Contacts of the helix formed by residues 91 - 98 (chain C) in PDB entry 3Q29
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 TYR 91 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90C LEU* 1.3 72.6 - - - +
92C PRO* 1.3 65.6 - - + +
93C PHE* 4.4 6.5 - - + +
94C THR* 2.6 46.7 + - + -
95C TRP* 3.4 4.4 + - - -
303C VAL 3.7 16.2 - - - -
304C ALA* 3.1 33.2 + - - -
305C LEU 4.0 1.4 + - - -
306C LYS* 3.3 49.4 + - + +
309C GLU* 3.8 23.5 + - - +
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Residues in contact with PRO 92 (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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90C LEU 3.4 4.5 - - - +
91C TYR* 1.3 88.3 - - + +
93C PHE* 1.3 62.6 + - - +
94C THR 3.1 0.2 + - - -
95C TRP* 3.2 14.4 + - + +
96C ASP* 3.0 33.4 + - - +
306C LYS* 4.6 10.8 - - - +
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Residues in contact with PHE 93 (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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91C TYR* 3.1 5.7 + - + +
92C PRO* 1.3 80.9 - - - +
94C THR* 1.3 75.6 + - + +
96C ASP* 3.4 14.9 + - + +
97C ALA* 3.2 17.8 + - + +
111C VAL* 3.9 25.8 - - + -
260C VAL* 4.8 2.2 - - + -
262C VAL* 4.0 14.6 - - + -
330C ILE* 3.4 50.7 - - + -
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Residues in contact with THR 94 (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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90C LEU* 3.8 2.6 - - - +
91C TYR* 2.6 44.3 + - + +
93C PHE* 1.3 86.4 - - + +
95C TRP* 1.3 64.5 + - - +
97C ALA* 3.2 18.8 + - - +
98C VAL* 3.5 2.9 - - - +
108C PRO* 3.5 32.5 - - - +
111C VAL* 4.1 16.4 - - + +
262C VAL* 4.6 4.7 - - + -
303C VAL 5.5 0.2 - - - +
304C ALA* 3.6 30.3 - - + +
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Residues in contact with TRP 95 (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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80C ILE* 3.9 22.2 - - + -
82C PRO* 4.0 9.6 - - + -
86C PHE* 3.8 20.9 - + - -
87C GLN* 2.8 56.9 + - + +
90C LEU* 3.2 35.7 - - + +
91C TYR 3.9 12.1 - - - -
92C PRO* 3.2 12.0 + - + +
94C THR* 1.3 77.3 + - - +
96C ASP* 1.3 65.7 + - - +
98C VAL* 2.9 26.9 + - + +
99C ARG* 3.4 24.8 + - - +
104C LEU* 4.0 19.9 - - + +
107C TYR* 4.0 3.6 - + - -
108C PRO* 3.5 21.8 - - + -
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Residues in contact with ASP 96 (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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92C PRO* 3.0 25.9 + - - +
93C PHE* 3.4 20.0 - - + +
94C THR 3.3 0.2 - - - -
95C TRP* 1.3 74.1 - - - +
97C ALA* 1.3 62.0 + - - +
99C ARG* 3.2 47.2 + - - +
333C ASN* 5.2 0.5 + - - -
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Residues in contact with ALA 97 (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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65C HIS* 3.5 33.0 - - + +
93C PHE* 3.2 13.4 + - + +
94C THR 3.2 12.0 + - - +
95C TRP 3.1 0.8 - - - -
96C ASP* 1.3 78.9 - - - +
98C VAL* 1.3 59.0 + - + +
99C ARG 3.4 2.0 + - - -
105C ILE* 5.3 0.3 - - - +
262C VAL* 3.6 34.5 - - + -
330C ILE* 5.5 2.7 - - + -
333C ASN* 3.6 12.7 + - - +
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Residues in contact with VAL 98 (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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65C HIS* 4.6 3.6 - - + -
94C THR 3.5 9.0 - - - +
95C TRP* 2.9 32.1 + - + +
97C ALA* 1.3 81.3 - - + +
99C ARG* 1.3 55.2 + - - -
104C LEU* 3.4 4.7 - - + -
105C ILE* 2.8 40.0 + - + +
106C ALA* 3.2 33.4 - - + +
108C PRO* 4.0 11.7 - - + -
264C SER* 3.3 35.4 - - - +
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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