Contacts of the strand formed by residues 89 - 96 (chain C) in PDB entry 3A2C
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 LYS 89 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80C GLN* 2.8 37.7 + - + +
81C ILE 3.1 5.8 - - - +
82C PHE* 3.8 10.5 - - + -
88C GLU* 1.3 102.8 - - + +
90C PHE* 1.3 69.7 + - - +
140C CYS* 3.6 23.6 + - + +
142C ASP* 2.7 29.4 + - - +
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Residues in contact with PHE 90 (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 TYR* 3.8 22.4 - + - -
80C GLN* 3.3 3.6 - - - -
81C ILE* 2.8 37.9 + - + +
83C ASN* 4.3 13.0 - - + -
86C THR* 5.9 0.9 - - + -
88C GLU* 3.9 39.7 - - + -
89C LYS* 1.3 80.7 - - - +
91C ALA* 1.3 61.2 + - - +
119C ARG* 5.0 4.5 - - - -
121C VAL* 3.5 34.8 - - + -
137C VAL* 3.7 18.8 - - + -
138C MET 3.2 18.6 - - - +
139C GLU* 4.3 4.9 - - - -
140C CYS* 3.8 8.1 - - - -
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Residues in contact with ALA 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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1C PDY 3.3 36.6 - - + +
78C VAL* 3.3 25.4 - - + -
79C LEU 3.3 5.4 - - - +
80C GLN* 4.5 1.3 - - - +
81C ILE* 4.7 0.2 - - - -
90C PHE* 1.3 74.4 - - - +
92C LEU* 1.3 58.6 + - - +
136C ILE 3.6 0.7 - - - +
137C VAL* 3.6 3.3 - - - -
138C MET* 2.9 36.2 + - + +
139C GLU 4.2 2.2 - - - +
140C CYS* 3.8 6.1 - - - +
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Residues in contact with LEU 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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59C ILE* 4.1 20.0 - - + -
65C VAL* 4.5 12.1 - - + -
69C VAL* 5.1 7.2 - - + -
70C LEU* 5.3 0.9 - - + -
77C LYS 3.8 2.4 - - - +
78C VAL* 3.2 8.0 - - - -
79C LEU* 2.6 41.9 + - + +
81C ILE* 3.4 33.4 - - + -
90C PHE 3.8 0.2 + - - -
91C ALA* 1.3 74.1 - - - +
93C LYS* 1.3 77.5 + - - +
94C MET* 4.3 18.2 - - + -
135C LEU* 4.1 17.5 - - + -
136C ILE 3.5 19.5 - - - +
137C VAL* 4.2 3.4 - - + -
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Residues in contact with LYS 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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76C GLY 6.1 2.2 - - - +
77C LYS 4.9 2.2 - - - -
78C VAL* 4.5 22.1 - - + +
92C LEU* 1.3 76.2 - - - +
94C MET* 1.3 67.2 + - - +
95C LEU* 4.2 20.8 + - + +
104C GLU* 3.2 30.2 + - - -
134C LEU 4.0 0.3 - - - +
135C LEU* 3.5 2.6 - - - -
136C ILE* 2.8 53.8 + - + +
138C MET* 4.8 18.2 - - + -
207C ASP* 4.0 24.8 + - - +
209C GLY* 5.6 1.0 - - - +
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Residues in contact with MET 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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70C LEU* 3.6 40.6 - - + +
73C GLY* 3.8 26.9 + - - +
74C ILE* 3.4 48.7 - - + +
76C GLY* 5.4 3.0 - - - -
77C LYS 5.4 0.2 + - - -
92C LEU* 4.3 14.1 - - + -
93C LYS* 1.3 80.8 - - - +
95C LEU* 1.3 70.2 + - - +
96C GLN 4.4 0.2 + - - -
128C TYR* 4.9 7.0 - - + -
133C CYS* 4.8 13.5 - - - -
134C LEU 3.6 4.7 - - - +
135C LEU* 4.2 22.2 - - + -
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Residues in contact with LEU 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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74C ILE* 5.1 1.1 - - - -
93C LYS* 4.2 20.6 + - + +
94C MET* 1.3 83.3 - - - +
96C GLN* 1.3 60.3 + - - +
101C ALA* 3.8 32.1 - - + +
104C GLU* 3.2 35.2 - - - +
105C VAL* 5.0 1.6 - - + -
133C CYS* 3.2 6.0 - - - +
134C LEU* 2.6 48.2 + - + +
136C ILE* 4.3 14.4 - - + -
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Residues in contact with GLN 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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74C ILE* 4.8 7.9 - - + +
94C MET 4.4 0.2 + - - -
95C LEU* 1.3 69.7 - - - +
97C ASP* 1.3 85.5 + - - +
98C CYS* 2.9 17.6 + - - +
101C ALA* 3.7 7.3 - - - +
131C ARG* 3.2 58.6 + - + +
132C LYS 4.2 3.9 - - - +
133C CYS* 4.0 5.8 - - + -
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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