Contacts of the helix formed by residues 126 - 138 (chain A) in PDB entry 5T46
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 LEU 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A SER* 4.0 15.9 - - - +
83A SER* 3.9 28.5 - - - +
117A LEU* 3.8 12.3 - - + -
121A GLN 3.1 5.3 + - - -
122A ARG* 3.4 24.9 + - + +
125A ASP* 1.3 76.1 - - - +
127A ASP* 1.3 58.6 + - - +
129A PHE* 3.8 1.5 - - - +
130A TRP* 2.9 28.9 + - - +
154A VAL* 3.8 14.6 - - + -
156A VAL* 4.3 7.4 - - + -
161A ASP* 3.6 38.4 - - + +
163A ILE* 3.8 21.1 - - + -
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Residues in contact with ASP 127 (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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76A TYR* 4.6 4.3 + - - +
81A LEU* 3.7 31.7 - - + +
82A SER* 3.3 11.8 + - - -
83A SER* 2.5 51.0 + - - -
122A ARG 4.5 1.2 + - - +
123A ARG 5.6 1.6 - - - +
125A ASP 3.4 0.4 - - - -
126A LEU* 1.3 76.3 - - - +
128A ARG* 1.3 57.4 + - - +
130A TRP* 3.5 6.5 + - - +
131A LEU* 3.0 31.0 + - - +
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Residues in contact with ARG 128 (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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124A SER 2.9 19.3 + - - +
125A ASP* 2.6 36.0 + - - +
126A LEU 3.3 0.4 - - - -
127A ASP* 1.3 79.8 - - - +
129A PHE* 1.3 80.6 + - - +
131A LEU* 3.9 4.8 - - - +
132A GLU* 3.0 29.2 + - - +
187A LEU 5.0 0.2 + - - -
188A GLY 5.4 2.4 + - - -
190A PRO* 6.0 1.0 - - - +
302A GOL 3.2 33.5 + - - +
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Residues in contact with PHE 129 (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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115A ILE* 3.8 15.0 - - + -
117A LEU* 4.2 10.3 - - + -
125A ASP* 2.9 36.8 + - + +
128A ARG* 1.3 104.5 - - - +
130A TRP* 1.3 59.4 + - - +
132A GLU* 3.4 1.1 + - - -
133A THR* 2.8 32.4 + - - -
163A ILE* 3.5 16.2 - - + -
187A LEU* 3.4 41.0 - - + +
188A GLY 4.8 0.9 - - - -
189A LEU* 3.8 20.2 - - + -
190A PRO* 4.6 8.5 - - + -
193A ILE* 3.9 23.1 - - + -
302A GOL 3.5 10.8 - - - -
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Residues in contact with TRP 130 (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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45A LEU* 4.8 4.3 - - + +
76A TYR* 5.1 7.4 - + - -
82A SER* 3.4 24.2 + - - +
91A TYR* 3.9 23.5 - + + +
92A SER 4.6 0.7 - - - -
93A LEU* 4.2 6.7 - - + -
126A LEU 2.9 18.1 + - - +
127A ASP* 3.9 5.2 - - - +
129A PHE* 1.3 74.5 - - - +
131A LEU* 1.3 66.8 + - - +
133A THR* 3.0 9.6 + - + -
134A LEU* 2.9 57.5 + - + +
152A ALA* 3.6 35.7 - - + -
153A VAL 3.6 23.8 - - - -
154A VAL* 3.5 30.4 - - + +
163A ILE* 3.7 19.0 - - + +
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Residues in contact with LEU 131 (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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72A PHE* 4.1 9.0 - - + -
73A TRP* 3.9 31.9 - - + -
76A TYR* 3.9 36.1 - - + +
127A ASP 3.0 18.0 + - - +
128A ARG* 3.9 5.2 - - - +
130A TRP* 1.3 77.5 - - - +
132A GLU* 1.3 64.7 + - - +
134A LEU* 3.1 7.7 + - + +
135A LEU* 2.9 42.5 + - + +
618B LEU* 4.5 11.2 - - + -
621B GLN* 5.3 2.7 - - - +
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Residues in contact with GLU 132 (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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128A ARG* 3.0 18.6 + - - +
129A PHE 3.7 4.9 - - - +
