Contacts of the helix formed by residues 62 - 79 (chain C) in PDB entry 4R0C
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 62 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58C HIS* 3.1 22.0 + - - -
59C SER* 3.2 17.5 + - - +
60C LEU 3.5 1.8 - - - -
61C LEU* 1.3 83.5 - - - +
63C ALA* 1.3 74.8 + - - +
64C ASP* 3.0 14.9 + - - +
65C GLY 3.1 19.4 + - - -
66C LEU* 3.0 20.0 + - - +
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Residues in contact with ALA 63 (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 ASP* 1.3 82.6 + - - +
64C ASP* 1.3 62.2 + - - +
66C LEU* 4.7 3.4 - - - -
67C ARG* 3.7 15.3 + - - +
275D ASP 5.5 4.5 - - - +
277D PRO* 3.5 35.8 - - + +
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Residues in contact with ASP 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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58C HIS* 4.6 6.7 - - + -
62C ASP* 3.0 14.6 + - - +
63C ALA* 1.3 80.7 - - - +
65C GLY* 1.3 61.7 + - - +
67C ARG* 2.9 28.5 + - - +
68C TYR* 3.2 16.8 + - - +
353C TYR* 3.4 14.5 + - - +
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Residues in contact with GLY 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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59C SER 3.6 12.3 - - - -
60C LEU* 2.9 21.1 - - - +
62C ASP* 3.1 11.1 + - - -
64C ASP* 1.3 75.1 - - - +
66C LEU* 1.3 54.4 + - - +
68C TYR* 3.2 3.6 + - - +
69C LEU* 2.7 35.7 + - - +
353C TYR* 3.6 15.0 + - - -
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Residues in contact with LEU 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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60C LEU 2.9 7.4 + - - +
61C LEU* 3.5 45.1 - - + +
62C ASP 3.0 15.0 + - - +
63C ALA* 4.7 1.6 - - - -
65C GLY* 1.3 70.6 - - - +
67C ARG* 1.3 61.7 + - - +
69C LEU* 3.3 11.8 + - + -
70C PHE* 2.8 46.0 + - + -
270D LEU* 3.8 29.4 - - + -
277D PRO* 4.2 20.2 - - + -
278D LEU* 4.8 1.1 - - - -
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Residues in contact with ARG 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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63C ALA* 3.7 10.7 + - - +
64C ASP* 2.9 35.0 + - - +
65C GLY 3.2 0.8 - - - -
66C LEU* 1.3 78.3 - - - +
68C TYR* 1.3 54.0 + - - +
70C PHE* 3.7 0.7 - - - +
71C THR* 2.8 55.5 + - + +
275D ASP 4.9 3.2 + - - -
276D ALA 3.8 6.7 + - - -
277D PRO* 2.9 48.6 + - - +
278D LEU* 4.7 4.5 - - - -
279D ARG 4.1 9.5 + - - -
281D PRO* 4.1 36.7 - - - +
290D PRO* 4.5 5.4 - - + +
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Residues in contact with TYR 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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60C LEU* 4.1 2.2 - - + -
64C ASP 3.2 10.5 + - - +
65C GLY 3.2 9.5 + - - +
67C ARG* 1.3 79.3 - - - +
69C LEU* 1.3 70.0 + - + +
71C THR* 3.2 6.5 + - - -
72C THR* 2.9 65.7 + - + -
76C ASN* 3.7 5.1 + - - -
349C ALA* 3.4 36.0 + - - +
350C TRP* 3.8 18.7 - + - -
353C TYR* 3.4 58.5 - + + +
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Residues in contact with LEU 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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33C LEU* 3.6 24.5 - - + -
60C LEU* 3.8 39.9 - - + +
61C LEU* 5.0 2.2 - - + -
65C GLY 2.7 22.8 + - - +
66C LEU* 3.4 19.1 - - + +
68C TYR* 1.3 79.7 - - + +
70C PHE* 1.3 67.5 + - + +
72C THR* 4.3 2.3 + - - -
73C LEU* 3.7 28.5 + - + +
350C TRP* 4.0 34.9 + - + +
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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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66C LEU* 2.8 40.8 + - + +
67C ARG 4.1 1.8 - - - +
69C LEU* 1.3 81.9 - - + +
71C THR* 1.3 61.6 + - - +
73C LEU* 4.7 5.4 + - - +
267D LEU* 5.7 1.8 - - + -
270D LEU* 3.7 28.3 - - + -
278D LEU* 3.6 35.7 - - + -
290D PRO* 5.1 14.4 - - + +
294D GLY* 5.6 6.4 - - - -
298D ILE* 4.1 25.8 - - + -
301D LEU* 5.3 15.3 - - + -
