Contacts of the helix formed by residues 54 - 59 (chain D) in PDB entry 3G4C
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 GLU 54 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211B LYS* 5.3 6.8 + - - -
310B FAD 4.6 3.6 + - - -
48D LEU 5.8 0.2 - - - +
49D MET* 6.0 6.5 - - - -
52D GLY* 3.1 24.4 + - - +
53D HIS* 1.3 73.7 - - - +
55D THR* 1.3 64.8 + - - +
56D PRO* 3.3 2.2 - - - -
57D PHE* 3.2 30.8 + - + +
58D GLU 4.0 0.7 + - - -
165D ARG* 2.8 61.3 + - + +
168D MET* 5.8 3.1 - - + -
209D ALA* 6.5 0.9 - - + -
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Residues in contact with THR 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ARG* 5.1 0.2 - - - +
80B ARG* 4.4 3.6 - - - +
310B FAD 3.3 44.7 + - - +
83C SER* 5.2 0.3 - - - -
84C TYR 4.3 8.9 + - - +
85C ASN* 3.4 18.9 + - - +
53D HIS* 5.1 0.3 - - - -
54D GLU* 1.3 78.6 + - - +
56D PRO* 1.4 72.2 - - - +
58D GLU* 3.0 34.4 + - - +
59D HIS* 3.5 7.4 + - - -
165D ARG* 3.7 20.9 - - - +
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Residues in contact with PRO 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C ASN* 3.6 17.9 - - - +
23D ALA* 3.5 37.8 - - + +
26D ALA* 4.3 0.9 - - + -
27D ALA* 3.8 18.2 - - + +
48D LEU* 4.0 16.8 - - + -
53D HIS* 3.3 21.8 - - + +
54D GLU 3.3 0.9 - - - -
55D THR* 1.4 96.3 - - - +
57D PHE* 1.3 58.7 + - + +
58D GLU 3.2 0.2 - - - -
59D HIS* 3.1 27.9 + - + +
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Residues in contact with PHE 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ALA* 3.7 20.4 - - + -
45D ILE* 4.0 17.0 - - + -
48D LEU* 4.0 26.0 - - + -
49D MET* 3.4 25.8 - - + -
53D HIS 3.7 15.9 - - - -
54D GLU* 3.2 26.9 + - + +
55D THR 3.1 1.0 - - - -
56D PRO* 1.3 72.8 - - - +
58D GLU* 1.3 59.5 + - - +
59D HIS 3.1 6.5 + - - -
60D ILE* 3.3 14.6 + - + +
164D ALA* 3.0 29.1 + - + +
165D ARG 4.1 4.5 - - - +
168D MET* 3.8 26.7 - - + -
201D THR* 3.8 33.0 - - + -
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Residues in contact with GLU 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ARG* 2.9 21.8 + - - -
310B FAD 3.5 17.9 + - - +
83C SER* 2.4 42.6 + - - +
84C TYR 4.9 0.3 + - - -
161C THR* 3.8 15.0 - - - +
55D THR* 3.0 22.4 + - - +
57D PHE* 1.3 77.1 - - - +
59D HIS* 1.3 56.2 + - - +
60D ILE 3.3 2.0 - - - +
61D VAL* 3.9 1.6 - - - +
163D ASN* 3.4 27.1 + - - +
165D ARG* 2.6 52.3 + - + -
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Residues in contact with HIS 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C THR* 4.3 11.3 + - + +
83C SER* 4.1 17.9 - - - -
84C TYR 4.2 2.0 + - - -
85C ASN* 2.7 25.9 + - - -
159C PHE* 3.9 32.1 - - + -
161C THR* 2.7 31.0 + - - +
17D MET* 3.3 22.2 - - - +
22D SER* 4.0 23.7 - - - +
26D ALA* 3.3 17.4 - - + +
55D THR 3.5 8.3 + - - -
56D PRO 3.1 22.9 - - - +
57D PHE 3.1 1.6 - - - -
58D GLU* 1.3 76.6 - - - +
60D ILE* 1.3 60.0 + - - +
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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