Contacts of the helix formed by residues 150 - 164 (chain A) in PDB entry 3V3E
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 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A GLY* 1.3 67.8 - - - -
151A TRP* 1.3 64.6 + - - +
152A ILE 3.2 3.1 - - - -
153A ASP* 3.0 29.7 + - - +
154A SER* 3.1 16.5 + - - +
237A GLN* 5.4 1.6 - - - +
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Residues in contact with TRP 151 (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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75A PHE* 3.7 29.8 - + - -
79A LEU* 4.5 4.3 - - + -
113A LEU* 4.0 17.0 - - + -
116A PHE* 3.9 16.6 - + - -
117A ILE* 3.8 25.8 - - + +
148A PHE* 3.5 35.6 + + - +
149A GLY 3.3 0.4 - - - -
150A ASP* 1.3 79.3 - - - +
152A ILE* 1.3 56.3 + - - +
154A SER* 3.2 1.2 + - - -
155A ILE* 2.8 53.4 + - + +
234A LEU* 2.9 21.1 + - + +
237A GLN* 3.6 38.6 - - + +
238A GLY* 3.5 27.6 - - - -
241A ARG* 4.4 7.9 - - + -
242A ILE* 5.8 0.4 - - + -
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Residues in contact with ILE 152 (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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120A LEU* 4.3 7.9 - - + -
131A LEU* 3.6 34.8 - - + -
133A PHE* 4.9 0.7 - - + -
141A ARG* 4.1 11.2 - - + +
144A CYS* 3.6 33.7 - - + -
145A ALA* 4.3 1.6 - - - +
148A PHE* 3.7 34.4 - - + +
149A GLY 3.6 14.8 + - - +
150A ASP 3.2 1.0 - - - -
151A TRP* 1.3 75.3 - - - +
153A ASP* 1.3 80.6 + - - +
155A ILE* 3.1 16.5 + - + +
156A LEU* 2.9 24.4 + - - +
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Residues in contact with ASP 153 (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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141A ARG* 3.3 39.0 + - - +
145A ALA* 5.7 3.4 - - - +
149A GLY 4.8 1.1 - - - +
150A ASP* 3.0 23.8 + - - +
152A ILE* 1.3 84.4 - - - +
154A SER* 1.3 60.9 + - - +
156A LEU* 3.3 7.1 + - - +
157A ALA* 3.2 19.9 + - - +
160A ARG* 5.1 1.7 + - - -
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Residues in contact with SER 154 (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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150A ASP* 3.1 11.9 + - - +
151A TRP 3.6 2.9 - - - -
153A ASP* 1.3 77.2 - - - +
155A ILE* 1.3 62.2 + - - +
157A ALA* 3.3 8.6 + - - +
158A PHE* 3.0 22.9 + - - +
234A LEU* 3.3 16.0 - - - +
237A GLN* 3.2 33.6 + - - -
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Residues in contact with ILE 155 (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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116A PHE* 4.7 2.5 - - + -
117A ILE* 4.2 22.9 - - + +
120A LEU* 4.0 34.5 - - + -
121A ALA* 4.2 7.6 - - + +
131A LEU* 4.7 6.5 - - + -
151A TRP* 2.8 62.8 + - + +
152A ILE* 3.1 20.4 + - + +
154A SER* 1.3 76.8 - - - +
156A LEU* 1.3 56.9 + - - +
158A PHE* 3.1 4.5 + - - +
159A SER* 2.8 25.6 + - - -
234A LEU* 4.1 11.2 - - + -
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Residues in contact with LEU 156 (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* 4.3 6.7 - - - -
126A PRO* 3.6 24.9 - - + +
129A GLY* 4.2 11.9 - - - -
130A LYS 4.0 10.1 - - - +
131A LEU* 3.8 41.3 - - + -
141A ARG* 3.8 30.7 - - + -
152A ILE 2.9 13.5 + - - +
153A ASP* 3.3 8.2 + - - +
155A ILE* 1.3 77.0 - - - +
157A ALA* 1.3 61.7 + - - +
159A SER* 3.2 7.3 - - - -
160A ARG* 3.1 42.7 + - - +
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Residues in contact with ALA 157 (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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153A ASP 3.2 11.6 + - - +
154A SER* 3.5 13.0 - - - +
155A ILE 3.3 0.2 - - - -
156A LEU* 1.3 75.6 - - - +
