Contacts of the helix formed by residues 67 - 80 (chain C) in PDB entry 7PRC
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 67 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48C GLU 5.5 3.8 - - - +
50C PRO* 4.0 9.7 + - + +
52C VAL* 3.1 15.8 - - - +
55C VAL* 3.9 26.1 - - + +
56C TYR* 3.1 35.0 + - + +
66C THR* 1.3 71.0 - - - +
68C ALA* 1.3 58.0 + - - +
70C PHE* 3.0 3.1 + - - +
71C LEU* 2.8 42.1 + - + +
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Residues in contact with ALA 68 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C VAL* 3.6 25.1 - - + +
46C LYS 3.9 7.0 - - - +
48C GLU* 3.7 23.3 + - - +
66C THR* 3.2 4.6 + - - +
67C GLU* 1.3 77.9 - - - +
69C GLU* 1.3 62.0 + - - +
71C LEU* 3.5 6.1 + - - +
72C ARG* 3.1 22.5 + - - +
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Residues in contact with GLU 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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45C VAL* 3.7 22.0 - - + +
47C ALA* 3.9 19.2 + - - +
64C ASN 4.7 0.7 - - - +
65C LEU* 3.6 24.7 - - + +
66C THR* 2.9 45.4 + - - +
68C ALA* 1.3 71.4 - - - +
70C PHE* 1.3 61.2 + - - +
72C ARG* 2.9 10.5 + - - +
73C THR* 2.8 32.5 + - - -
327C GLU* 5.9 1.8 - - + -
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Residues in contact with PHE 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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52C VAL* 3.7 25.6 - - + -
56C TYR* 3.8 13.7 - + - -
59C VAL* 3.6 33.2 - - + -
62C LEU* 3.8 30.1 - - + -
65C LEU* 3.9 9.3 - - + +
66C THR 3.0 12.9 + - - +
67C GLU* 3.0 8.5 + - - +
69C GLU* 1.3 76.4 - - - +
71C LEU* 1.3 64.8 + - + +
73C THR* 3.2 4.8 + - - -
74C MET* 2.9 33.1 + - + +
337C HEM 3.2 57.2 - + + -
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Residues in contact with LEU 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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56C TYR* 3.6 24.9 - - - +
67C GLU* 2.8 29.7 + - + +
68C ALA* 4.2 5.2 - - - +
70C PHE* 1.3 77.5 - - + +
72C ARG* 1.3 59.7 + - - +
74C MET* 3.2 3.4 + - + +
75C THR* 2.8 35.9 + - - +
337C HEM 3.8 39.4 - - + +
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Residues in contact with ARG 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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41C ALA* 4.7 1.0 - - - +
42C LEU* 3.0 42.2 + - + +
43C ALA 2.9 27.0 + - - -
44C ALA* 4.4 11.5 - - - +
45C VAL* 4.1 21.0 - - + +
68C ALA 3.1 13.5 + - - +
69C GLU* 2.9 13.5 + - - +
71C LEU* 1.3 75.2 - - - +
73C THR* 1.3 63.5 + - - +
75C THR* 3.4 3.8 + - - -
76C ALA* 3.0 20.6 + - - +
324C ASP* 3.0 37.4 + - - +
325C TYR* 3.4 24.7 - - + -
326C PRO* 5.6 0.2 - - - +
327C GLU* 4.4 9.1 + - - -
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Residues in contact with THR 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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62C LEU* 4.1 25.8 - - + -
65C LEU* 3.6 4.7 - - - +
69C GLU 2.8 14.7 + - - -
70C PHE* 3.2 9.8 + - - -
72C ARG* 1.3 75.4 + - - +
74C MET* 1.3 60.0 + - + +
76C ALA* 3.0 8.1 + - + +
77C ILE* 2.8 43.0 + - + +
80C TRP* 6.2 1.6 - - + -
325C TYR* 5.1 1.3 - - + -
327C GLU* 2.7 41.0 + - + +
328C LEU* 5.0 8.3 - - + -
