Contacts of the helix formed by residues 61 - 73 (chain C) in PDB entry 5U0A
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 LEU 61 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59C ILE* 3.2 10.4 - - + +
60C PRO* 1.3 90.5 - - + +
62C PRO* 1.3 62.0 - - - +
63C PRO* 4.1 8.1 - - + -
64C GLY* 2.8 13.0 + - - +
65C ALA* 2.8 25.5 + - - +
153C TRP* 4.8 9.0 - - + -
183C TRP* 4.5 21.1 - - + +
184C HIS* 3.4 38.6 - - + +
187C ALA* 4.5 17.3 - - + -
390C TRP* 5.0 14.1 - - + +
20N MET* 6.4 2.9 - - + -
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Residues in contact with PRO 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ILE 5.2 0.2 - - - +
60C PRO 3.2 11.7 - - - +
61C LEU* 1.3 84.2 - - - +
63C PRO* 1.3 60.4 - - + +
65C ALA 3.8 0.7 - - - +
66C ALA* 2.8 28.4 + - - +
191C TYR* 5.1 0.4 - - - -
377C PHE* 3.4 40.1 - - + +
378C GLY 4.7 2.9 - - - +
379C PHE* 6.1 0.4 - - - -
390C TRP* 3.3 44.9 - - + +
391C PHE 4.1 9.0 - - - +
392C THR* 3.8 17.0 - - + -
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Residues in contact with PRO 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C LEU* 3.4 12.8 - - + -
62C PRO* 1.3 96.5 - - + +
64C GLY* 1.3 65.9 + - - +
66C ALA* 2.9 12.3 + - - +
67C VAL* 3.0 18.4 + - - +
153C TRP* 5.5 5.2 - - + +
187C ALA* 3.8 18.2 - - + -
191C TYR* 3.0 40.2 - - + -
379C PHE* 4.7 10.5 - - + -
390C TRP* 4.5 22.4 - - + -
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Residues in contact with GLY 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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59C ILE* 4.0 14.3 - - - +
61C LEU* 2.8 15.5 + - - +
63C PRO* 1.3 76.5 - - - +
65C ALA* 1.3 56.8 + - - +
68C LEU* 2.9 26.5 + - - +
183C TRP 4.2 16.2 - - - -
186C LEU* 3.0 20.4 - - - +
187C ALA* 4.0 3.4 - - - +
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Residues in contact with ALA 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 ILE* 3.7 20.9 - - + +
61C LEU 2.8 17.6 + - - +
62C PRO 4.0 0.2 - - - +
64C GLY* 1.3 73.9 - - - -
66C ALA* 1.3 58.2 + - - +
68C LEU* 3.7 8.1 - - + -
69C TRP* 2.9 43.5 + - + +
377C PHE* 3.4 35.0 - - + -
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Residues in contact with ALA 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C PRO 2.8 16.5 + - - +
63C PRO 2.9 3.6 + - - +
65C ALA* 1.3 78.9 - - - +
67C VAL* 1.3 60.7 + - + +
70C ARG* 3.2 29.0 + - - +
191C TYR* 3.1 29.6 - - + +
215C LEU* 5.1 1.8 - - + -
220C SER* 3.5 24.7 - - - +
222C HIS* 3.8 6.8 + - - -
377C PHE* 4.0 6.0 - - + -
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Residues in contact with VAL 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 PRO 3.0 12.9 + - - +
66C ALA* 1.3 76.1 - - - +
68C LEU* 1.3 64.6 + - - +
70C ARG* 3.0 11.9 + - + +
71C ILE* 2.9 31.2 + - + +
133C LEU* 5.9 1.1 - - + -
186C LEU* 3.3 42.4 - - + +
189C LEU* 5.5 1.1 - - + -
190C GLY* 3.6 23.3 - - - +
191C TYR* 4.7 3.6 - - + -
215C LEU* 4.7 10.1 - - + -
273C LEU* 4.5 13.5 - - + -
276C PHE* 4.9 9.9 - - + -
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Residues in contact with LEU 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C TRP* 3.5 31.2 - - + -