158A PHE* 1.3 58.7 + - - +
160A ARG* 3.2 24.4 + - - +
161A SER* 2.9 27.1 + - - -
230A GLU* 5.5 0.2 - - - -
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Residues in contact with PHE 158 (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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117A ILE* 4.4 4.3 - - + -
118A LEU* 4.0 29.6 - - + -
121A ALA* 3.6 20.0 - - + -
154A SER 3.0 6.5 + - - +
155A ILE 3.6 3.4 - - - +
157A ALA* 1.3 75.2 - - - +
159A SER* 1.3 55.5 + - - +
161A SER* 3.8 5.8 - - - -
162A LEU* 2.6 51.5 + - + +
227A LYS* 4.0 32.5 - - + -
230A GLU* 3.7 25.8 - - + +
231A LEU* 4.1 23.6 - - + -
234A LEU* 3.3 33.4 - - + -
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Residues in contact with SER 159 (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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121A ALA* 2.6 38.8 + - - +
124A SER* 3.9 3.9 + - - -
126A PRO* 3.1 25.9 - - - +
155A ILE 2.8 13.4 + - - -
156A LEU* 3.2 21.5 - - - -
158A PHE* 1.3 76.0 - - - +
160A ARG* 1.4 49.0 + - - -
162A LEU* 3.2 1.7 + - - +
163A HIS* 2.8 43.3 + - - -
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Residues in contact with ARG 160 (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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126A PRO* 3.1 48.6 + - + +
127A GLY* 4.9 1.0 - - - +
129A GLY* 5.7 0.4 - - - -
141A ARG* 6.3 0.4 - - - +
153A ASP 5.1 1.4 + - - -
156A LEU* 3.1 24.0 + - - +
157A ALA* 3.2 33.0 + - - +
159A SER* 1.4 73.1 - - - +
161A SER* 1.3 64.9 + - - +
163A HIS* 3.1 5.7 + - - +
164A SER* 2.9 27.1 + - - -
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Residues in contact with SER 161 (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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157A ALA 2.9 17.8 + - - -
158A PHE* 3.1 7.9 + - - -
160A ARG* 1.3 74.9 - - - +
162A LEU* 1.3 60.6 + - - +
164A SER* 2.9 24.7 + - - -
165A LEU* 4.0 1.7 + - - +
227A LYS* 3.2 34.3 + - - +
230A GLU* 2.8 28.5 + - - -
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Residues in contact with LEU 162 (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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118A LEU* 3.9 24.2 - - + +
121A ALA* 4.2 5.8 - - + -
122A TYR* 3.9 47.2 - - + +
158A PHE* 2.6 35.1 + - + +
159A SER* 3.6 4.5 - - - +
161A SER* 1.3 75.5 + - - +
163A HIS* 1.3 63.2 + - - +
165A LEU* 3.2 21.6 + - + +
166A LEU 4.0 1.9 + - - -
167A VAL* 4.2 25.5 + - + +
172A PHE* 4.4 4.0 - - + -
224A LEU* 5.7 5.2 - - + -
227A LYS* 5.0 6.1 - - + -
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Residues in contact with HIS 163 (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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121A ALA 3.2 12.3 - - - -
122A TYR* 2.9 41.7 - + - -
124A SER 3.0 21.2 + - - -
125A LYS* 4.1 6.9 + - + -
126A PRO* 3.8 16.4 - - + -
159A SER* 2.8 30.1 + - - +
160A ARG* 3.1 5.1 + - - +
162A LEU* 1.3 76.2 - - - +
164A SER* 1.3 56.4 + - - +
165A LEU 3.1 0.2 - - - -
166A LEU* 3.0 31.7 + - - +
167A VAL 5.9 0.2 - - - +
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Residues in contact with SER 164 (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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160A ARG 2.9 16.5 + - - -
161A SER* 2.9 15.8 + - - -
162A LEU 3.1 0.2 - - - -
163A HIS* 1.3 76.3 - - - +
165A LEU* 1.3 65.6 + - - +
166A LEU* 3.4 10.9 - - - +
227A LYS* 4.0 10.7 + - - -
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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
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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