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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
----------------------------------------------------------
67C ARG* 2.8 37.3 + - + +
68C TYR* 3.3 11.6 + - - -
70C PHE* 1.3 77.9 - - - +
72C THR* 1.3 66.1 + - - +
73C LEU 3.6 0.8 + - - -
74C VAL 5.3 0.5 + - - -
75C GLY 5.6 0.5 + - - -
290D PRO* 4.0 31.2 - - + -
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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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68C TYR* 2.9 52.8 + - + +
69C LEU* 4.3 2.3 + - - -
71C THR* 1.3 86.2 - - - +
73C LEU* 1.3 67.4 + - - +
74C VAL 3.2 2.8 + - - -
75C GLY* 3.3 4.7 + - - +
76C ASN* 3.0 40.5 + - - -
350C TRP* 5.2 0.9 + - - -
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Residues in contact with LEU 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 LEU* 3.7 16.1 + - + +
70C PHE* 4.7 4.9 + - - +
71C THR 3.6 2.4 - - - -
72C THR* 1.3 78.9 + - - +
74C VAL* 1.3 66.2 + - + +
76C ASN* 3.6 2.6 + - - +
77C PHE* 3.7 1.0 + - - +
342C PHE* 4.2 11.9 - - + -
346C GLN* 2.7 53.3 + - + +
350C TRP* 4.1 21.1 - - + +
88D VAL* 4.1 23.6 - - + -
297D VAL* 4.2 15.9 - - + -
301D LEU* 6.3 4.5 - - + -
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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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71C THR 5.3 0.4 + - - -
72C THR 3.3 0.6 - - - -
73C LEU* 1.3 75.7 - - + +
75C GLY* 1.3 66.8 + - - +
77C PHE* 3.0 6.8 + - - +
78C THR* 3.0 24.4 + - + +
84D GLY* 3.5 32.1 - - - +
85D VAL* 3.6 27.1 - - + +
88D VAL* 4.0 21.8 - - + -
297D VAL* 4.5 8.7 - - + -
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Residues in contact with GLY 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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71C THR 5.6 0.4 + - - -
72C THR* 3.3 7.3 + - - +
74C VAL* 1.3 78.6 - - - +
76C ASN* 1.3 57.3 + - - +
78C THR* 3.8 8.7 - - - -
79C GLY* 2.9 29.1 + - - -
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Residues in contact with ASN 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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68C TYR* 3.7 7.0 + - - -
72C THR* 3.0 39.8 + - - +
73C LEU* 3.7 1.3 - - - +
75C GLY* 1.3 76.2 - - - +
77C PHE* 1.3 60.1 + - - +
79C GLY 4.3 0.3 - - - -
80C PHE* 3.3 15.8 + - - +
345C ALA* 3.3 23.3 - - - +
346C GLN* 3.0 30.9 + - - +
349C ALA* 3.4 26.2 - - + +
350C TRP* 4.2 4.8 - - - +
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Residues in contact with PHE 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 LEU 3.7 5.8 + - - +
74C VAL* 3.0 8.9 + - - +
76C ASN* 1.3 78.6 - - - +
78C THR* 1.3 76.9 + - + +
80C PHE* 3.1 18.9 + - + +
83C LEU* 3.6 24.7 - - + +
338C LEU* 3.7 30.7 - - + -
341C MET* 4.2 3.8 - - + -
342C PHE* 3.4 55.4 - + + -
345C ALA* 4.0 6.3 - - + -
346C GLN* 4.1 1.3 - - - +
84D GLY 4.7 0.4 - - - -
87D LEU* 4.0 30.5 - - + -
88D VAL* 3.9 19.1 - - + -
91D LEU* 5.6 3.4 - - + -
331D MET* 5.7 2.9 - - - -
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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 VAL* 3.0 15.7 + - - +
75C GLY* 3.8 8.3 - - - -
77C PHE* 1.3 94.9 - - + +
79C GLY* 1.3 57.6 + - - +
80C PHE 3.4 3.4 + - - +
83C LEU* 4.4 9.3 - - + +
84C GLY 5.3 1.2 + - - -
78D THR* 3.3 49.2 + - - +
79D GLY* 5.5 0.2 - - - -
83D LEU* 5.3 6.5 - - + -
84D GLY* 3.4 33.7 - - - +
87D LEU* 6.0 0.7 - - + -
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Residues in contact with GLY 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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75C GLY 2.9 18.1 + - - -
76C ASN 4.3 1.1 - - - -
78C THR* 1.3 77.5 + - - +
80C PHE* 1.3 63.6 + - - +
81C ALA* 3.3 4.7 + - - -
189C GLU* 3.8 5.9 - - - +
78D THR* 5.4 0.7 - - - -
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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
------------------------------------------------------------
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