Contacts of the helix formed by residues 96 - 111 (chain A) in PDB entry 4GBM
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 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A MET* 4.3 2.2 - - - -
95A LEU* 1.3 78.7 - - - +
97A ALA* 1.3 63.9 + - - +
98A THR* 4.0 9.7 - - - -
99A ALA* 3.0 24.9 + - - +
100A SER* 3.1 17.2 + - - -
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Residues in contact with ALA 97 (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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86A GLN* 3.7 20.5 - - - +
90A MET* 3.7 23.9 - - + -
96A ASP* 1.3 74.6 - - - +
98A THR* 1.3 58.0 + - - +
100A SER* 3.5 1.9 + - - -
101A GLN* 3.0 29.5 + - - +
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Residues in contact with THR 98 (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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96A ASP* 3.3 10.3 + - - -
97A ALA* 1.3 79.2 - - - +
99A ALA* 1.3 56.3 + - - +
101A GLN* 3.4 15.9 + - - +
102A ALA* 3.0 28.5 + - + +
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Residues in contact with ALA 99 (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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95A LEU* 4.0 26.3 - - + +
96A ASP* 3.0 21.7 + - - +
98A THR* 1.3 74.0 - - - +
100A SER* 1.3 66.0 + - - +
102A ALA* 3.3 7.9 + - - +
103A LEU* 3.0 22.5 + - - +
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Residues in contact with SER 100 (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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86A GLN* 2.7 36.3 + - - -
89A PHE* 3.2 15.5 - - - +
90A MET* 3.6 21.8 - - - -
95A LEU* 4.0 13.1 - - - +
96A ASP 3.1 9.0 + - - -
97A ALA 3.8 3.8 - - - -
99A ALA* 1.3 75.7 - - - +
101A GLN* 1.3 61.6 + - - +
103A LEU* 3.2 6.8 + - - +
104A ILE* 3.0 25.6 + - - +
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Residues in contact with GLN 101 (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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86A GLN* 3.9 22.1 - - - +
97A ALA 3.0 19.2 + - - +
98A THR* 3.7 14.1 - - - +
99A ALA 3.3 0.2 - - - -
100A SER* 1.3 77.8 - - - +
102A ALA* 1.3 56.8 + - - +
104A ILE* 3.3 9.1 + - + +
105A LYS* 2.9 59.4 + - + +
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Residues in contact with ALA 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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98A THR* 3.0 19.1 + - + +
99A ALA* 3.5 9.0 - - - +
100A SER 3.3 0.2 - - - -
101A GLN* 1.3 75.6 - - - +
103A LEU* 1.3 62.5 + - - +
105A LYS* 3.5 9.2 + - - +
106A ASP* 3.1 21.3 + - - +
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Residues in contact with LEU 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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89A PHE* 3.7 41.1 - - + -
93A LYS* 3.8 26.2 - - + -
95A LEU* 4.5 3.8 - - + -
99A ALA 3.0 12.5 + - - +
100A SER* 3.2 8.5 + - - +
102A ALA* 1.3 74.9 - - - +
104A ILE* 1.3 66.8 + - - +
106A ASP* 3.0 20.6 + - + +
107A LEU* 3.1 35.4 + - + +
120A MET* 5.3 4.5 - - - -
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Residues in contact with ILE 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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69A MET* 4.3 13.2 - - + -
72A ARG* 4.7 0.4 - - - +
85A LEU* 4.0 9.6 - - + -
86A GLN* 3.6 37.2 - - + +
89A PHE* 3.8 22.7 - - + -
100A SER 3.0 15.4 + - - +
101A GLN* 3.7 7.6 - - - +
103A LEU* 1.3 74.1 - - - +
105A LYS* 1.3 59.0 + - + +
107A LEU* 3.1 10.5 + - + +
108A GLU* 3.0 46.9 + - - +
416A SO4 3.9 27.6 - - - +
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Residues in contact with LYS 105 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A GLN* 6.1 2.2 - - - +
101A GLN* 2.9 53.3 + - + +
102A ALA* 3.7 9.0 - - - +
104A ILE* 1.3 75.9 - - + +
106A ASP* 1.3 56.9 + - - +
108A GLU* 3.3 21.3 + - - +
109A SER* 2.9 29.5 + - - -
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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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102A ALA 3.1 12.4 + - - +
103A LEU* 3.0 17.2 + - + +
105A LYS* 1.3 76.0 - - - +
107A LEU* 1.3 68.5 + - + +
109A SER* 2.8 24.2 + - - -
110A GLN* 3.0 18.9 + - - +
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Residues in contact with LEU 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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69A MET* 3.9 18.0 - - + +
89A PHE* 4.1 22.0 - - + -
103A LEU* 3.1 27.1 + - + +
104A ILE* 3.1 10.7 + - - +
106A ASP* 1.3 80.5 - - - +
108A GLU* 1.3 58.2 + - - +
110A GLN* 3.6 1.9 + - - +
111A ASN 3.0 20.1 + - - -
112A LEU* 3.2 30.9 + - + +
117A VAL* 4.2 16.8 - - + -
120A MET* 3.7 41.5 - - + -
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Residues in contact with GLU 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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69A MET* 3.9 34.2 - - + +
70A LYS* 3.0 28.7 + - + +
72A ARG* 4.3 10.0 + - - -
73A GLN* 3.5 35.1 - - + +
104A ILE* 3.0 31.3 + - - +
105A LYS* 3.6 29.3 + - - +
107A LEU* 1.3 75.2 - - - +
109A SER* 1.3 61.9 + - - +
111A ASN* 3.1 7.8 + - - -
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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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70A LYS* 3.1 19.9 + - - +
105A LYS 2.9 13.8 + - - -
106A ASP* 2.8 31.4 + - - -
108A GLU* 1.3 76.0 - - - +
110A GLN* 1.3 60.3 + - - +
111A ASN* 4.6 0.2 - - - +
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Residues in contact with GLN 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 ASP* 3.0 18.7 + - - +
107A LEU* 4.2 4.0 - - - +
109A SER* 1.3 80.0 + - - +
111A ASN* 1.3 69.4 + - - +
112A LEU* 3.6 28.6 - - + +
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Residues in contact with ASN 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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68A THR* 3.1 30.2 + - - +
70A LYS* 2.9 51.3 + - + +
107A LEU 3.0 6.0 + - - -
108A GLU* 3.1 14.0 + - - +
110A GLN* 1.3 82.4 - - - +
112A LEU* 1.3 68.7 + - - +
113A SER 3.6 0.5 + - - -
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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