Contacts of the helix formed by residues 125 - 139 (chain B) in PDB entry 3U7X
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 125 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B LEU* 4.7 1.6 - - + -
121B GLN* 2.8 40.3 + - + +
123B ARG 3.6 0.4 - - - -
124B SER* 1.3 100.8 + - - +
126B LEU* 1.3 64.9 + - - +
127B ASP 3.4 2.0 - - - -
128B ARG* 3.4 22.0 + - - +
129B PHE* 2.9 57.0 + - + +
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B SER* 3.9 15.3 - - - +
83B SER* 3.7 32.8 - - - +
117B LEU* 3.8 23.6 - - + -
121B GLN 3.0 6.4 + - - +
122B ARG* 3.5 25.3 + - + +
125B ASP* 1.3 75.7 - - - +
127B ASP* 1.3 58.2 + - - +
129B PHE* 3.7 1.6 - - - +
130B TRP* 2.9 31.9 + - - +
154B VAL* 3.6 25.4 - - + -
156B VAL* 4.5 4.7 - - + -
161B ASP* 3.7 30.7 - - + +
163B ILE* 3.8 9.1 - - + +
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Residues in contact with ASP 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TYR* 4.6 3.7 + - - +
81B LEU* 3.9 30.6 - - + +
82B SER* 3.5 11.2 + - - -
83B SER* 2.5 52.2 + - - -
122B ARG 4.7 2.5 + - - +
123B ARG 5.6 1.2 - - - +
125B ASP 3.4 0.2 - - - -
126B LEU* 1.3 76.6 - - - +
128B ARG* 1.3 57.6 + - - +
130B TRP* 3.8 5.8 - - - +
131B LEU* 2.9 30.7 + - - +
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Residues in contact with ARG 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B SER 3.4 25.3 + - - +
125B ASP* 3.4 20.7 + - - +
126B LEU 3.4 0.4 - - - -
127B ASP* 1.3 78.8 - - - +
129B PHE* 1.3 74.2 + - + +
131B LEU* 3.4 6.6 + - - +
132B GLU* 3.0 32.8 + - + +
187B LEU 5.0 6.1 + - - -
56D ARG* 6.1 3.6 - - - +
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Residues in contact with PHE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ILE* 4.2 14.4 - - + -
117B LEU* 4.0 24.7 - - + -
125B ASP* 2.9 47.1 + - + +
128B ARG* 1.3 96.1 - - + +
130B TRP* 1.3 52.7 + - - +
132B GLU* 3.4 2.5 + - + +
133B THR* 2.6 38.4 + - - +
163B ILE* 3.5 14.1 - - + -
187B LEU* 3.5 43.8 - - + +
188B GLY 5.7 0.4 - - - -
189B LEU* 3.4 30.7 - - + -
227B UNX 4.4 2.5 - - - -
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Residues in contact with TRP 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 4.8 4.5 - - + +
76B TYR* 5.0 7.4 - + - -
79B ILE* 6.3 0.8 - - - +
82B SER* 3.4 25.7 + - - +
91B TYR* 3.9 24.7 - + + -
93B LEU* 4.3 6.3 - - + -
126B LEU 2.9 18.8 + - - +
127B ASP* 3.9 4.3 - - - +
129B PHE* 1.3 73.2 - - - +
131B LEU* 1.3 66.2 + - - +
133B THR* 3.3 7.1 + - + -
134B LEU* 3.0 58.8 + - + +
152B ALA* 3.7 39.5 - - + -
153B VAL 3.7 6.7 - - - -
154B VAL* 3.6 42.5 - - + +
163B ILE* 3.7 18.1 - - + +
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE* 4.1 15.7 - - + -
73B TRP* 3.9 25.4 - - + -
76B TYR* 3.9 37.4 + - + +
127B ASP 2.9 19.1 + - - +
128B ARG* 3.9 6.1 - - - +
130B TRP* 1.3 75.8 - - - +
132B GLU* 1.3 57.4 + - - +
134B LEU* 3.3 6.0 + - + +
135B LEU* 3.0 44.1 + - + +
60D MET* 3.9 26.0 - - + -
63D ARG* 6.3 1.3 - - - -
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ARG* 3.0 22.1 + - + +
129B PHE* 3.6 6.3 - - + +
131B LEU* 1.3 77.6 - - - +
133B THR* 1.3 55.7 + - - +
135B LEU* 3.3 6.9 + - - +
136B CYS* 2.9 34.0 + - - -
186B ARG* 2.9 71.4 + - + +
