Contacts of the helix formed by residues 69 - 78 (chain C) in PDB entry 6I3N
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 ASP 69 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30C ARG* 5.0 1.4 - - - +
31C ARG* 5.9 2.8 - - - +
34C SER* 2.8 35.7 + - - -
38C ASN* 3.7 9.8 + - - +
68C ALA* 1.3 78.9 - - + +
70C PRO* 1.3 69.3 - - - +
71C THR 3.7 0.9 + - - -
72C GLY* 3.1 18.4 + - - -
73C ARG* 3.3 28.0 + - - +
63D GLN* 5.9 2.8 - - - +
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Residues in contact with PRO 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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38C ASN* 3.8 19.5 - - + +
47C TRP* 3.5 39.2 - - + +
64C LEU* 3.3 23.4 - - - +
65C GLU 4.6 6.1 - - - +
67C GLN 3.6 14.4 - - - +
68C ALA* 4.6 0.4 - - - -
69C ASP* 1.3 85.3 - - - +
71C THR* 1.3 59.9 + - - +
73C ARG* 3.8 5.2 - - + +
74C LEU* 2.9 29.0 + - - +
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Residues in contact with THR 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 4.1 17.3 - - + +
34C SER* 3.8 17.3 - - - +
37C LEU* 3.9 20.0 - - + -
38C ASN* 3.5 29.2 + - - +
47C TRP* 3.6 13.8 - - + +
50C LEU* 5.6 4.3 - - + -
69C ASP* 3.2 1.5 - - - -
70C PRO* 1.3 76.6 - - - +
72C GLY* 1.3 60.3 - - - +
74C LEU* 3.3 8.2 + - + +
75C LEU* 2.9 38.9 + - + +
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Residues in contact with GLY 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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30C ARG* 4.7 14.5 + - - -
34C SER* 3.9 4.0 + - - -
69C ASP* 3.1 26.6 + - - -
71C THR* 1.3 78.0 - - - +
73C ARG* 1.3 63.0 + - - +
75C LEU* 3.3 6.6 + - - +
76C ASP* 2.9 36.1 + - - +
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Residues in contact with ARG 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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30C ARG* 6.0 2.6 - - - +
64C LEU* 3.9 11.2 - - + +
67C GLN* 3.4 46.0 - - + +
68C ALA 4.0 5.9 + - - +
69C ASP* 3.3 38.1 + - - +
70C PRO* 4.1 3.1 - - + +
72C GLY* 1.3 78.7 + - - +
74C LEU* 1.3 60.5 + - - +
76C ASP* 2.5 35.4 + - - +
77C ALA* 2.9 28.9 + - - +
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Residues in contact with LEU 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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47C TRP* 3.6 38.8 - - + +
50C LEU* 4.5 8.7 - - + -
51C ALA* 3.7 16.2 - - + +
54C MET* 3.6 21.1 - - + -
56C PHE* 3.6 27.1 - - + -
64C LEU* 3.7 21.0 - - + +
70C PRO 2.9 19.5 + - - +
71C THR* 3.4 8.5 - - + +
73C ARG* 1.3 77.1 - - - +
75C LEU* 1.3 59.6 + - + +
77C ALA* 3.4 1.8 + - - +
78C TRP* 3.0 28.9 + - - +
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Residues in contact with LEU 75 (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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22C LEU* 3.7 22.6 - - + +
25C LEU* 5.4 2.7 - - + -
30C ARG* 3.4 42.2 - - + +
33C LEU* 4.0 24.2 - - + -
50C LEU* 5.5 5.6 - - + -
54C MET* 5.5 1.6 - - + -
71C THR* 2.9 30.8 + - + +
72C GLY 3.3 2.4 + - - +
74C LEU* 1.3 78.1 - - + +
76C ASP* 1.3 65.4 + - - +
78C TRP* 3.4 9.3 + - + +
79C GLN* 3.2 29.1 + - - +
89C LEU* 4.2 23.1 - - + -
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Residues in contact with ASP 76 (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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30C ARG* 3.9 16.3 + - - -
72C GLY 2.9 15.6 + - - +
73C ARG* 2.5 45.8 + - - +
74C LEU 3.3 0.2 - - - -
75C LEU* 1.3 76.8 - - - +
77C ALA* 1.3 62.1 + - - +
79C GLN* 3.3 27.5 + - + +
80C GLY 4.7 0.7 + - - -
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Residues in contact with ALA 77 (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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56C PHE* 4.0 22.1 - - + -
64C LEU* 5.0 10.1 - - + -
73C ARG 2.9 18.7 + - - +
74C LEU* 3.4 5.6 + - - +
76C ASP* 1.3 76.5 - - - +
78C TRP* 1.3 58.1 + - - +
79C GLN 3.3 1.7 + - - -
80C GLY 4.4 4.0 + - - +
81C ARG* 3.7 15.9 - - - +
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Residues in contact with TRP 78 (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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22C LEU* 3.7 34.3 - - + +
54C MET* 3.4 55.9 + - + +
56C PHE* 4.0 10.3 - + + -
74C LEU 3.0 17.2 + - - +
75C LEU* 3.4 11.4 + - + +
76C ASP 3.2 0.4 - - - -
77C ALA* 1.3 77.9 - - - +
79C GLN* 1.3 64.1 + - - +
80C GLY 3.6 0.4 - - - -
81C ARG* 3.6 27.7 - - + +
83C GLY* 4.4 2.1 - - - +
84C ALA* 3.2 33.4 - - + +
85C SER 3.8 11.4 - - - -
88C ARG* 3.7 31.4 - - + -
89C LEU* 3.9 20.0 - - + -
92C LEU* 4.2 3.8 - - + -
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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