Contacts of the helix formed by residues 90 - 100 (chain C) in PDB entry 1Y9D
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 90 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59C GLU* 3.4 26.5 - - + +
60C GLU* 4.5 0.2 - - - +
63C ALA* 3.1 22.3 - - + +
79C CYS* 4.1 10.1 - - + -
80C PHE 3.9 19.3 - - - +
81C GLY 4.2 9.0 - - - +
86C GLY 3.9 5.8 - - - +
87C GLY* 2.9 16.7 + - - +
89C HIS* 1.3 75.8 - - - +
91C MET* 1.3 63.8 + - - +
92C ASN 3.5 0.2 - - - -
93C GLY 3.0 14.8 + - - -
94C LEU* 3.0 23.2 + - + -
106C ALA* 4.0 18.8 - - + -
108C ILE* 3.7 31.0 - - + -
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Residues in contact with MET 91 (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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88A THR* 4.5 12.8 - - - +
91A MET* 4.5 18.8 - - + -
87C GLY 4.1 6.7 - - - +
88C THR* 3.1 18.4 - - - +
89C HIS 3.2 1.8 - - - -
90C LEU* 1.3 76.7 - - - +
92C ASN* 1.3 63.3 + - - +
94C LEU* 3.1 6.0 + - + -
95C TYR* 2.8 59.6 + - + -
129C ILE* 3.7 26.0 - - + +
130C TYR* 3.0 44.9 - - + -
133C VAL* 4.5 10.1 - - - -
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Residues in contact with ASN 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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85A PRO* 3.0 29.7 + - - +
88A THR* 2.7 26.4 + - - +
89A HIS* 3.2 28.5 + - + -
60C GLU* 3.8 17.9 - - + +
64C MET* 4.0 2.7 - - + -
89C HIS 4.6 2.0 + - - -
90C LEU 3.3 1.0 + - - -
91C MET* 1.3 74.8 - - - +
93C GLY* 1.3 59.8 + - - +
96C ASP* 3.2 23.6 + - - +
419C PHE* 3.8 11.3 - - - -
421C THR* 2.9 31.5 + - - +
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Residues in contact with GLY 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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60C GLU* 4.6 2.2 + - - +
63C ALA* 3.6 25.1 - - - +
64C MET* 3.6 25.2 - - - +
67C ALA* 3.9 1.7 - - - +
90C LEU 3.0 7.9 + - - -
92C ASN* 1.3 76.8 - - - +
94C LEU* 1.3 59.0 + - - +
96C ASP* 3.5 4.5 + - - +
97C ALA* 3.1 25.3 + - - +
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Residues in contact with LEU 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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63C ALA* 4.2 4.5 - - + -
79C CYS* 4.1 16.8 - - - -
90C LEU* 3.0 27.7 + - + +
91C MET* 3.6 9.4 - - + +
93C GLY* 1.3 76.5 - - - +
95C TYR* 1.3 60.4 + - - +
97C ALA* 3.3 1.7 + - - -
98C ARG 2.9 23.2 + - - -
104C VAL* 4.0 26.5 - - + -
106C ALA* 4.2 12.1 - - + -
130C TYR* 4.3 17.0 - - + -
133C VAL* 3.5 30.8 - - + +
163C VAL* 3.3 28.1 - - + +
165C VAL* 4.4 0.9 - - + -
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Residues in contact with TYR 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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88A THR* 4.1 17.9 - - + -
91A MET* 6.4 0.2 - - + -
124A MET* 4.7 2.2 - - - -
129A ILE* 3.5 26.2 - - + +
91C MET* 2.8 45.7 + - + +
94C LEU* 1.3 74.0 - - - +
96C ASP* 1.3 53.5 + - - +
98C ARG* 3.2 29.5 + - - +
99C GLU* 2.8 40.5 + - - +
129C ILE 5.5 2.4 + - - -
132C ASP* 2.7 38.8 + - - +
133C VAL* 3.6 25.8 + - + -
419C PHE* 3.4 36.6 - + + -
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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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64C MET* 5.0 2.2 - - + +
67C ALA* 3.6 13.0 - - - +
71C LYS* 2.6 25.9 + - - -
92C ASN 3.2 20.0 + - - +
93C GLY* 3.6 6.7 - - - +
94C LEU 3.2 0.2 - - - -
95C TYR* 1.3 77.8 - - - +
97C ALA* 1.3 56.8 + - - +
99C GLU* 4.4 0.2 - - - +
100C ASP* 3.0 32.7 + - - +
416C SER* 2.5 41.8 + - - +
419C PHE* 3.7 10.6 - - - +
421C THR* 4.2 7.9 - - + -
424C VAL* 4.6 7.1 - - + +
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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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67C ALA* 4.0 3.4 - - + -
93C GLY 3.1 14.1 + - - +
94C LEU* 3.3 7.2 + - - +
96C ASP* 1.3 75.7 + - - +
98C ARG* 1.3 65.9 + - - +
101C HIS* 2.9 3.8 + - - -
102C VAL* 2.9 48.8 + - + +
104C VAL* 3.5 32.8 - - + -
161C GLN 4.4 0.3 - - - +
163C VAL* 4.0 8.7 - - + -
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Residues in contact with ARG 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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124A MET* 3.6 23.6 - - - +
125A ASN 5.3 1.8 + - - +
129A ILE* 5.7 0.2 - - - +
94C LEU 2.9 16.9 + - - +
95C TYR* 3.6 27.4 - - - +
97C ALA* 1.3 76.8 - - - +
99C GLU* 1.3 86.0 + - - +
101C HIS* 3.3 24.0 + - - +
132C ASP* 2.8 47.9 + - - -
133C VAL* 3.4 25.4 - - + +
135C ASP* 5.3 9.4 - - - +
161C GLN 4.8 0.3 - - - +
162C GLY* 4.8 7.4 - - - -
163C VAL* 4.0 6.2 - - + +
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Residues in contact with GLU 99 (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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124A MET* 4.4 14.7 - - - +
95C TYR* 2.8 24.1 + - - +
96C ASP 4.4 0.2 - - - +
98C ARG* 1.3 116.5 + - - +
100C ASP* 1.3 60.2 + - - +
101C HIS* 3.1 19.0 + - - -
418C LEU* 3.7 28.4 - - + +
419C PHE* 3.7 40.2 - - + +
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Residues in contact with ASP 100 (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 LYS* 3.1 35.3 + - + -
96C ASP* 3.0 21.7 + - - +
97C ALA 4.6 0.4 - - - +
99C GLU* 1.3 74.3 - - - +
101C HIS* 1.3 72.5 + - - +
102C VAL* 3.5 10.8 + - + +
417C ASN* 3.0 34.2 + - - +
418C LEU* 2.9 29.6 + - - +
419C PHE 5.3 0.4 - - - -
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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