Contacts of the helix formed by residues 64 - 70 (chain A) in PDB entry 2FG5
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 GLN 64 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A THR* 2.9 30.6 + - + +
36A PRO* 3.5 28.3 - - - +
37A THR 4.4 6.4 - - - +
38A ILE* 4.6 2.3 - - - +
62A ALA* 3.4 1.8 - - + -
63A GLY* 1.3 78.3 - - - +
65A GLU* 1.3 59.3 + - - +
66A ARG* 3.2 32.8 + - - +
67A PHE* 2.9 42.7 + - + +
68A HIS* 3.9 2.8 - - - -
302A GNP 4.1 2.7 + - - +
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Residues in contact with GLU 65 (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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63A GLY 3.6 2.0 + - - -
64A GLN* 1.3 70.6 - - - +
66A ARG* 1.3 58.7 + - - +
67A PHE 3.1 5.5 + - - -
68A HIS* 3.2 44.5 + - + +
69A SER 4.8 0.5 + - - -
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Residues in contact with ARG 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE* 4.1 18.2 - - - +
64A GLN* 3.2 38.2 + - + +
65A GLU* 1.3 73.6 - - - +
67A PHE* 1.3 98.9 + - + +
68A HIS 3.6 0.4 - - - -
69A SER* 3.3 18.8 + - - -
70A LEU* 4.9 2.1 - - - +
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Residues in contact with PHE 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A THR 4.0 3.8 - - - -
38A ILE* 3.8 20.6 - - + -
39A GLY* 3.3 29.2 - - - +
62A ALA* 3.5 34.9 - - + +
64A GLN* 2.9 34.4 + - + +
66A ARG* 1.3 124.0 - - + +
68A HIS* 1.3 58.7 + - - +
69A SER 3.0 3.1 - - - -
70A LEU* 2.8 48.3 + - + +
71A ALA* 3.5 4.7 + - - +
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Residues in contact with HIS 68 (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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13A ASP* 5.3 5.3 + - - -
62A ALA 5.3 1.6 + - - -
63A GLY 3.1 28.6 + - - -
64A GLN 3.9 0.6 + - - -
65A GLU* 3.2 41.5 + - + +
67A PHE* 1.3 77.0 - - - +
69A SER* 1.3 56.9 + - - +
70A LEU 3.0 5.6 + - - -
71A ALA* 3.1 23.8 + - - +
72A PRO* 3.8 5.4 - - - +
95A THR* 6.4 1.1 - - + -
99A TRP* 3.6 31.4 - + + -
102A GLU* 4.8 5.4 - - - +
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Residues in contact with SER 69 (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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65A GLU 4.8 0.4 + - - -
66A ARG 3.3 19.8 + - - -
68A HIS* 1.3 77.1 - - - +
70A LEU* 1.3 70.5 + - - +
72A PRO* 4.5 9.0 - - - +
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Residues in contact with LEU 70 (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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39A GLY* 4.9 11.7 - - - +
66A ARG 4.9 1.6 - - - +
67A PHE* 2.8 39.9 + - + +
69A SER* 1.3 92.6 - - - +
71A ALA* 1.3 64.7 + - - +
72A PRO* 3.6 3.1 - - - -
73A MET* 3.4 39.1 - - + +
74A TYR* 3.5 15.5 - - + +
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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