.9 41.4 + - + -
57G LEU* 3.2 18.8 + - + +
59G GLY* 1.3 77.0 - - - +
61G LEU* 1.3 61.8 + - + +
62G GLY 3.4 0.3 + - - -
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Residues in contact with LEU 61 (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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28E TRP* 4.3 11.2 - - + -
29E ILE* 4.6 2.9 - - + -
91E MET* 4.7 8.1 - - + -
93E TYR* 3.2 68.7 + - + -
103E LYS* 3.6 7.6 + - - -
105E ILE* 3.8 21.3 - - + -
57G LEU* 2.8 48.9 + - + +
58G LEU 4.1 0.2 - - - +
60G PHE* 1.3 76.9 - - - +
62G GLY* 1.3 63.0 + - - +
63G LEU* 3.4 29.2 - - + +
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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