Contacts of the helix formed by residues 67 - 77 (chain C) in PDB entry 5UHE
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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62C GLU* 3.0 41.2 + - - +
65C ILE* 3.5 24.0 - - - -
66C GLY* 1.3 80.5 - - - +
68C PRO* 1.3 75.7 - - - +
69C ARG* 3.8 4.5 + - - -
70C TRP* 2.9 19.6 + - - +
71C ARG* 3.4 5.2 + - - +
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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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66C GLY 4.4 1.6 - - - +
67C SER* 1.3 87.6 - - - +
69C ARG* 1.3 64.8 + - + +
71C ARG* 3.1 20.1 + - + +
72C GLU* 3.1 26.7 + - - +
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Residues in contact with ARG 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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58C THR* 5.0 6.3 - - - +
62C GLU* 3.0 41.4 + - - +
67C SER* 3.2 3.6 - - - -
68C PRO* 1.3 79.9 - - + +
70C TRP* 1.3 57.7 + - - +
72C GLU* 4.0 12.5 - - - +
73C SER* 3.2 25.0 + - - -
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Residues in contact with TRP 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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59C ASP 4.9 4.3 - - - -
62C GLU* 3.8 19.3 + - + +
63C TRP* 3.6 40.6 - + + -
66C GLY* 3.6 24.2 - - - -
67C SER* 2.9 12.8 + - - +
69C ARG* 1.3 79.0 - - - +
71C ARG* 1.3 89.9 + - + +
72C GLU 3.2 0.4 - - - -
73C SER* 3.1 9.3 + - - -
74C ALA* 2.6 37.7 + - + +
79C ASP* 5.7 1.6 + - - -
82C PRO* 3.5 28.7 - - + -
83C VAL 3.3 35.4 - - - -
84C GLY* 3.3 7.6 - - - -
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Residues in contact with ARG 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C GLY* 3.2 25.1 + - - -
67C SER 3.4 3.1 + - - +
68C PRO* 3.1 13.0 + - + +
70C TRP* 1.3 97.1 - - + +
72C GLU* 1.3 57.8 + - + +
74C ALA* 3.3 7.7 + - - +
75C ALA* 2.8 26.2 + - - +
82C PRO* 3.8 38.0 + - + +
87C GLU* 3.6 24.4 + - - -
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Residues in contact with GLU 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 PRO* 3.1 24.5 + - - +
69C ARG* 4.0 9.6 - - - +
71C ARG* 1.3 76.0 - - + +
73C SER* 1.3 55.7 + - - +
74C ALA 3.2 0.2 - - - -
75C ALA* 3.1 8.3 + - - +
76C GLU* 2.8 46.4 + - + +
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Residues in contact with SER 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ASP* 5.3 4.0 + - - -
69C ARG 3.2 18.3 + - - -
70C TRP* 3.1 13.1 + - - -
72C GLU* 1.3 77.8 - - - +
74C ALA* 1.3 58.9 + - - +
76C GLU* 4.5 7.0 - - - +
77C ARG* 3.1 54.4 + - - +
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Residues in contact with ALA 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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70C TRP* 2.6 27.3 + - + +
71C ARG* 3.4 9.0 - - - +
72C GLU 3.2 0.2 - - - -
73C SER* 1.3 74.9 - - - +
75C ALA* 1.3 57.2 + - - +
77C ARG* 5.6 0.2 - - - +
78C GLY 3.2 1.2 + - - -
79C ASP* 2.5 53.0 + - + +
82C PRO* 3.6 33.0 - - + -
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Residues in contact with ALA 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 ARG 2.8 14.9 + - - +
72C GLU* 3.1 12.3 + - - +
74C ALA* 1.3 74.8 - - - +
76C GLU* 1.3 61.7 + - + +
78C GLY* 2.9 20.4 + - - -
79C ASP 4.8 2.2 - - - +
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Residues in contact with GLU 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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72C GLU* 2.8 28.9 + - + +
73C SER* 4.3 5.9 - - - +
75C ALA* 1.3 74.0 - - + +
77C ARG* 1.3 62.5 + - + +
78C GLY* 3.1 0.9 + - - -
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Residues in contact with ARG 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ASP* 4.0 20.8 + - - +
73C SER* 3.1 33.5 + - - +
74C ALA* 5.6 0.2 - - - +
76C GLU* 1.3 76.2 - - + +
78C GLY* 1.3 60.7 + - - +
79C ASP* 3.2 22.9 - - - +
505C ARG* 4.1 45.7 - - - +
506C VAL 4.0 13.7 + - - -
507C ASN* 4.8 0.6 - - - +
508C PRO* 3.7 30.3 - - - +
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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