Contacts of the helix formed by residues 96 - 111 (chain D) in PDB entry 2GTP
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 96 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87D GLY* 4.4 5.2 - - - +
90D LEU* 3.6 13.6 + - + -
91D LYS* 4.0 36.7 - - + +
94D PHE* 3.8 12.3 - - - -
95D SER* 1.3 83.6 + - - +
97D GLU* 1.3 69.0 + - + +
98D ASN 3.0 0.9 + - - -
99D ILE* 3.0 11.8 - - + +
100D GLU* 3.0 44.6 + - - +
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Residues in contact with GLU 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A THR* 4.0 4.7 + - - -
207A GLU* 4.5 2.3 - - - +
210A LYS* 2.7 36.1 + - - -
94D PHE 4.0 0.9 - - - +
95D SER* 3.1 17.2 - - - -
96D GLU* 1.3 79.2 + - + +
98D ASN* 1.3 72.1 + - - +
100D GLU* 4.3 11.2 - - - -
101D PHE* 2.9 31.0 + - - +
127D PHE* 3.8 2.8 - - - -
134D LYS* 3.6 42.4 - - + +
135D GLN 4.0 14.5 - - - +
136D ILE* 4.0 4.7 - - + +
137D ASN 5.2 0.9 + - - -
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Residues in contact with ASN 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A THR* 3.4 38.0 + - - +
90D LEU* 4.8 0.6 - - + +
95D SER* 3.2 14.3 + - - +
96D GLU 3.0 0.8 + - - -
97D GLU* 1.3 91.0 + - - +
99D ILE* 1.3 57.8 + - - +
101D PHE* 3.5 1.8 - - - +
102D TRP* 3.0 23.9 + - - +
136D ILE* 4.2 6.0 - - - +
137D ASN 4.5 0.9 + - - -
165D ILE* 3.4 45.4 - - + +
168D LEU* 3.8 12.2 - - - +
169D MET* 3.7 17.7 - - + +
173D SER* 5.1 0.6 + - - -
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Residues in contact with ILE 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D LEU* 3.8 16.6 - - + -
83D GLN* 3.8 24.2 - - + +
86D PHE* 3.7 27.8 - - + -
87D GLY* 4.3 12.6 - - - +
90D LEU* 3.8 16.5 - - + +
96D GLU* 3.0 20.1 + - + +
98D ASN* 1.3 76.2 - - - +
100D GLU* 1.3 72.8 + - + +
102D TRP* 3.2 7.9 + - + +
103D LEU* 2.9 46.7 + - + +
169D MET* 3.6 9.9 - - - -
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Residues in contact with GLU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D GLU* 3.0 40.5 + - + +
97D GLU* 4.0 9.0 - - - +
99D ILE* 1.3 82.1 - - + +
101D PHE* 1.3 57.1 + - - +
103D LEU* 3.4 10.5 + - + +
104D ALA* 2.9 28.4 + - - +
127D PHE* 3.9 19.3 - - + -
134D LYS* 4.8 9.9 - - - +
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Residues in contact with PHE 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D GLU 2.9 19.5 + - - +
98D ASN 3.5 3.1 - - - +
100D GLU* 1.3 74.7 - - - +
102D TRP* 1.3 67.9 + - - +
104D ALA* 3.0 3.8 + - - +
105D CYS* 2.9 48.9 + - - -
123D ILE* 3.7 19.1 - - + -
127D PHE* 3.5 34.5 - + + -
128D VAL* 4.2 6.3 - - + -
136D ILE* 3.4 39.7 - - + -
158D PHE* 4.3 7.9 - + + -
161D ALA* 3.9 32.5 - - + -
162D GLN* 3.9 2.2 - - - -
165D ILE* 3.9 14.6 - - + -
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Residues in contact with TRP 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D LEU* 3.8 50.5 - - + -
83D GLN* 4.6 4.9 - - - -
98D ASN 3.0 14.7 + - - +
99D ILE* 3.6 10.1 - - + +
101D PHE* 1.3 79.3 - - - +
103D LEU* 1.3 82.2 + - + +
105D CYS* 3.3 1.8 + - - -
106D GLU* 3.0 48.2 + - + +
162D GLN* 3.2 51.1 + - + +
165D ILE* 5.3 2.0 - - + -
166D TYR* 4.0 29.0 - + + +
169D MET* 4.1 14.8 - - + -
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Residues in contact with LEU 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D GLN* 3.3 35.0 - - + +
