Contacts of the strand formed by residues 79 - 83 (chain C) in PDB entry 3QI6
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 PHE 79 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72C ALA* 3.9 6.1 - - - -
77C ALA* 3.2 2.1 - - - +
78C ALA* 1.3 106.0 - - + +
80C GLY* 1.3 57.4 + - - +
222C VAL* 3.3 7.3 - - - +
223C THR* 3.0 42.2 + - + +
224C ASN 3.6 15.3 - - - -
225C ASP 4.1 2.7 - - - -
226C GLU* 3.5 50.7 - - + -
229C ASP* 3.5 33.4 - - + +
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Residues in contact with GLY 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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68C GLU* 3.4 40.7 + - - +
71C LEU* 5.4 0.9 - - - -
72C ALA* 3.9 5.2 - - - +
79C PHE* 1.3 74.8 - - - +
81C ARG* 1.4 71.9 + - - +
221C LEU 3.3 8.7 - - - -
222C VAL* 4.1 8.5 - - - -
229C ASP* 4.3 0.4 - - - +
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Residues in contact with ARG 81 (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 THR 5.0 6.5 + - - -
64C ARG* 5.1 0.8 - - - +
68C GLU* 3.4 13.5 + - - +
71C LEU* 5.0 2.1 - - - +
80C GLY* 1.4 75.7 + - - -
82C ALA* 1.3 60.7 + - - +
83C PHE* 3.5 22.3 - - + -
220C ALA* 3.1 7.2 - - - +
221C LEU* 2.7 36.9 + - + +
222C VAL* 5.1 0.2 - - - +
229C ASP* 3.0 42.1 + - - +
230C GLN* 4.3 7.1 + - - -
232C PHE* 4.1 15.9 - - + -
233C ALA* 3.4 30.1 - - - +
236C GLN* 2.9 31.5 + - - +
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Residues in contact with ALA 82 (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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64C ARG* 3.9 2.9 - - + -
67C LEU* 3.6 31.4 - - + -
68C GLU* 2.9 21.9 + - + +
71C LEU* 4.1 6.7 - - + -
81C ARG* 1.3 72.6 - - - +
83C PHE* 1.3 65.0 + - - +
219C GLY 3.4 9.4 - - - +
220C ALA* 4.5 0.2 - - - +
236C GLN* 3.1 19.1 + - - +
241C ALA 4.5 0.5 - - - +
242C VAL* 4.6 0.2 - - - +
243C PRO* 3.5 20.5 - - + +
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Residues in contact with PHE 83 (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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81C ARG* 3.5 39.3 - - + -
82C ALA* 1.3 77.1 - - - +
84C SER* 1.3 61.3 + - - +
85C SER 3.2 15.0 - - - +
88C ALA* 4.0 10.8 - - + -
89C ALA* 3.7 19.1 - - + +
92C CYS* 3.5 37.2 - - + -
218C GLY* 3.5 3.6 - - - -
219C GLY 3.0 27.0 + - - +
221C LEU* 3.8 18.6 - - + -
232C PHE* 4.6 1.1 - - + -
235C LEU 5.4 0.2 - - - -
236C GLN* 3.9 25.6 - - + -
241C ALA* 3.1 23.6 - - + +
243C PRO* 3.9 13.8 - - - +
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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