Contacts of the helix formed by residues 104 - 113 (chain A) in PDB entry 3GBN
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 ASP 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A PHE 3.6 1.0 + - - -
103A ILE* 1.3 87.1 - - - +
105A TYR* 1.3 59.5 + - - +
106A GLU* 3.3 6.3 + - - +
107A GLU* 3.3 17.0 + - + +
108A LEU 3.0 21.7 + - - -
211A ARG* 5.6 1.4 + - - -
234A TRP* 3.1 20.5 + - + +
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Residues in contact with TYR 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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65A ASN* 4.1 8.4 + - - -
66A ILE* 3.6 11.0 + - + +
67A ALA* 3.3 42.4 + - + +
102A PHE* 3.3 47.0 + + + +
103A ILE 3.2 3.2 + - - -
104A ASP* 1.3 74.6 - - - +
106A GLU* 1.3 81.3 + - + +
108A LEU* 3.1 8.8 + - + +
109A ARG* 3.0 70.5 + - + +
69B GLU* 4.9 4.3 - - - -
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Residues in contact with GLU 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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104A ASP* 3.3 3.1 - - - -
105A TYR* 1.3 90.4 + - + +
107A GLU* 1.3 63.4 + - + +
109A ARG* 3.3 12.0 + - - +
110A GLU* 3.0 20.4 + - - +
69B GLU* 3.2 50.4 + - + +
70B PHE* 3.7 5.9 - - - +
71B ASN* 3.5 37.3 + - - +
74B GLU* 4.7 4.9 - - - +
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Residues in contact with GLU 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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104A ASP* 3.3 21.2 + - + +
105A TYR 3.2 0.4 - - - -
106A GLU* 1.3 77.7 - - + +
108A LEU* 1.3 65.8 + - - +
110A GLU* 3.0 15.9 + - - +
111A GLN* 2.9 34.5 + - + +
234A TRP* 4.0 15.2 - - + -
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Residues in contact with LEU 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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66A ILE* 5.3 2.9 - - + -
70A LEU* 3.8 19.5 - - + -
102A PHE* 4.0 21.5 - - + -
104A ASP 3.0 8.6 + - - +
105A TYR* 3.1 14.3 + - + +
107A GLU* 1.3 74.8 - - - +
109A ARG* 1.3 57.2 + - + +
111A GLN* 3.1 8.1 + - + -
112A LEU* 3.0 46.7 + - + +
177A LEU* 3.8 25.6 - - + -
179A LEU* 4.2 6.3 - - + -
234A TRP* 3.7 42.8 - - + +
236A LEU* 5.9 0.4 - - + -
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Residues in contact with ARG 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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65A ASN* 5.2 0.6 - - - +
66A ILE* 3.8 15.3 - - + +
89A GLU* 2.9 44.0 + - - -
105A TYR* 3.0 59.8 + - + +
106A GLU* 3.5 12.1 - - - +
107A GLU 3.2 0.2 - - - -
108A LEU* 1.3 76.2 - - - +
110A GLU* 1.3 61.7 + - - +
112A LEU* 3.4 3.9 + - - +
113A SER* 3.2 19.4 + - - -
267A ILE* 3.4 37.6 - - + +
269A THR* 5.5 2.2 + - - -
69B GLU* 3.2 43.2 + - + +
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Residues in contact with GLU 110 (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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106A GLU 3.0 12.1 + - - +
107A GLU* 3.0 21.2 + - - +
109A ARG* 1.3 76.9 - - - +
111A GLN* 1.3 64.5 + - + +
113A SER* 3.3 21.0 - - - -
114A SER* 4.2 2.9 + - - -
67B GLY 4.6 2.9 - - - +
68B LYS* 2.6 54.4 + - - +
69B GLU 5.4 0.5 + - - -
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Residues in contact with GLN 111 (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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107A GLU* 2.9 26.7 + - - +
108A LEU* 3.1 14.1 + - + +
110A GLU* 1.3 78.3 - - - +
112A LEU* 1.3 62.2 + - + +
114A SER* 3.3 7.0 + - - -
115A VAL* 3.6 3.2 - - - +
234A TRP* 4.1 22.5 - - + -
236A LEU* 3.5 18.5 - - + +
260A LEU* 6.2 0.9 - - + -
262A ARG* 2.7 54.7 + - - +
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Residues in contact with LEU 112 (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 ILE* 3.5 23.6 - - + -
69A TRP* 4.7 13.9 - - + -
70A LEU* 3.4 35.4 - - + -
84A TRP* 5.6 0.4 - - + -
87A ILE* 4.3 14.1 - - + +
108A LEU* 3.0 30.0 + - + +
109A ARG* 3.9 4.9 - - - +
110A GLU 3.3 0.6 - - - -
111A GLN* 1.3 73.1 - - + +
113A SER* 1.3 60.7 + - - +
114A SER 3.1 2.2 - - - -
115A VAL* 2.9 49.8 + - + +
118A PHE* 5.8 2.2 - - + -
177A LEU* 4.8 10.8 - - + -
260A LEU* 5.2 5.8 - - + -
265A SER* 5.0 0.5 + - - -
267A ILE* 4.3 10.1 - - + -
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Residues in contact with SER 113 (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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109A ARG 3.2 10.3 + - - -
110A GLU* 3.3 22.0 - - - -
111A GLN 3.2 0.2 - - - -
112A LEU* 1.3 78.1 - - - +
114A SER* 1.3 55.7 + - - +
115A VAL 3.4 0.4 - - - -
265A SER* 3.0 35.9 + - - +
266A GLY* 3.3 22.6 + - - -
267A ILE* 4.0 9.5 + - - +
66B VAL* 3.5 18.7 - - - +
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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