99D ILE* 2.9 39.6 + - + +
100D GLU* 3.8 9.6 - - + +
102D TRP* 1.3 89.8 - - + +
104D ALA* 1.3 66.3 + - - +
106D GLU* 3.3 8.5 + - + +
107D ASP* 3.1 23.4 + - - +
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Residues in contact with ALA 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D GLU 2.9 18.0 + - - +
101D PHE* 3.0 5.8 + - - +
103D LEU* 1.3 77.2 - - - +
105D CYS* 1.3 55.6 + - - +
107D ASP* 3.6 6.3 + - - +
108D TYR* 3.0 27.7 + - - +
123D ILE* 3.6 23.7 - - + +
127D PHE* 4.0 20.4 - - + -
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Residues in contact with CYS 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D PHE* 2.9 54.0 + - - -
102D TRP 3.6 1.6 - - - +
104D ALA* 1.3 73.9 - - - +
106D GLU* 1.3 64.1 + - - +
108D TYR* 3.1 9.9 + - - +
109D LYS* 2.9 28.7 + - - +
123D ILE* 4.9 1.6 - - - -
158D PHE* 3.6 24.5 - - + -
162D GLN* 3.5 32.5 - - + +
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Residues in contact with GLU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D TRP* 3.0 48.8 + - + +
103D LEU* 3.3 12.5 + - + +
105D CYS* 1.3 75.6 - - - +
107D ASP* 1.3 61.5 + - - +
109D LYS* 3.0 46.7 + - - +
110D LYS* 3.4 36.3 + - - +
162D GLN* 3.3 8.6 + - - +
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Residues in contact with ASP 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D LEU 3.1 16.0 + - - +
104D ALA* 4.0 6.6 - - - +
106D GLU* 1.3 75.0 - - - +
108D TYR* 1.3 63.3 + - - +
110D LYS* 3.1 17.1 + - - +
111D THR* 2.8 35.1 + - - -
119D LYS* 4.2 13.5 - - - +
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Residues in contact with TYR 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D ALA 3.0 19.4 + - - +
105D CYS* 3.1 8.9 + - - +
107D ASP* 1.3 78.2 + - - +
109D LYS* 1.3 63.4 - - + +
111D THR* 3.2 21.8 + - - -
116D LEU* 3.6 31.7 - - + +
119D LYS* 3.8 18.8 - - + -
120D ALA* 3.6 24.9 - - + -
123D ILE* 3.7 20.0 - - + -
153D PRO* 3.3 21.7 - - - +
154D THR 2.9 28.4 + - - -
155D PRO* 3.5 21.0 - - + +
157D CYS* 3.8 13.1 - - + +
158D PHE* 4.2 10.1 - + + -
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Residues in contact with LYS 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D CYS* 2.9 18.1 + - - +
106D GLU* 3.0 31.6 + - - +
107D ASP 3.2 0.4 - - - -
108D TYR* 1.3 81.3 - - + +
110D LYS* 1.3 63.2 + - + +
111D THR 3.5 5.4 + - - +
116D LEU* 5.7 0.2 - - - +
155D PRO* 3.8 30.4 - - + +
156D THR* 5.8 0.2 - - - -
158D PHE 6.1 0.2 - - - -
159D ASP* 3.4 21.2 + - - +
162D GLN* 2.6 31.6 + - - -
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Residues in contact with LYS 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D GLU* 3.4 36.1 + - - +
107D ASP* 3.1 13.8 + - - +
109D LYS* 1.3 75.5 - - + +
111D THR* 1.3 64.7 + - - +
112D GLU* 4.6 7.1 - - - +
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Residues in contact with THR 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D ASP* 2.8 32.0 + - - -
108D TYR* 3.2 20.5 + - - -
109D LYS 3.9 6.1 - - - +
110D LYS* 1.3 82.1 - - - +
112D GLU* 1.3 73.7 + - - +
113D SER 3.8 1.0 + - - -
115D LEU* 4.4 15.5 - - + -
116D LEU* 3.7 22.2 - - + +
119D LYS* 3.8 23.1 - - + +
155D PRO* 6.1 1.2 - - - +
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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