Contacts of the helix formed by residues 147 - 161 (chain A) in PDB entry 5XVO
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 ARG 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A ILE* 4.6 2.2 - - + -
135A MET* 3.9 26.9 - - + +
138A GLU* 3.1 61.1 + - - +
139A LEU* 3.9 12.3 - - + -
140A ARG 5.7 0.4 - - - +
143A ASP* 2.9 12.7 + - - +
145A ALA* 2.3 44.8 + - + +
146A ASN* 1.3 75.2 + - - +
148A GLU* 1.3 60.1 + - - +
149A GLY 3.2 1.6 - - - -
150A HIS* 3.7 19.7 + - - +
151A ALA* 2.8 33.9 + - - +
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Residues in contact with GLU 148 (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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105A TRP* 4.0 20.5 - - - -
109A ILE* 3.4 29.4 - - + +
112A LYS* 3.4 27.4 + - - +
113A ILE* 4.1 13.5 - - - +
116A GLN* 4.8 1.7 - - - +
139A LEU* 4.7 0.6 - - + +
143A ASP* 2.9 15.9 + - + +
146A ASN* 5.0 2.5 + - - +
147A ARG* 1.3 79.2 - - - +
149A GLY* 1.3 58.5 + - - +
151A ALA* 3.5 2.8 - - - +
152A ALA* 2.9 28.0 + - + +
203A LYS* 5.4 1.7 + - - -
219A GLU* 3.4 15.1 - - - +
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Residues in contact with GLY 149 (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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146A ASN* 2.9 27.8 - - - +
148A GLU* 1.3 80.6 - - - +
150A HIS* 1.3 61.6 + - - +
152A ALA* 3.8 6.3 - - - +
153A ARG* 3.1 32.9 + - - +
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Residues in contact with HIS 150 (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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135A MET* 4.1 13.8 - - + +
146A ASN* 3.1 33.3 + - + +
147A ARG* 3.4 25.7 + - - +
149A GLY* 1.3 75.3 - - - +
151A ALA* 1.3 64.5 + - - +
153A ARG* 3.4 31.5 + - - +
154A SER* 3.1 24.1 + - - -
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Residues in contact with ALA 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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113A ILE* 4.3 17.0 - - + -
116A GLN* 4.3 10.5 - - - +
132A LEU* 4.1 18.1 - - + +
135A MET* 3.6 20.1 - - + -
147A ARG 2.8 18.8 + - - +
148A GLU 3.5 5.2 - - - +
150A HIS* 1.3 79.7 - - - +
152A ALA* 1.3 57.0 + - - +
154A SER* 3.4 2.8 + - - -
155A TYR* 2.9 31.0 + - - +
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Residues in contact with ALA 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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112A LYS* 4.7 9.9 - - - +
116A GLN* 4.2 17.9 + - - +
148A GLU* 2.9 17.7 + - + +
149A GLY* 3.8 7.6 - - - +
150A HIS 3.3 0.2 - - - -
151A ALA* 1.3 73.7 - - - +
153A ARG* 1.3 66.2 + - - +
155A TYR* 3.3 6.4 + - - +
156A PHE* 2.9 41.7 + - + -
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Residues in contact with ARG 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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149A GLY 3.1 20.4 + - - +
150A HIS* 3.4 33.1 + - - +
152A ALA* 1.3 77.0 - - - +
154A SER* 1.3 57.8 + - - +
156A PHE* 3.5 4.0 + - - +
157A ASN* 3.0 51.9 + - - +
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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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120A LEU* 5.8 0.2 - - - +
128A LYS* 4.2 18.9 + - - +
131A ALA* 5.6 1.9 - - - +
132A LEU* 4.0 15.3 - - - +
