Contacts of the strand formed by residues 106 - 113 (chain C) in PDB entry 3AQQ
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 GLU 106 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64C LYS* 3.0 32.1 + - - +
65C GLY 3.7 8.3 - - - +
66C VAL* 4.7 8.5 - - + +
104C GLY 3.2 6.7 + - - +
105C ASP* 1.3 72.5 - - - +
107C VAL* 1.3 63.6 + - - +
128C ILE* 3.4 2.1 - - - +
129C THR* 2.8 34.2 + - - +
130C HIS* 2.9 41.4 + - + +
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Residues in contact with VAL 107 (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 LYS* 3.2 8.4 - - - +
65C GLY* 2.9 50.4 + - - +
66C VAL* 3.8 1.8 - - - +
67C CYS* 4.5 6.7 - - + +
79C ILE* 3.8 29.6 - - + -
101C PRO* 6.4 0.9 - - + -
105C ASP* 3.5 13.7 - - + +
106C GLU* 1.3 83.7 - - - +
108C THR* 1.3 67.3 + - - +
109C TYR* 4.3 3.4 - - + -
126C VAL* 4.4 10.3 - - + -
127C VAL 3.0 13.5 - - - +
128C ILE* 4.2 15.0 - - + -
129C THR* 3.3 3.5 + - - -
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Residues in contact with THR 108 (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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62C VAL* 3.9 18.0 - - + +
63C TYR 3.1 10.1 - - - +
64C LYS* 4.1 15.9 - - + -
107C VAL* 1.3 78.8 - - - +
109C TYR* 1.3 64.7 + - - +
125C GLU 3.7 1.8 + - - +
126C VAL* 3.4 2.4 - - - +
127C VAL* 2.8 52.2 + - - +
129C THR* 3.9 20.4 - - + -
58D SER* 5.3 2.6 + - - -
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Residues in contact with TYR 109 (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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62C VAL* 3.6 6.5 - - - +
63C TYR* 2.9 50.1 + - + +
64C LYS 3.4 30.9 + - - -
65C GLY* 3.7 5.8 - - - -
79C ILE* 4.2 10.3 - - + -
81C PRO* 3.7 18.0 - - - +
88C ILE* 4.4 9.1 - - + +
107C VAL* 4.2 9.9 - - + -
108C THR* 1.3 81.7 - - - +
110C LYS* 1.3 74.1 + - - +
111C MET* 3.4 41.3 - - + +
123C ALA* 3.9 13.7 - - + -
124C VAL 3.7 4.5 - - - +
125C GLU 3.8 4.5 - - - -
126C VAL* 3.6 24.2 - - + -
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Residues in contact with LYS 110 (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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56B ARG* 3.4 27.4 - - - +
57C ALA 3.0 28.5 - - - +
58C SER* 3.3 14.0 + - - -
60C GLY 3.5 11.2 - - - +
61C PRO 4.0 7.4 - - - +
62C VAL* 3.9 17.0 - - + -
109C TYR* 1.3 79.1 - - - +
111C MET* 1.3 62.5 + - - +
123C ALA* 3.5 4.0 - - - -
124C VAL* 2.7 50.2 + - + +
125C GLU* 2.7 34.5 + - + +
110D LYS* 4.2 16.0 - - - +
125D GLU* 4.5 1.6 + - - -
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Residues in contact with MET 111 (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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116B PRO* 4.2 18.2 - - - +
117B LYS 5.2 0.7 - - - -
118B ASN* 3.3 22.4 + - - +
57C ALA* 3.3 15.1 - - - +
61C PRO 4.8 0.6 + - - -
63C TYR* 3.7 34.8 - - + -
81C PRO* 5.0 6.1 - - + -
88C ILE* 3.9 20.6 - - + -
109C TYR* 3.4 43.1 - - + +
110C LYS* 1.3 72.7 - - - +
112C CYS* 1.3 65.3 + - - +
121C LEU* 3.9 26.2 - - + -
122C GLN 3.4 7.9 - - - +
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Residues in contact with CYS 112 (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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117B LYS 4.6 3.3 + - - -
118B ASN* 5.5 1.8 - - - -
49C ARG* 3.9 29.4 - - - -
53C ALA* 3.9 21.8 - - - -
57C ALA* 3.8 13.0 - - + +
111C MET* 1.3 80.1 - - - +
113C SER* 1.3 75.3 + - - +
114C ILE* 5.6 0.9 - - - -
121C LEU* 4.4 1.9 - - - +
122C GLN* 2.8 42.3 + - + +
124C VAL* 4.2 8.7 - - + -
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Residues in contact with SER 113 (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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117B LYS* 3.3 31.6 + - - +
118B ASN 4.6 2.5 + - - -
119B GLU* 3.9 15.1 + - - +
53C ALA* 5.4 2.9 - - - +
56C ARG* 5.1 4.5 + - - -
112C CYS* 1.3 83.3 - - - +
114C ILE* 1.3 62.5 + - - +
118C ASN 4.7 1.5 + - - -
119C GLU* 4.0 19.7 - - - -
120C LYS 3.0 11.0 - - - -
121C LEU* 3.9 10.3 - - - +
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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