Contacts of the helix formed by residues 54 - 59 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A LEU 5.5 0.2 - - - +
49A MET* 6.1 6.1 - - - -
52A GLY* 3.2 28.4 + - - +
53A HIS* 1.3 70.9 - - - +
55A THR* 1.3 64.8 + - - +
56A PRO* 3.2 3.8 - - - -
57A PHE* 3.2 30.1 + - + +
58A GLU 3.9 0.3 + - - -
165A ARG* 3.0 54.4 + - + +
168A MET* 5.8 3.8 - - + -
209A ALA* 6.2 0.2 - - - +
211C LYS* 5.3 6.9 + - - -
305C FAD 5.0 1.9 + - - -
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Residues in contact with THR 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A HIS* 5.0 1.2 - - - +
54A GLU* 1.3 77.4 + - - +
56A PRO* 1.3 74.9 - - - +
58A GLU* 3.0 34.2 + - - +
59A HIS* 3.7 1.6 + - - -
165A ARG* 3.6 20.0 - - - +
83B SER* 5.1 0.5 - - - -
84B TYR 4.5 4.5 - - - -
85B ASN* 3.4 24.9 + - - -
78C ARG* 5.0 1.8 - - - +
80C ARG* 4.5 3.6 - - - +
305C FAD 3.2 46.1 + - - +
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Residues in contact with PRO 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ALA* 3.5 37.8 - - + +
26A ALA* 4.3 1.1 - - + -
27A ALA* 4.2 9.0 - - + +
48A LEU* 3.9 27.8 - - + -
53A HIS* 3.2 21.1 - - + +
54A GLU 3.2 1.1 - - - -
55A THR* 1.3 98.8 - - - +
57A PHE* 1.3 61.0 + - + +
59A HIS* 3.3 20.5 + - + +
60A ILE 4.7 0.2 + - - -
85B ASN* 3.6 19.7 - - - +
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Residues in contact with PHE 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ALA* 3.6 22.2 - - + -
45A ILE* 4.0 15.9 - - + -
48A LEU* 3.9 27.6 - - + -
49A MET* 3.7 24.9 - - + -
53A HIS 3.8 15.3 - - - -
54A GLU* 3.2 23.6 + - + +
55A THR 3.2 0.2 + - - -
56A PRO* 1.3 71.8 - - - +
58A GLU* 1.3 63.4 + - - +
59A HIS 3.1 3.0 + - - -
60A ILE* 3.3 12.3 + - + +
164A ALA* 3.1 27.1 + - + +
165A ARG 4.0 4.9 - - - +
168A MET* 3.9 25.1 - - + -
201A THR* 3.6 36.6 - - + -
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Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A THR* 3.0 23.2 + - - +
57A PHE* 1.3 77.8 - - - +
59A HIS* 1.3 58.2 + - - +
60A ILE 3.2 1.7 - - - +
61A VAL* 3.8 6.4 - - - +
163A ASN* 3.3 27.3 + - - +
165A ARG* 2.7 49.3 + - + -
83B SER* 2.3 41.1 + - - +
161B THR* 4.1 7.1 - - - +
80C ARG* 2.8 27.0 + - - -
305C FAD 3.4 19.1 + - - +
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Residues in contact with HIS 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A MET* 3.6 18.6 - - - +
18A GLY* 4.8 0.2 - - - -
22A SER* 3.9 24.2 + - - +
26A ALA* 3.4 13.1 - - + +
55A THR 3.7 5.0 + - - -
56A PRO 3.3 21.7 + - - +
57A PHE 3.1 1.4 - - - -
58A GLU* 1.3 76.6 - - - +
60A ILE* 1.3 60.6 + - - +
61A VAL* 4.1 3.1 - - - -
63B THR* 4.4 9.9 + - + +
83B SER* 3.8 27.6 - - - -
84B TYR 4.1 0.8 - - - -
85B ASN* 2.7 34.8 + - - +
159B PHE* 4.0 21.7 - - + +
161B THR* 2.6 34.4 + - - +
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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