Contacts of the helix formed by residues 120 - 137 (chain B) in PDB entry 4OE4
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 PRO 120 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118B ASN 3.3 7.6 - - - +
119B LEU* 1.3 95.9 - - + +
121B PHE* 1.3 60.4 + - - +
122B TYR* 3.1 7.6 - - + +
123B ASP* 2.8 44.6 + - - +
124B ARG* 3.0 9.9 + - - +
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Residues in contact with PHE 121 (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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119B LEU 3.5 1.8 + - - -
120B PRO* 1.3 72.5 - - - +
122B TYR* 1.3 65.1 + - + +
124B ARG* 3.7 20.7 - - - +
125B SER* 2.8 51.1 + - - -
174B VAL* 3.4 25.4 - - + -
177B ALA* 3.5 19.5 - - + -
178B SER* 3.5 33.0 - - - -
181B TYR* 3.4 34.5 - + + -
226B LEU* 4.2 14.8 - - + -
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Residues in contact with TYR 122 (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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120B PRO* 3.0 5.5 + - + +
121B PHE* 1.3 84.8 - - + +
123B ASP* 1.3 77.3 + - - +
125B SER* 3.6 5.2 + - - -
126B ALA* 3.1 29.8 + - + +
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Residues in contact with ASP 123 (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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119B LEU* 3.8 23.6 - - + -
120B PRO* 2.8 35.5 + - - +
122B TYR* 1.3 93.1 - - - +
124B ARG* 1.3 65.2 + - - +
125B SER 3.2 0.2 - - - -
126B ALA* 3.1 18.2 + - - +
127B ILE* 3.3 16.1 + - - +
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Residues in contact with ARG 124 (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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116B TRP* 3.4 61.4 + - + +
117B TYR* 3.7 16.2 + - - +
119B LEU* 2.8 41.4 + - + +
120B PRO* 3.0 3.3 + - - +
121B PHE* 3.7 20.1 - - + +
123B ASP* 1.3 75.1 - - - +
125B SER* 1.3 63.6 + - - +
127B ILE* 3.4 7.9 + - - +
128B PHE* 3.2 22.2 - - - -
181B TYR* 2.9 38.4 + - - -
226B LEU* 2.9 33.7 + - + +
227B MET 3.8 4.0 + - - -
228B GLY* 3.8 9.5 - - - +
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Residues in contact with SER 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B PHE* 2.8 54.7 + - - -
122B TYR* 3.7 6.7 - - - -
124B ARG* 1.3 75.5 - - - +
126B ALA* 1.3 65.2 + - - +
128B PHE* 3.0 4.5 + - - +
129B LEU* 2.9 29.8 + - - +
174B VAL* 3.7 23.5 - - - +
226B LEU* 3.8 10.4 - - - +
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Residues in contact with ALA 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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122B TYR* 3.1 23.6 + - + +
123B ASP* 3.1 13.8 + - - +
125B SER* 1.3 76.4 - - - +
127B ILE* 1.3 58.5 + - + +
129B LEU* 4.1 8.4 - - - +
130B LYS* 2.8 33.7 + - - +
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Residues in contact with ILE 127 (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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116B TRP* 3.8 17.0 - - + -
119B LEU* 4.4 7.6 - - + -
123B ASP 3.3 13.6 + - - +
124B ARG 3.5 5.6 - - - +
126B ALA* 1.3 78.1 - - + +
128B PHE* 1.3 64.1 + - + +
131B ALA* 3.0 23.6 + - - +
250B LEU* 4.1 13.7 - - + +
253B ALA* 3.3 27.4 - - - +
254B GLY 3.5 19.3 - - - +
255B LEU* 3.8 30.1 - - + +
256B PRO* 3.8 17.3 - - + -
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Residues in contact with PHE 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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116B TRP* 4.1 22.2 - + - -
124B ARG 3.2 23.1 - - - -
125B SER 3.0 6.2 + - - +
127B ILE* 1.3 78.8 - - + +
129B LEU* 1.3 61.6 + - - +
131B ALA* 3.3 2.1 + - - +
132B ALA* 3.0 23.7 + - - +
170B PHE* 3.2 49.7 - + + -
174B VAL* 4.8 4.3 - - + -
221B ILE* 5.4 0.4 - - + -
222B GLY* 3.8 20.4 - - - -
225B ALA* 3.8 24.2 - - + -
226B LEU* 3.8 23.6 - - + -
250B LEU* 3.7 23.6 - - + -
255B LEU* 4.6 5.6 - - + -
260B ILE* 4.3 11.7 - - + -