131A LEU* 1.3 78.2 - - - +
133A THR* 1.3 63.0 + - - +
135A LEU* 3.3 9.5 + - - +
136A CYS* 3.0 24.6 + - - -
186A ARG* 3.1 55.0 + - + +
187A LEU* 4.4 7.0 - - + +
302A GOL 2.2 37.9 + - - +
614B ARG* 2.9 31.6 + - - +
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Residues in contact with THR 133 (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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129A PHE 2.8 18.8 + - - -
130A TRP* 3.0 19.0 + - + -
132A GLU* 1.3 73.2 - - - +
134A LEU* 1.3 65.6 + - - +
136A CYS* 3.2 4.2 + - - +
137A LEU* 3.1 23.5 + - + +
152A ALA* 3.5 31.4 - - + -
163A ILE* 3.6 6.2 - - + +
165A ILE* 3.8 12.1 - - + -
183A TYR* 2.7 40.4 + - + +
187A LEU* 4.0 0.7 - - - +
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Residues in contact with LEU 134 (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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45A LEU* 5.2 4.5 - - + -
72A PHE* 3.9 31.6 - - + -
76A TYR* 4.0 18.8 - - + -
93A LEU* 3.8 32.8 - - + -
130A TRP* 2.9 62.2 + - + +
131A LEU* 3.5 7.4 - - - +
133A THR* 1.3 75.4 - - - +
135A LEU* 1.3 57.8 + - - +
137A LEU* 3.2 7.3 + - + +
138A ILE* 2.9 34.1 + - - +
152A ALA* 5.8 0.2 - - + -
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Residues in contact with LEU 135 (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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72A PHE* 4.1 16.4 - - + -
73A TRP* 4.0 22.9 - - + -
131A LEU* 2.9 29.5 + - + +
132A GLU* 3.7 17.3 - - - +
134A LEU* 1.3 72.8 - - - +
136A CYS* 1.3 60.7 + - - +
138A ILE* 4.1 5.4 - - + -
139A GLY* 2.9 28.8 + - - -
141A SER* 3.9 2.3 + - - -
186A ARG* 4.0 11.7 + - - +
614B ARG* 4.2 18.4 - - + +
617B LEU* 3.8 23.2 - - + +
618B LEU* 4.2 28.7 - - + -
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Residues in contact with CYS 136 (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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132A GLU* 3.0 19.8 + - - -
133A THR* 3.2 9.6 + - - +
135A LEU* 1.3 76.9 - - - +
137A LEU* 1.3 66.2 + - + +
140A GLU* 3.3 1.6 + - - -
141A SER* 3.1 34.6 + - - +
142A PHE* 3.8 33.0 - - + -
146A SER* 4.8 0.2 + - - -
165A ILE* 4.8 1.3 - - + -
183A TYR* 4.5 9.6 - - - -
186A ARG* 3.8 44.0 - - - -
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Residues in contact with LEU 137 (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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43A TRP* 3.4 38.6 - - + -
93A LEU* 3.7 23.1 - - + +
133A THR* 3.1 18.1 + - + +
134A LEU* 3.2 8.9 + - + +
136A CYS* 1.3 77.8 - - - +
138A ILE* 1.3 64.1 - - - +
140A GLU* 3.1 17.5 + - - +
142A PHE* 4.6 3.1 - - + -
146A SER* 5.3 0.2 + - - -
149A VAL* 4.0 18.2 - - + -
151A GLY 3.7 4.7 - - - -
152A ALA* 3.7 33.9 - - + +
165A ILE* 3.9 30.1 - - + -
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Residues in contact with ILE 138 (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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39A LEU* 3.6 33.5 - - + +
40A GLN 4.9 1.0 + - - -
43A TRP* 3.9 18.1 + - + +
66A PHE* 3.9 24.9 - - + -
69A VAL* 5.4 1.3 - - - -
72A PHE* 3.5 43.5 - - + -
93A LEU* 4.0 14.4 - - + -
134A LEU 2.9 24.3 + - - +
135A LEU* 4.0 13.9 - - + +
137A LEU* 1.3 72.8 - - - +
139A GLY* 1.3 63.0 + - - +
140A GLU* 3.5 8.8 + - - +
612B TYR* 4.6 2.4 - - - -
617B LEU* 4.1 17.5 - - + -
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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