Contacts of the helix formed by residues 63 - 71 (chain C) in PDB entry 3A13
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 63 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62C TYR* 1.3 77.1 - - - +
64C GLN* 1.3 67.3 + - - +
65C GLU* 3.2 17.6 + - + +
66C ARG* 3.2 63.6 + - - +
67C TRP 3.3 9.5 + - - -
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Residues in contact with GLN 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C PRO* 3.8 24.6 - - - +
62C TYR* 3.2 34.7 + - - +
63C GLU* 1.3 73.0 - - - +
65C GLU* 1.3 64.0 + - - +
67C TRP* 3.3 21.9 + - + +
68C ALA* 2.9 25.6 + - - +
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Residues in contact with GLU 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C GLU* 3.2 18.8 - - + +
64C GLN* 1.3 80.7 - - - +
66C ARG* 1.3 63.3 + - - +
68C ALA* 3.5 4.0 + - - +
69C ASP* 3.0 26.3 + - - +
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Residues in contact with ARG 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C TYR* 4.9 6.1 - - - +
63C GLU* 3.2 53.8 + - - +
65C GLU* 1.3 77.8 - - - +
67C TRP* 1.3 64.6 + - - +
69C ASP* 3.2 7.9 + - - +
70C LEU* 3.1 48.6 + - + +
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Residues in contact with TRP 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C TYR* 3.5 47.1 - + + -
12C TYR* 3.5 18.1 + + - -
52C THR* 3.4 39.9 + - + +
53C GLY* 5.2 0.2 - - - -
58C LEU* 6.3 1.4 - - - +
62C TYR* 3.7 37.6 + + + -
63C GLU 3.3 4.2 + - - +
64C GLN* 3.5 26.7 - - - +
66C ARG* 1.3 79.5 - - - +
68C ALA* 1.3 78.5 + - + +
70C LEU* 3.1 15.8 + - - +
71C SER* 3.0 21.0 + - - -
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Residues in contact with ALA 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C TYR* 3.2 26.8 + - - +
64C GLN 2.9 19.3 + - - +
65C GLU* 4.0 4.7 - - - +
67C TRP* 1.3 84.4 - - + +
69C ASP* 1.3 61.8 + - - +
70C LEU 3.3 0.5 + - - -
71C SER* 3.4 16.7 + - - +
73C LYS* 5.2 7.6 + - - -
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Residues in contact with ASP 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C GLU 3.0 19.2 + - - +
66C ARG* 3.2 8.7 + - - +
68C ALA* 1.3 77.0 - - - +
70C LEU* 1.3 62.6 + - - +
71C SER 3.5 1.8 + - - +
92C PRO* 3.7 15.2 - - - +
94C HIS* 2.7 35.0 + - - -
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Residues in contact with LEU 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C SER* 4.4 5.0 - - - -
52C THR* 3.8 15.5 - - + +
66C ARG* 3.1 39.1 + - + +
67C TRP* 3.1 5.6 + - - +
68C ALA 3.1 0.4 - - - -
69C ASP* 1.3 83.7 - - - +
71C SER* 1.3 62.1 + - - +
72C ALA 3.7 1.2 + - - -
91C TYR* 6.0 0.5 - - - -
92C PRO* 3.9 14.7 - - - +
94C HIS* 3.7 43.5 - - + +
95C ALA* 4.0 23.3 - - + +
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Residues in contact with SER 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C TYR* 3.9 19.4 - - - -
12C TYR* 3.8 12.8 - - - -
51C SER* 4.1 0.2 - - - -
52C THR* 2.6 28.7 + - - -
67C TRP* 3.0 17.0 + - - -
68C ALA* 3.4 12.9 + - - +
69C ASP 3.5 1.6 - - - +
70C LEU* 1.3 78.2 - - - +
72C ALA* 1.3 64.9 + - - +
73C LYS* 4.2 16.6 - - - +
90C ALA 4.6 0.3 - - - +
92C PRO* 4.3 7.8 - - - +
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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