Contacts of the helix formed by residues 131 - 145 (chain D) in PDB entry 2GTL
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 131 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126C GLN* 4.5 4.5 - - - +
13D GLU* 5.7 0.3 - - - +
16D LYS* 2.9 46.6 + - + +
20D GLN* 3.2 11.4 + - - +
129D HIS 3.0 5.4 + - - +
130D PHE* 1.3 66.5 - - - +
132D PHE* 1.3 63.7 + - - +
133D GLY* 3.5 6.2 + - - -
134D ALA* 3.1 29.9 + - + +
135D TRP* 3.1 25.0 + - + -
60L ASN* 5.2 0.2 + - - -
62L TYR* 5.5 0.2 - - - -
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Residues in contact with PHE 132 (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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119D LEU* 4.2 25.3 - - + +
130D PHE* 3.0 26.9 + + - -
131D ASP* 1.3 69.7 + - - +
133D GLY* 1.3 66.3 + - - +
135D TRP* 3.0 2.9 + - - +
136D HIS* 2.8 49.6 + + + -
59L ASP 3.9 22.0 - - - -
60L ASN* 3.4 19.7 - - + +
61L ILE* 5.0 5.8 - - + -
62L TYR* 3.2 52.8 - + + +
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Residues in contact with GLY 133 (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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13D GLU* 5.4 1.3 - - - -
131D ASP* 3.2 6.5 + - - -
132D PHE* 1.3 77.5 - - - +
134D ALA* 1.3 63.7 + - - +
136D HIS* 3.7 2.8 - - - +
137D ASP* 3.0 31.0 + - - +
57L ARG* 5.9 1.1 - - - -
60L ASN* 2.8 27.3 - - - +
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Residues in contact with ALA 134 (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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9D CYS* 4.6 0.5 - - - -
13D GLU* 3.6 38.9 + - + +
16D LYS* 4.2 5.6 - - + -
17D VAL* 3.9 7.9 - - + -
131D ASP* 3.1 34.9 + - + +
133D GLY* 1.3 73.8 - - - +
135D TRP* 1.3 58.9 + - - +
137D ASP* 3.8 3.2 - - - +
138D CYS* 2.8 32.4 + - - +
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Residues in contact with TRP 135 (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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16D LYS 5.9 0.2 - - - -
17D VAL* 3.4 40.4 - - + +
20D GLN* 2.8 29.2 - - + +
21D TRP* 3.5 45.8 - + + -
81D ILE* 4.0 9.6 - - + -
118D LEU* 4.9 3.8 - - + -
119D LEU* 3.6 17.3 - - + -
122D LEU* 3.2 34.3 - - + -
126D LEU* 4.8 2.0 - - + -
130D PHE* 3.2 19.0 - + + -
131D ASP* 3.1 21.7 + - + -
132D PHE 3.0 6.5 + - - +
134D ALA* 1.3 73.2 - - + +
136D HIS* 1.3 61.5 + - - +
138D CYS 2.8 1.0 + - - -
139D VAL* 2.5 67.3 + - + +
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Residues in contact with HIS 136 (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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115D LEU* 4.2 14.0 - - + +
119D LEU* 3.7 23.6 - - + +
132D PHE* 2.8 43.7 + + + +
133D GLY* 3.7 3.8 - - - +
135D TRP* 1.3 73.8 - - - +
137D ASP* 1.3 67.5 + - - +
139D VAL* 5.4 0.7 - - - -
140D ASP* 2.9 49.9 + - - +
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Residues in contact with ASP 137 (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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8D GLU* 3.6 36.4 + - - +
9D CYS* 4.1 7.7 + - - +
13D GLU* 3.4 20.8 - - - +
133D GLY* 3.0 21.0 + - - +
134D ALA* 3.8 3.6 - - - +
136D HIS* 1.3 85.6 - - - +
138D CYS* 1.3 60.6 + - - +
140D ASP* 4.0 3.0 - - - +
141D GLN* 3.8 15.6 + - - +
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Residues in contact with CYS 138 (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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9D CYS* 2.0 46.7 - - - -
13D GLU 4.3 2.9 - - - -
14D SER* 4.3 0.9 - - - -
17D VAL* 4.1 12.1 - - + -
84D LEU* 3.3 37.8 - - + +