135A MET* 4.5 12.2 - - - +
150A HIS 3.1 14.3 + - - -
151A ALA 3.6 4.9 - - - -
153A ARG* 1.3 77.4 - - - +
155A TYR* 1.3 66.5 + - - +
157A ASN* 3.1 6.3 + - - +
158A THR* 2.9 29.8 + - - +
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Residues in contact with TYR 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 GLN* 3.2 62.4 - - + +
119A HIS* 2.8 29.0 + - - +
120A LEU* 3.8 19.4 - - + +
132A LEU* 4.2 5.8 - - + +
151A ALA 2.9 19.5 + - - +
152A ALA* 3.4 4.9 - - - +
154A SER* 1.3 76.0 + - - +
156A PHE* 1.3 90.4 + + - +
158A THR* 3.1 9.1 + - - -
159A LEU* 3.1 39.5 + - + +
223A PRO* 4.2 3.5 - - - +
226A ASP* 2.8 34.0 + - - +
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Residues in contact with PHE 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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116A GLN* 4.9 3.8 - - - -
152A ALA* 2.9 39.2 + - + +
153A ARG* 4.1 4.3 - - - +
155A TYR* 1.3 97.9 - + - +
157A ASN* 1.3 62.5 + - - +
159A LEU* 4.5 1.6 - - + -
160A PHE* 2.9 56.8 + + - +
164A PHE* 3.8 22.0 - + + -
166A ARG* 3.9 27.6 - - + -
176A LEU* 3.8 19.3 - - + -
180A TYR* 3.7 22.2 - - - -
226A ASP* 4.4 6.1 - - - -
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Residues in contact with ASN 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 ARG* 3.0 38.7 + - - +
154A SER* 3.1 6.5 + - - +
156A PHE* 1.3 76.9 - - - +
158A THR* 1.3 62.9 + - + +
161A GLY* 2.6 43.0 + - - +
162A ASN* 3.3 31.6 + - + +
164A PHE* 3.0 24.8 - - - +
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Residues in contact with THR 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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120A LEU* 3.5 18.5 - - - +
125A TYR* 3.5 33.3 + - + -
128A LYS* 2.7 50.9 - - + +
154A SER* 2.9 21.0 + - - +
155A TYR* 3.1 10.0 + - - -
157A ASN* 1.3 83.5 - - + +
159A LEU* 1.3 59.0 + - - +
161A GLY 4.4 1.2 + - - -
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Residues in contact with LEU 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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119A HIS* 3.7 19.5 - - + +
120A LEU* 3.8 20.2 - - + -
123A ARG* 4.2 15.7 - - + -
125A TYR* 4.6 6.9 + - + -
155A TYR* 3.1 52.2 + - + +
156A PHE* 3.9 0.7 - - + +
157A ASN 3.3 0.2 - - - -
158A THR* 1.3 79.2 - - - +
160A PHE* 1.3 86.9 + - + +
161A GLY 3.6 0.2 - - - -
226A ASP* 5.1 2.7 - - + -
230A TYR* 3.4 43.4 + - + -
233A ARG* 4.6 3.1 - - - -
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Residues in contact with PHE 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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156A PHE* 2.9 39.0 + + - +
159A LEU* 1.3 90.6 - - + +
161A GLY* 1.3 62.7 + - - +
163A ASP* 5.3 2.3 - - - +
164A PHE* 3.5 42.5 + + + +
172A ILE* 3.7 42.4 - - + -
176A LEU* 4.6 1.3 - - + -
226A ASP* 5.1 1.8 - - + -
229A ILE* 4.3 15.3 - - + -
230A TYR* 4.2 18.8 - + + -
233A ARG* 3.8 31.2 - - + +
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Residues in contact with GLY 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 ASN* 2.6 30.1 + - - +
158A THR 4.4 1.4 + - - -
159A LEU 3.6 1.4 - - - -
160A PHE* 1.3 75.1 - - - +
162A ASN* 1.3 61.9 + - - -
163A ASP* 3.1 8.7 - - - -
164A PHE* 3.2 15.9 + - - +
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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