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Residues in contact with MET 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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62C LEU* 4.4 9.4 - - + -
70C PHE* 2.9 30.4 + - + +
71C LEU* 3.2 10.1 + - - +
73C THR* 1.3 76.3 - - - +
75C THR* 1.3 51.4 + - - +
77C ILE* 3.6 21.8 - - + +
78C THR* 2.5 37.7 + - - -
111C LEU* 5.1 0.7 - - + -
337C HEM 2.2 112.9 - - + +
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Residues in contact with THR 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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42C LEU* 3.7 26.5 - - + -
71C LEU* 2.8 20.9 + - - +
72C ARG* 4.4 1.2 - - - -
74C MET* 1.3 75.6 - - - +
76C ALA* 1.3 58.9 + - - +
78C THR* 3.1 8.8 + - - -
79C GLU* 2.9 30.5 + - + +
337C HEM 4.0 15.4 - - + +
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Residues in contact with ALA 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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42C LEU* 3.6 6.5 - - + +
72C ARG 3.0 13.8 + - - +
73C THR* 3.0 10.2 + - + +
75C THR* 1.3 74.0 - - - +
77C ILE* 1.3 65.3 + - - +
79C GLU* 2.9 12.8 + - - +
80C TRP* 2.9 42.7 + - + -
325C TYR* 3.6 33.4 - - + +
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Residues in contact with ILE 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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73C THR* 2.8 26.9 + - + +
74C MET* 3.6 28.0 - - + +
76C ALA* 1.3 75.5 - - - +
78C THR* 1.3 61.4 + - - +
80C TRP* 3.0 12.6 + - + -
81C VAL* 2.9 27.4 + - + +
107C ALA* 5.9 0.7 - - + -
111C LEU* 3.9 28.7 - - + -
132C CYS* 4.5 7.6 - - - -
328C LEU* 6.1 0.7 - - + -
337C HEM 4.0 33.9 - - + -
338C HEM 3.8 27.1 - - + -
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Residues in contact with THR 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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74C MET 2.5 22.5 + - - -
75C THR* 3.1 8.9 + - - -
77C ILE* 1.3 75.2 - - - +
79C GLU* 1.3 59.6 + - - +
82C SER* 3.0 24.0 + - - +
83C PRO* 2.9 31.7 - - + +
86C GLY* 3.7 27.8 - - - -
87C CYS 3.8 2.5 - - - +
337C HEM 3.0 35.9 - - + +
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Residues in contact with GLU 79 (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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39C PRO* 3.6 38.2 - - + +
40C PRO* 4.1 10.3 - - - +
42C LEU* 4.4 20.5 - - - +
75C THR* 2.9 13.8 + - + +
76C ALA* 3.2 18.0 - - - +
78C THR* 1.3 79.9 - - - +
80C TRP* 1.3 63.6 + - + +
83C PRO* 3.8 21.3 - - + +
133C TYR* 5.1 1.0 - - - -
138C GLY* 4.6 2.4 - - - -
325C TYR* 4.5 2.1 + - - -
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Residues in contact with TRP 80 (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 TYR* 4.0 7.9 - - - -
39C PRO* 4.2 14.9 + - + +
40C PRO 5.8 0.2 + - - -
73C THR* 6.2 2.0 - - + -
76C ALA* 2.9 33.5 + - + +
77C ILE* 3.7 7.9 - - + +
79C GLU* 1.3 90.7 + - - +
81C VAL* 1.3 59.9 + - - +
131C THR* 3.8 24.2 - - + -
132C CYS* 3.5 29.6 - - + -
133C TYR* 3.5 42.6 - + + +
136C HIS* 3.9 4.7 - - - +
138C GLY* 2.7 31.5 + - - -
321C ARG* 4.9 4.9 - - + -
325C TYR* 3.6 44.6 + + + -
328C LEU* 3.9 19.7 - - + -
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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