Contacts of the helix formed by residues 151 - 163 (chain A) in PDB entry 3VWJ
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 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A VAL 5.1 0.2 - - - +
148A LEU* 3.6 11.7 + - - +
149A ASN 3.5 0.2 - - - -
150A GLN* 1.3 74.7 - - - +
152A LYS* 1.3 63.6 + - - +
153A TRP 3.6 1.2 + - - -
154A THR* 3.0 31.4 + - - +
155A ARG* 3.2 26.6 + - - +
303A DB3 2.2 54.7 + - - -
95C ARG* 4.8 0.7 - - - -
96C GLY* 3.6 17.6 + - - -
97C SER* 3.9 10.7 + - - +
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Residues in contact with LYS 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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150A GLN 2.9 10.2 + - - +
151A ASP* 1.3 70.7 + - - +
153A TRP* 1.3 67.9 + - - +
155A ARG* 3.2 32.8 + - - +
156A GLU* 3.2 38.5 + - + +
96C GLY* 4.6 2.2 + - - -
101D GLY* 5.3 15.6 - - - +
102D LEU* 6.5 0.7 - - + -
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Residues in contact with TRP 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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69A ILE* 6.2 4.5 - - + -
151A ASP* 3.5 1.0 + - - -
152A LYS* 1.3 80.5 - - - +
154A THR* 1.3 59.7 + - - +
156A GLU* 3.6 6.6 + - + +
157A THR* 2.2 73.7 + - + -
160A TRP* 6.4 0.4 - + - -
303A DB3 3.5 72.2 - - + +
30C SER* 5.9 0.4 - - - +
51C PHE* 4.3 30.0 - + - -
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Residues in contact with THR 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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131A TRP* 5.3 9.4 - - + +
148A LEU 5.9 0.7 - - - +
151A ASP* 3.0 34.2 + - + -
152A LYS 3.3 0.6 - - - -
153A TRP* 1.3 82.8 - - - +
155A ARG* 1.3 65.0 + - + +
157A THR* 3.2 6.0 + - - -
158A VAL* 3.0 30.4 + - + +
303A DB3 3.4 60.6 + - + +
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Residues in contact with ARG 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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126A PHE* 3.4 27.7 - - + -
129A THR* 3.0 22.0 + - - +
130A SER* 2.3 40.6 + - - -
131A TRP* 4.5 11.4 - - + +
148A LEU 4.2 7.0 - - - +
149A ASN* 3.5 40.1 + - - +
150A GLN 5.7 0.2 + - - -
151A ASP 3.2 16.5 + - - +
152A LYS* 3.2 26.5 + - - +
154A THR* 1.3 80.3 - - - +
156A GLU* 1.3 62.8 + - + +
158A VAL* 3.6 0.6 + - - -
159A GLN* 3.5 11.5 + - - +
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Residues in contact with GLU 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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152A LYS* 3.2 48.2 + - + +
153A TRP* 4.1 6.3 - - + +
155A ARG* 1.3 78.0 - - + +
157A THR* 1.3 59.0 + - - +
159A GLN* 3.2 22.3 + - - +
160A TRP* 2.8 28.4 + - - +
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Residues in contact with THR 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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69A ILE* 5.3 5.8 - - + -
153A TRP* 2.2 70.7 + - + -
154A THR* 3.2 5.1 + - - -
156A GLU* 1.3 76.2 - - - +
158A VAL* 1.3 64.0 + - - +
160A TRP* 3.4 27.0 + - + +
161A LEU* 3.2 36.4 + - + +
303A DB3 5.0 9.4 - - + -
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Residues in contact with VAL 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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114A PHE* 4.3 15.5 - - + -
126A PHE* 3.6 30.3 - - + -
131A TRP* 4.6 15.3 - - + -
154A THR* 3.0 25.2 + - + +
155A ARG* 3.9 6.1 - - - +
156A GLU 3.2 0.2 - - - -
157A THR* 1.3 74.5 - - - +
159A GLN* 1.3 54.3 + - - +
161A LEU* 3.0 7.2 + - - +
162A LEU* 2.7 52.5 + - + +
303A DB3 3.8 27.6 - - + -
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Residues in contact with GLN 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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126A PHE* 4.0 15.5 - - + -
128A GLY 3.6 5.2 - - - +
129A THR* 3.3 38.1 + - - +
155A ARG 3.5 11.1 + - - +
156A GLU* 3.2 28.2 + - - +
158A VAL* 1.3 77.2 - - - +
160A TRP* 1.3 58.5 + - - +
161A LEU 3.0 0.2 - - - -
162A LEU* 4.4 5.2 - - - +
163A ASN* 3.0 38.6 + - + +
164A GLY 4.0 0.7 + - - -
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Residues in contact with TRP 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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65A THR* 5.0 12.8 - - + -
69A ILE* 3.9 20.0 - - + -
153A TRP* 6.4 0.4 - + - -
156A GLU 2.8 18.0 + - - +
157A THR* 3.6 22.7 - - + +
158A VAL 3.2 0.4 - - - -
159A GLN* 1.3 71.7 - - - +
161A LEU* 1.3 73.8 + - + +
164A GLY* 4.3 3.4 + - - +
165A THR* 2.4 39.4 + - + -
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Residues in contact with LEU 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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66A LEU* 6.3 1.8 - - + -
69A ILE* 4.6 22.7 - - + -
70A PHE* 5.0 8.5 - - + -
157A THR* 3.2 19.5 - - + +
158A VAL* 3.0 6.6 + - - +
159A GLN 3.0 0.6 - - - -
160A TRP* 1.3 103.8 - - + +
162A LEU* 1.3 62.3 + - + +
163A ASN 3.5 0.4 - - - -
165A THR* 3.4 26.8 + - + +
166A CYS* 2.6 35.0 + - + +
303A DB3 4.0 26.9 - - + -
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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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100A ALA* 5.2 1.6 - - + -
101A GLY 3.8 29.4 - - - +
102A CYS* 4.7 0.5 - - - +
112A ASN* 3.4 39.1 + - + +
113A PHE* 4.1 7.2 - - - +
114A PHE* 4.0 28.9 - - + -
126A PHE* 4.1 11.0 - - + +
158A VAL* 2.7 44.2 + - + +
159A GLN* 4.4 2.9 - - - +
161A LEU* 1.3 78.5 - - + +
163A ASN* 1.3 58.2 + - + +
166A CYS* 4.3 7.4 - - + +
167A PRO* 3.2 19.4 - - - +
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Residues in contact with ASN 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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110A SER* 5.3 3.8 + - - +
112A ASN* 4.2 12.5 + - - +
159A GLN* 3.0 19.4 + - + +
162A LEU* 1.3 78.1 - - + +
164A GLY* 1.3 57.0 + - - +
167A PRO* 3.6 12.7 - - - +
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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