134D ALA 2.8 16.0 + - - +
135D TRP 2.8 4.0 + - - +
137D ASP* 1.3 75.8 - - - +
139D VAL* 1.3 64.2 + - - +
140D ASP 3.1 1.7 + - - -
141D GLN* 3.4 17.4 + - - +
142D ILE* 3.6 11.9 + - - +
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Residues in contact with VAL 139 (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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17D VAL* 5.0 4.7 - - + -
77D LEU* 5.0 6.7 - - + -
81D ILE* 5.1 4.0 - - + -
114D PHE* 5.8 1.8 - - + -
115D LEU* 3.4 27.8 - - + -
118D LEU* 4.2 17.7 - - + -
119D LEU* 5.1 0.2 - - + -
135D TRP* 2.5 57.6 + - + +
138D CYS* 1.3 70.1 - - - +
140D ASP* 1.3 66.5 + - - +
142D ILE* 2.8 28.4 + - + +
143D ILE* 3.0 18.3 + - + +
160D HEM 5.8 0.4 - - + -
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Residues in contact with ASP 140 (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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112D ASP* 5.6 1.4 - - - +
115D LEU* 4.0 17.5 - - + +
136D HIS* 2.9 44.9 + - - +
137D ASP* 4.0 5.6 - - - +
138D CYS 3.1 0.2 - - - -
139D VAL* 1.3 76.0 - - - +
141D GLN* 1.3 55.2 + - - +
143D ILE* 2.7 29.7 + - - +
144D ASP* 3.1 36.2 + - - +
147D LYS* 5.3 1.6 + - - -
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Residues in contact with GLN 141 (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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8D GLU* 5.8 0.4 - - - +
9D CYS* 3.7 33.5 + - - +
84D LEU* 5.7 2.0 - - - +
90D LEU* 3.7 25.5 - - + +
94D LEU* 3.9 10.3 - - + +
137D ASP 3.8 7.6 + - - +
138D CYS* 3.4 12.0 + - - +
139D VAL 3.2 0.2 - - - -
140D ASP* 1.3 76.6 - - - +
142D ILE* 1.3 60.5 + - + +
144D ASP* 4.1 8.9 + - - +
145D GLY* 3.7 12.8 + - - -
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Residues in contact with ILE 142 (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* 4.8 10.3 - - + -
80D THR* 3.4 34.1 - - + +
81D ILE* 3.9 14.6 - - + +
84D LEU* 3.5 31.2 - - + -
90D LEU* 4.7 6.1 - - + -
94D LEU* 3.3 31.5 - - + +
138D CYS 3.6 13.9 - - - +
139D VAL* 2.8 17.3 + - + +
141D GLN* 1.3 77.0 - - + +
143D ILE* 1.3 66.5 + - - +
145D GLY 3.6 1.6 + - - -
146D ILE* 3.4 15.4 - - + +
160D HEM 5.2 5.6 - - + -
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Residues in contact with ILE 143 (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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111D PHE* 3.3 41.1 - - + +
112D ASP* 4.8 2.7 - - - +
114D PHE* 4.7 5.4 - - + -
115D LEU* 3.2 49.1 - - + +
139D VAL* 3.0 15.6 + - + +
140D ASP* 2.7 16.0 + - - +
142D ILE* 1.3 68.5 - - - +
144D ASP* 1.3 54.5 + - - +
145D GLY 3.0 1.8 - - - -
146D ILE* 2.6 30.7 + - - +
147D LYS* 2.7 30.4 + - - -
160D HEM 4.2 16.6 - - + -
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Residues in contact with ASP 144 (chain D).
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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98D LYS* 5.0 5.7 + - - -
140D ASP* 3.1 33.9 + - - +
141D GLN* 4.3 7.6 + - - +
143D ILE* 1.3 75.7 - - - +
145D GLY* 1.3 58.0 + - - +
146D ILE 3.0 4.7 + - - -
147D LYS* 3.1 43.4 + - - +
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Residues in contact with GLY 145 (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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94D LEU* 3.5 27.4 - - - +
95D ALA* 4.4 1.4 + - - -
98D LYS* 3.5 22.2 - - - +
141D GLN 3.7 8.5 + - - -
142D ILE 3.6 7.0 + - - -
143D ILE 2.9 2.0 + - - -
144D ASP* 1.3 78.3 - - - +
146D ILE* 1.3 61.1 + - - +
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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