Contacts of the helix formed by residues 67 - 74 (chain C) in PDB entry 4I6N
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 SER 67 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A CYS* 3.4 13.6 - - - +
65C ASP* 3.0 18.5 + - - +
66C ASP* 1.3 80.6 + - - +
68C PRO* 1.4 69.1 - - - +
69C GLN* 2.8 29.3 + - - +
70C THR* 3.5 12.7 + - - -
184C ARG* 3.4 25.6 - - - -
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Residues in contact with PRO 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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68A PRO* 3.6 27.9 - - + +
71A CYS* 4.3 0.4 - - + -
72A THR* 3.8 24.2 - - + -
66C ASP 3.6 0.9 - - - +
67C SER* 1.4 87.4 - - - +
69C GLN* 1.3 83.4 + - - +
71C CYS* 3.2 15.2 + - - +
72C THR* 3.2 17.0 + - + +
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Residues in contact with GLN 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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67C SER* 2.8 25.9 + - - +
68C PRO* 1.3 97.1 - - - +
70C THR* 1.3 59.1 + - - +
71C CYS 3.1 0.2 - - - -
72C THR* 3.4 9.0 - - - +
73C ASP* 2.8 53.1 + - - +
74C VAL 4.0 0.5 + - - -
173C TYR* 3.5 17.5 + - - +
184C ARG* 4.3 11.4 + - - +
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Residues in contact with THR 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A CYS* 4.3 7.6 - - - -
65C ASP* 2.7 26.6 + - - +
67C SER* 3.5 8.7 + - - -
68C PRO 3.2 0.2 - - - -
69C GLN* 1.3 79.2 - - - +
71C CYS* 1.3 60.0 + - - +
74C VAL* 3.8 20.3 + - - +
173C TYR* 3.5 10.8 + - + -
181C ALA* 4.8 4.3 - - + -
182C PRO* 3.6 51.2 - - + +
184C ARG* 3.5 16.3 - - - +
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Residues in contact with CYS 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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66A ASP* 3.6 21.2 - - - +
67A SER 3.5 22.9 - - - +
70A THR* 4.2 11.2 - - - -
71A CYS* 2.1 56.3 - - + -
181A ALA* 6.2 1.6 - - - -
68C PRO 3.2 8.6 + - - +
69C GLN 3.1 0.2 - - - -
70C THR* 1.3 81.8 - - - +
72C THR* 1.3 60.2 + - - +
74C VAL 4.8 4.6 + - - +
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Residues in contact with THR 72 (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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66A ASP* 3.3 31.7 - - - +
68A PRO* 3.6 28.5 - - + -
68C PRO* 3.2 11.9 + - + +
69C GLN* 3.4 14.9 - - - +
71C CYS* 1.3 78.0 - - - +
73C ASP* 1.3 82.9 + - - +
74C VAL 3.8 0.2 - - - -
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Residues in contact with ASP 73 (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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69C GLN* 2.8 36.0 + - + +
72C THR* 1.3 108.8 + - - +
74C VAL* 1.3 62.3 + - + +
75C TYR 4.1 0.9 + - - -
96C ASN* 4.4 1.9 - - - +
168C VAL* 3.5 26.0 - - + +
169C ASN* 3.9 27.1 - - - +
173C TYR* 4.6 2.7 + - - +
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Residues in contact with VAL 74 (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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69C GLN 4.2 3.6 - - - +
70C THR* 3.8 16.2 + - - +
71C CYS 4.8 3.7 + - - +
72C THR 3.8 0.6 - - - -
73C ASP* 1.3 86.8 - - + +
75C TYR* 1.3 74.8 + - - +
76C PHE* 3.7 3.6 + - - +
96C ASN* 3.6 14.8 - - - +
123C ARG* 4.5 5.7 + - - -
168C VAL* 4.2 8.5 - - + -
173C TYR* 3.5 46.2 - - + +
175C LEU* 4.2 11.2 - - + -
182C PRO* 3.7 21.1 - - + +
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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