Contacts of the strand formed by residues 64 - 71 (chain C) in PDB entry 3EBL
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 64 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56C ASN 3.7 5.8 - - - -
57C ALA 2.6 28.6 + - - -
59C PRO* 3.2 22.6 - - - +
62C GLY 4.4 0.2 - - - -
63C VAL* 1.3 75.3 - - - +
65C SER* 1.3 61.6 + - - +
66C PHE* 4.3 17.4 - - - -
80C ILE 3.9 0.2 - - - +
81C TYR* 3.3 4.2 - - - -
82C ARG* 3.0 35.0 + - - -
83C ALA 4.8 5.2 + - - -
139C ARG* 4.7 0.7 - - - +
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Residues in contact with SER 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C PRO 4.4 0.5 + - - -
55C ALA* 3.3 6.3 - - - +
56C ASN* 2.8 50.5 + - - -
57C ALA 3.7 0.3 + - - -
64C SER* 1.3 75.0 - - - +
66C PHE* 1.3 73.0 + - - +
79C ARG* 4.1 10.6 - - - -
80C ILE 3.1 9.6 - - - -
81C TYR* 3.8 24.9 - - - -
135C ASP* 4.8 0.3 + - - -
139C ARG* 3.3 14.1 + - - -
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Residues in contact with PHE 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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55C ALA* 4.0 2.9 - - - -
57C ALA* 3.8 27.4 - - + -
64C SER* 4.3 20.9 - - - -
65C SER* 1.3 86.6 - - - +
67C ASP* 1.3 67.9 + - - +
68C HIS* 5.7 0.9 - - + -
78C VAL 3.8 0.7 - - - +
79C ARG* 3.4 1.6 - - - -
80C ILE* 2.9 58.5 + - + +
82C ARG* 5.0 13.0 - - + -
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Residues in contact with ASP 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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55C ALA* 3.6 14.0 + - + +
66C PHE* 1.3 73.5 - - - +
68C HIS* 1.3 64.5 + - - +
77C GLU* 3.7 23.3 - - - +
78C VAL 3.6 2.9 - - - +
79C ARG* 2.8 55.1 + - - +
153C ASN* 5.6 1.2 + - - -
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Residues in contact with HIS 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 PHE* 4.7 1.6 - - + +
67C ASP* 1.3 78.3 + - - +
69C ILE* 1.3 83.2 + - - +
70C ILE* 3.6 9.3 + - + -
77C GLU* 3.5 6.2 - - - +
78C VAL* 3.0 34.8 + - + +
80C ILE* 4.1 18.8 - - + -
175C TRP* 3.6 39.2 + + - -
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Residues in contact with ILE 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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68C HIS* 1.3 92.6 + - - +
70C ILE* 1.3 59.6 + - - +
71C ASP 3.7 23.8 - - - +
72C GLN* 3.8 18.6 - - + +
75C GLY* 4.4 13.7 - - - +
76C LEU 3.4 14.6 - - - +
77C GLU* 3.3 31.9 - - + +
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Residues in contact with ILE 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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68C HIS* 3.6 13.7 + - + -
69C ILE* 1.3 73.4 - - - +
71C ASP* 1.3 59.9 + - - +
72C GLN 4.3 0.4 - - - -
76C LEU* 2.8 38.8 + - + +
78C VAL* 3.7 33.4 - - + -
171C THR* 4.2 10.8 - - + +
172C ALA* 3.6 31.6 - - + +
175C TRP* 3.6 49.3 - - + +
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Residues in contact with ASP 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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69C ILE* 3.5 3.5 - - - +
70C ILE* 1.3 81.5 - - - +
72C GLN* 1.3 57.7 + - - +
73C SER* 3.2 26.1 + - - -
74C VAL* 3.6 18.4 - - - +
75C GLY* 2.9 9.5 + - - -
76C LEU* 2.9 43.6 + - + +
171C THR* 4.2 22.6 + - + +
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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