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Residues in contact with LEU 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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125B SER* 2.9 22.2 + - - +
126B ALA* 4.1 6.3 - - - +
128B PHE* 1.3 73.6 - - - +
130B LYS* 1.3 65.6 + - - +
132B ALA* 3.3 4.6 + - - +
133B ASP* 2.9 32.3 + - - +
170B PHE 4.4 0.2 - - - +
171B ARG* 3.8 41.1 - - + +
174B VAL* 4.0 29.6 - - + -
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Residues in contact with LYS 130 (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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126B ALA 2.8 21.2 + - - +
127B ILE* 3.8 4.7 - - - +
129B LEU* 1.3 76.2 - - - +
131B ALA* 1.3 57.5 + - - +
133B ASP* 3.3 5.4 + - + -
134B LEU* 2.9 56.6 + - + +
252B GLU 5.3 2.2 + - - -
253B ALA* 3.6 27.3 + - + +
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Residues in contact with ALA 131 (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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127B ILE 3.0 18.6 + - - +
128B PHE 3.5 5.6 - - - +
129B LEU 3.2 0.4 - - - -
130B LYS* 1.3 74.2 - - - +
132B ALA* 1.3 65.2 + - - +
134B LEU* 3.2 3.0 + - - +
135B ILE* 2.9 31.9 + - + +
170B PHE* 4.2 6.7 - - + -
246B LEU* 5.7 0.2 - - + -
249B VAL* 3.9 20.4 - - + -
250B LEU* 3.7 25.8 - - + -
253B ALA* 3.8 6.9 - - + +
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Residues in contact with ALA 132 (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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128B PHE 3.0 16.3 + - - +
129B LEU* 3.7 7.0 - - - +
131B ALA* 1.3 76.8 - - - +
133B ASP* 1.3 58.5 + - - +
135B ILE* 3.3 4.9 + - - +
136B SER* 2.9 31.1 + - - -
166B LEU* 4.7 2.9 - - - -
167B SER* 3.2 36.0 + - - +
170B PHE* 4.1 15.8 - - + -
171B ARG* 4.0 9.0 - - + +
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Residues in contact with ASP 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 LEU* 2.9 29.8 + - - +
130B LYS* 4.1 5.6 - - + +
132B ALA* 1.3 74.7 - - - +
134B LEU* 1.3 58.8 + - - +
136B SER* 3.4 3.3 + - - -
137B THR* 2.7 40.7 + - + +
171B ARG* 2.9 35.6 + - - +
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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
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130B LYS* 2.9 55.5 + - + +
131B ALA 3.2 3.8 + - - +
133B ASP* 1.3 73.8 - - - +
135B ILE* 1.3 64.6 + - - +
137B THR* 3.8 4.7 - - - +
138B LYS* 3.1 32.2 + - + -
139B TYR* 2.8 35.1 + - + -
249B VAL* 4.2 14.6 - - + -
252B GLU* 3.9 26.5 - - + +
253B ALA* 4.3 12.6 - - + +
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Residues in contact with ILE 135 (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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131B ALA* 2.9 20.4 + - + +
132B ALA* 3.7 5.2 - - - +
134B LEU* 1.3 76.9 - - - +
136B SER* 1.3 57.9 + - - +
139B TYR* 4.5 7.9 - - + -
140B ARG* 3.1 27.4 - - - -
143B MET* 4.1 20.0 - - + -
162B CYS 3.3 24.7 - - - +
163B ILE* 3.5 13.6 - - + +
166B LEU* 3.6 30.3 - - + -
167B SER* 5.0 1.3 - - - +
246B LEU* 4.0 20.6 - - + -
249B VAL* 3.8 25.4 - - + -
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Residues in contact with SER 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 ALA 2.9 18.6 + - - -
133B ASP* 3.9 8.5 - - - -
134B LEU 3.2 0.4 - - - -
135B ILE* 1.3 77.4 - - - +
137B THR* 1.3 64.8 + - - +
140B ARG* 2.8 32.1 + - - +
163B ILE* 3.9 18.0 - - - +
167B SER* 2.9 17.3 + - - -
171B ARG* 3.8 10.2 + - - -
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Residues in contact with THR 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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133B ASP* 2.7 26.7 + - + +
134B LEU* 3.7 4.9 + - - +
135B ILE 3.2 0.6 - - - -
136B SER* 1.3 86.1 - - - +
138B LYS* 1.3 78.8 + - - +
139B TYR 2.9 3.3 + - - -
140B ARG* 2.9 16.9 + - - +
141B TYR* 5.2 4.5 - - - -
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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