Contacts of the helix formed by residues 96 - 111 (chain A) in PDB entry 3GHG
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 GLY 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A GLU* 4.5 7.1 + - - -
95A ARG* 1.3 79.5 - - - +
97A ASP* 1.3 55.0 + - - +
98A PHE 3.1 3.1 - - - -
99A SER* 2.4 36.8 + - - -
100A SER* 2.8 11.9 + - - -
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Residues in contact with ASP 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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92A GLU 5.4 0.4 + - - -
93A ILE 3.6 21.7 + - - +
94A LEU* 3.4 31.8 - - + +
95A ARG 3.8 0.2 - - - -
96A GLY* 1.3 74.7 - - - +
98A PHE* 1.3 71.7 + - + +
100A SER* 2.6 32.2 + - - -
101A ALA* 2.7 23.5 + - - +
125B TRP* 4.7 0.5 - - - -
68C TYR* 5.4 1.6 - - - -
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Residues in contact with PHE 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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94A LEU* 4.0 17.0 + - + +
95A ARG 6.0 1.1 - - - +
96A GLY 3.1 1.0 - - - -
97A ASP* 1.3 95.3 - - - +
99A SER* 1.3 58.4 + - - +
100A SER 3.4 0.2 - - - -
101A ALA* 4.0 11.9 - - + -
102A ASN* 4.0 14.0 + - - +
124B LEU* 5.3 9.4 - - + -
125B TRP* 3.6 23.8 - + - -
128B ARG* 3.4 77.7 + - + +
129B GLN* 3.5 29.8 - - + -
132B VAL* 4.5 9.4 - - + -
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Residues in contact with SER 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 ARG 4.6 4.6 + - - -
96A GLY* 2.4 35.0 + - - -
98A PHE* 1.3 67.6 + - - +
100A SER* 1.3 56.1 + - - -
102A ASN* 2.8 29.2 + - - +
103A ASN* 3.2 19.5 + - - +
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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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96A GLY 2.8 8.0 + - - -
97A ASP* 2.6 31.5 + - - -
99A SER* 1.3 76.3 - - - +
101A ALA* 1.3 59.2 + - - +
102A ASN 3.4 0.7 - - - -
103A ASN* 3.6 10.8 + - - +
104A ARG* 2.9 26.6 + - - +
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Residues in contact with ALA 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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97A ASP* 2.7 15.6 + - - +
98A PHE* 4.2 16.6 - - + +
99A SER 3.4 0.2 - - - -
100A SER* 1.3 77.5 + - - +
102A ASN* 1.3 55.2 + - - +
104A ARG* 3.2 19.8 - - - +
105A ASP* 2.6 28.9 - - - +
128B ARG* 4.7 11.0 - - - +
132B VAL* 5.9 5.6 - - + -
79C ILE* 4.5 0.3 - - - +
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Residues in contact with ASN 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 PHE 4.0 7.9 + - - +
99A SER* 2.8 36.8 + - - +
101A ALA* 1.3 76.2 - - - +
103A ASN* 1.3 86.5 + - - +
105A ASP* 3.2 19.3 + - - +
106A ASN* 3.2 12.6 + - - +
109A ASN* 4.3 2.1 - - - +
128B ARG* 5.5 3.5 - - - +
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Residues in contact with ASN 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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99A SER 3.2 15.7 + - - +
100A SER* 3.6 12.2 + - - +
101A ALA 3.3 0.2 - - - -
102A ASN* 1.3 105.5 + - - +
104A ARG* 1.3 64.6 + - - +
105A ASP 3.1 0.4 - - - -
106A ASN* 3.1 39.6 + - - +
107A THR* 4.5 1.0 + - - -
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Residues in contact with ARG 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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100A SER 2.9 16.0 + - - +
101A ALA* 3.2 21.3 - - - +
103A ASN* 1.3 76.4 - - - +
105A ASP* 1.3 58.8 + - - +
106A ASN 3.6 0.2 + - - -
107A THR* 4.2 8.3 + - - -
108A TYR* 4.2 4.0 + - - +
78C MET* 3.1 36.3 - - - +
79C ILE* 3.3 40.1 - - + +
80C ASP* 2.7 47.3 + - - +
83C THR* 4.5 5.0 + - - +
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Residues in contact with ASP 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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101A ALA 2.6 24.7 - - - +
102A ASN* 3.2 12.5 + - - +
103A ASN 3.1 0.8 - - - -
104A ARG* 1.3 75.3 - - - +
106A ASN* 1.3 51.2 + - - +
107A THR 3.1 2.9 - - - -
108A TYR* 2.5 20.6 + - + +
109A ASN* 2.3 55.5 + - - +
79C ILE* 2.9 20.0 - - - +
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Residues in contact with ASN 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 ASN* 3.2 14.7 - - - +
103A ASN* 3.1 36.2 + - - +
105A ASP* 1.3 75.7 - - - +
107A THR* 1.3 61.0 + - - +
109A ASN* 3.3 21.7 + - - +
110A ARG* 2.8 32.8 + - - +
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Residues in contact with THR 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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103A ASN 4.5 1.1 + - - -
104A ARG 4.2 5.9 + - - -
105A ASP 3.1 0.8 - - - -
106A ASN* 1.3 75.8 - - - +
108A TYR* 1.3 59.8 + - - +
110A ARG* 4.6 3.4 + - - +
111A VAL* 2.9 64.9 + - + +
112A SER 3.3 1.6 + - - -
83C THR* 3.1 32.7 - - + +
86C SER* 5.4 0.3 + - - -
87C ARG* 5.9 6.7 - - + +
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Residues in contact with TYR 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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104A ARG 4.2 1.7 + - - +
105A ASP* 2.5 34.5 + - + +
107A THR* 1.3 72.4 - - - +
109A ASN* 1.3 57.9 + - - +
112A SER* 1.7 48.3 + - - -
116A ARG* 5.0 5.7 + - - -
140B ASN* 3.4 25.6 + - + +
142B TYR* 5.2 12.1 - + - -
143B SER* 3.8 19.1 + - - -
79C ILE* 4.0 18.2 - - + -
82C ALA* 3.6 24.5 - - + -
83C THR* 3.5 22.6 + - - +
86C SER* 5.9 1.8 - - - -
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Residues in contact with ASN 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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102A ASN 4.3 1.7 - - - +
105A ASP* 2.3 59.8 + - - +
106A ASN* 3.3 18.4 + - - +
107A THR 3.2 0.2 - - - -
108A TYR* 1.3 71.3 - - - +
110A ARG* 1.3 64.2 + - + +
113A GLU* 3.0 23.9 - - - +
116A ARG* 4.9 0.9 + - - -
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Residues in contact with ARG 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 ASN* 2.8 41.4 + - - +
107A THR* 5.0 2.6 + - - +
109A ASN* 1.3 82.2 - - + +
111A VAL* 1.3 74.9 + - + +
112A SER 3.0 4.5 - - - -
113A GLU* 2.8 22.1 + - - -
114A ASP* 2.9 32.8 + - - +
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Residues in contact with VAL 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 THR* 2.9 46.3 + - + +
110A ARG* 1.3 91.5 - - + +
112A SER* 1.3 51.0 + - - +
114A ASP* 5.6 0.9 - - - -
115A LEU* 2.6 52.0 - - + +
86C SER* 3.9 15.0 + - - +
87C ARG* 5.1 7.6 - - + +
90C LEU* 4.3 14.4 - - + -
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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