28C LEU* 4.5 11.2 - - + -
44C LEU* 5.7 0.2 - - + -
57C VAL* 5.2 5.4 - - + +
59C ILE* 3.8 17.3 - - + -
64C GLY 2.9 19.9 + - - +
65C ALA* 3.0 9.4 + - - +
67C VAL* 1.3 78.8 - - - +
69C TRP* 1.3 68.9 + - + +
71C ILE* 3.0 24.8 - - + +
72C LEU* 2.8 56.0 + - + +
186C LEU* 3.3 9.8 - - + +
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Residues in contact with TRP 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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56C ASP* 3.2 22.4 - - - -
57C VAL* 3.5 18.4 + - + -
65C ALA* 2.9 33.7 + - + +
68C LEU* 1.3 84.3 - - + +
70C ARG* 1.3 56.4 + - - +
72C LEU* 4.0 16.5 - - + +
73C ALA* 3.1 28.7 + - - +
222C HIS* 3.5 31.4 - + + +
224C LEU* 5.0 2.9 - - + -
228C LEU* 4.4 11.0 - - + -
231C SER* 4.8 3.1 - - - -
232C LEU* 3.7 26.2 - - + -
235C ASN* 3.4 24.6 + - - +
312C TYR* 4.5 2.6 + - - -
375C ARG* 3.0 32.9 - - - +
377C PHE* 3.5 21.6 - + - -
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Residues in contact with ARG 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 ALA 3.2 17.4 + - - +
67C VAL* 3.0 20.5 + - + +
68C LEU 3.0 0.2 - - - -
69C TRP* 1.3 77.4 - - - +
71C ILE* 1.3 61.3 + - - +
73C ALA* 3.5 3.7 + - - +
74C LEU 3.4 3.5 + - - -
215C LEU* 3.9 26.6 - - - +
220C SER* 3.2 33.5 - - - -
222C HIS* 4.1 4.4 + - - -
271C LEU* 2.9 66.8 + - + +
272C ARG* 4.6 3.2 - - - +
273C LEU* 3.9 8.1 - - + -
310C ASP* 2.5 40.2 + - - -
312C TYR* 3.6 24.8 - - + +
313C LEU* 4.5 4.8 - - - +
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Residues in contact with ILE 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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27C TRP* 5.7 0.7 - - + -
44C LEU* 4.2 15.0 - - + -
67C VAL* 2.9 24.3 + - + +
68C LEU* 3.0 38.6 - - + +
70C ARG* 1.3 72.9 - - - +
72C LEU* 1.3 84.3 + - + +
73C ALA 3.1 1.3 - - - -
74C LEU* 2.8 19.9 + - - +
75C ILE* 3.2 20.4 + - + +
132C TRP* 5.7 9.0 - - + +
133C LEU* 5.2 11.0 - - + -
186C LEU* 4.9 7.4 - - + -
249C TRP* 4.4 17.2 - - + -
273C LEU* 3.8 30.3 - - + -
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Residues in contact with LEU 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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28C LEU* 5.4 4.7 - - + -
44C LEU* 4.1 32.1 - - + -
47C VAL* 5.2 14.4 - - + -
48C LEU* 4.2 19.5 - - + -
57C VAL* 5.6 3.1 - - + -
68C LEU* 2.8 43.1 + - + +
69C TRP* 4.3 26.5 - - + +
71C ILE* 1.3 77.2 - - + +
73C ALA* 1.3 61.0 + - - +
74C LEU 3.3 0.5 + - - -
75C ILE* 3.3 8.3 + - + +
76C THR* 3.1 27.3 + - - +
228C LEU* 5.7 1.8 - - + -
232C LEU* 4.5 17.0 - - + -
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Residues in contact with ALA 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 TRP 3.1 21.6 + - - +
70C ARG 3.6 6.7 - - - +
71C ILE 3.1 0.4 - - - -
72C LEU* 1.3 76.9 - - - +
74C LEU* 1.3 56.4 + - - +
77C ALA* 2.3 37.7 - - + +
78C ARG 3.6 1.0 + - - -
232C LEU* 5.0 3.4 - - - +
235C ASN* 4.0 28.9 - - + +
236C ILE* 4.4 5.9 - - - +
237C PRO* 5.4 0.6 - - + +
267C LEU* 4.8 2.6 - - - +
271C LEU* 4.2 10.0 - - + +
312C TYR* 4.0 5.6 - - - +
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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