Contacts of the helix formed by residues 101 - 109 (chain A) in PDB entry 3BDW
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 ASN 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A ARG* 5.3 2.4 + - - -
99A LEU* 3.2 10.0 - - - +
100A GLN* 1.3 91.0 + - - +
102A THR* 1.3 64.2 + - - +
103A ASP* 3.4 24.4 + - - +
104A GLU* 3.1 28.7 + - - +
140A LEU* 4.6 11.9 - - - -
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Residues in contact with THR 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LEU* 4.6 3.4 - - + +
101A ASN* 1.3 70.2 - - - +
103A ASP* 1.3 69.0 + - - +
104A GLU 3.0 6.7 + - - -
105A LEU* 3.4 13.0 + - - +
106A ASP* 4.1 4.0 + - - -
140A LEU* 4.1 24.8 - - + +
141A PHE* 6.1 0.2 - - + -
155A TYR* 3.3 30.5 + - + +
157A PRO 5.3 4.3 - - - +
158A ASN 6.1 0.2 - - - -
159A GLY* 4.6 12.6 - - - +
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Residues in contact with ASP 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A TYR* 4.0 1.2 - - - -
69A ARG* 3.7 24.0 + - - +
101A ASN* 3.3 13.3 + - - +
102A THR* 1.3 83.6 + - - +
104A GLU* 1.3 62.9 + - - +
105A LEU 3.3 0.4 - - - -
106A ASP* 3.0 33.6 + - + +
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Residues in contact with GLU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A TYR* 3.3 24.5 - - - -
69A ARG* 4.5 9.6 - - - +
71A ASN* 4.8 2.5 - - - +
73A TYR* 2.9 31.8 + - + +
97A LEU* 3.6 9.4 - - - +
98A GLN 3.2 10.0 - - - +
99A LEU* 3.9 8.7 - - + -
100A GLN* 3.0 38.1 + - - +
101A ASN* 3.1 20.5 + - - +
102A THR 3.0 0.4 - - - -
103A ASP* 1.3 78.1 - - - +
105A LEU* 1.3 60.7 + - + +
107A PHE* 3.9 0.5 - - - -
175A LYS* 3.0 24.2 + - - -
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A TYR* 3.8 28.5 - - + -
97A LEU* 3.6 29.6 - - + -
99A LEU* 4.6 7.8 - - + +
102A THR 3.4 9.4 + - - +
103A ASP 3.3 0.4 - - - -
104A GLU* 1.3 82.8 - - + +
106A ASP* 1.3 65.3 + - - +
107A PHE* 3.3 15.0 - - + -
108A MET* 3.1 44.0 + - + -
109A SER* 3.4 9.5 + - - -
155A TYR* 4.6 16.4 - - + -
157A PRO* 4.5 15.2 - - + +
173A ILE* 3.6 11.2 - - + -
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Residues in contact with ASP 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A TYR* 3.8 13.5 + - - +
69A ARG* 4.9 2.0 + - - +
102A THR 4.8 1.3 - - - -
103A ASP* 3.0 34.1 + - - +
104A GLU 3.4 1.2 + - - -
105A LEU* 1.3 74.7 - - - +
107A PHE* 1.3 54.6 + - - +
108A MET 2.8 11.6 + - - -
109A SER* 2.8 34.6 + - - -
135B LYS* 3.5 21.3 + - - +
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Residues in contact with PHE 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL* 3.6 25.4 - - + -
68A TYR* 3.4 42.1 - + + -
73A TYR* 4.1 14.4 - + + -
75A ILE* 4.8 1.8 - - + -
104A GLU 3.9 10.3 - - - -
105A LEU* 3.9 13.2 - - + -
106A ASP* 1.3 76.1 - - - +
108A MET* 1.3 79.8 + - + +
109A SER 3.6 0.6 + - - -
124B ILE* 3.8 29.4 - - + -
133B ILE* 3.7 20.0 - - + +
135B LYS* 3.8 13.2 - - - +
169B ILE* 3.1 49.5 - - + +
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Residues in contact with MET 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ILE* 4.0 32.8 - - + -
105A LEU* 3.1 51.1 + - + +
106A ASP 2.8 3.0 + - - -
107A PHE* 1.3 93.7 - - + +
109A SER* 1.3 60.9 + - - +
110A SER 3.2 3.1 - - - -
111A SER* 3.2 17.3 + - - -
115A TYR* 4.6 7.0 - - - -
157A PRO* 3.1 26.4 - - + +
173A ILE* 4.3 1.8 - - + -
168B ILE* 4.2 5.2 - - - +
169B ILE* 3.7 27.6 - - + -
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Residues in contact with SER 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A LEU 3.4 4.9 + - - -
106A ASP* 2.8 29.4 + - - -
107A PHE 3.6 1.0 + - - -
108A MET* 1.3 76.8 - - - +
110A SER* 1.3 60.2 + - - +
111A SER 3.3 1.2 + - - -
157A PRO* 4.1 14.4 - - - -
158A ASN* 3.6 20.7 + - - +
135B LYS* 3.6 21.2 - - - +
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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