187B LEU* 4.3 9.9 - - + +
56D ARG* 3.1 34.1 + - - +
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Residues in contact with THR 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B PHE 2.6 23.9 + - - -
130B TRP* 3.4 16.4 - - + -
132B GLU* 1.3 71.6 - - - +
134B LEU* 1.3 65.0 + - - +
136B CYS* 3.2 5.1 + - - +
137B LEU* 3.1 27.0 + - + +
152B ALA* 3.5 31.0 - - + -
163B ILE* 3.7 5.2 - - + +
165B ILE* 3.8 13.2 - - + -
183B TYR* 2.8 39.8 + - - +
187B LEU* 4.2 0.3 - - - +
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 5.0 5.4 - - + -
72B PHE* 3.9 31.9 - - + -
76B TYR* 3.9 21.1 - - + -
93B LEU* 3.7 31.6 - - + -
130B TRP* 3.0 62.3 + - + +
131B LEU* 3.5 8.3 - - - +
133B THR* 1.3 74.7 - - - +
135B LEU* 1.3 58.4 + - - +
137B LEU* 3.3 6.9 + - + +
138B ILE* 3.0 35.5 + - - +
152B ALA* 5.6 0.2 - - + -
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE* 4.0 26.5 - - + -
73B TRP* 4.1 7.2 - - + -
131B LEU* 3.0 28.3 + - + +
132B GLU* 3.6 16.8 - - - +
134B LEU* 1.3 74.1 - - - +
136B CYS* 1.3 61.7 - - - +
138B ILE* 4.2 5.2 - - + -
139B GLY* 2.9 28.9 + - - -
141B SER* 3.9 2.3 + - - -
186B ARG* 4.3 5.5 + - - +
56D ARG* 3.9 26.0 - - + +
59D LEU* 3.7 36.2 - - + +
60D MET* 4.0 22.7 - - + -
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Residues in contact with CYS 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B GLU 2.9 19.0 + - - -
133B THR* 3.5 10.3 - - - +
135B LEU* 1.3 75.9 - - - +
137B LEU* 1.3 63.0 + - + +
140B GLU* 3.2 2.4 + - - -
141B SER* 3.0 38.3 + - - +
142B PHE* 3.8 30.8 - - + -
146B SER* 4.8 0.2 + - - -
165B ILE* 4.9 1.6 - - + -
183B TYR* 4.5 9.4 - - - -
186B ARG* 3.8 43.0 - - - +
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B TRP* 3.2 43.5 - - + -
93B LEU* 3.8 16.6 - - + +
133B THR* 3.1 19.8 + - + +
134B LEU* 3.6 9.0 - - - +
135B LEU 3.3 0.2 - - - -
136B CYS* 1.3 74.4 - - - +
138B ILE* 1.3 65.6 + - - +
140B GLU* 3.1 17.7 + - - +
142B PHE* 4.6 3.6 - - + -
149B VAL* 4.0 16.2 - - + -
151B GLY 3.7 5.6 - - - -
152B ALA* 3.6 35.0 - - + +
165B ILE* 3.9 30.5 - - + -
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Residues in contact with ILE 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 3.7 39.6 - - + +
40B GLN 4.8 2.3 + - - -
43B TRP* 3.7 14.8 + - - +
66B PHE* 3.9 17.3 - - + -
69B VAL* 5.3 1.3 - - + -
72B PHE* 3.5 46.9 - - + -
93B LEU* 3.8 23.3 - - + -
134B LEU 3.0 17.4 + - - +
135B LEU* 4.1 13.9 - - + +
137B LEU* 1.3 74.4 - - - +
139B GLY* 1.3 61.2 + - - +
140B GLU* 3.5 9.2 + - - +
52D ILE 4.8 0.3 - - - +
54D TYR* 4.7 2.6 - - - -
59D LEU* 4.3 13.5 - - + -
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Residues in contact with GLY 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B LEU 2.9 19.4 + - - -
136B CYS 4.0 0.2 - - - -
138B ILE* 1.3 78.7 - - - +
140B GLU* 1.3 71.6 + - - +
141B SER* 3.4 3.3 + - - -
52D ILE 4.5 0.2 - - - -
53D ILE* 3.4 3.7 - - - +
54D TYR* 3.1 44.5 + - - +
59D LEU* 4.2 6.7 - - - -
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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
------------------------------------------------------------
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