Contacts of the helix formed by residues 140 - 156 (chain A) in PDB entry 2VDY
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 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A ASN* 3.2 30.0 + - + +
138A PHE 4.1 0.2 - - - -
139A GLN* 1.3 76.4 - - - +
141A TRP* 1.3 58.7 + - - +
142A ALA* 3.7 9.7 + - - +
143A THR* 2.6 36.2 + - + +
144A ALA* 3.0 21.7 + - - +
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Residues in contact with TRP 141 (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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136A MET* 3.2 29.2 - - + -
138A PHE 4.2 9.9 - - - +
139A GLN 3.6 5.0 + - - +
140A ASP* 1.3 72.1 + - - +
142A ALA* 1.3 60.9 + - - +
144A ALA* 3.7 11.7 - - + -
145A SER* 2.8 49.3 + - - -
148A ILE* 4.7 4.7 - - + -
164A PHE* 3.6 27.8 - + - +
168A ASP 4.2 9.8 + - - +
169A SER* 3.7 6.0 - - - -
170A PRO* 3.7 40.2 - - + -
171A ALA 3.7 12.3 - - - -
174A VAL* 4.4 6.1 - - + -
345A GLU* 3.3 27.4 - - - -
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Residues in contact with ALA 142 (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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140A ASP* 3.3 9.6 + - - +
141A TRP* 1.3 78.0 - - - +
143A THR* 1.3 60.4 + - - +
145A SER* 3.5 6.3 + - - -
146A ARG* 3.2 40.9 + - - +
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Residues in contact with THR 143 (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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137A ASN* 5.7 0.9 - - + -
140A ASP* 2.6 33.9 + - - -
141A TRP 3.3 0.4 - - - -
142A ALA* 1.3 75.4 - - - +
144A ALA* 1.3 60.3 + - - +
146A ARG* 3.1 22.8 + - - +
147A GLN* 2.8 34.5 + - + +
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Residues in contact with ALA 144 (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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136A MET* 3.6 33.7 - - + -
137A ASN 3.8 10.5 - - - +
140A ASP 3.0 17.9 + - - +
141A TRP* 3.3 12.3 + - + +
143A THR* 1.3 77.8 - - - +
145A SER* 1.3 57.2 + - - +
147A GLN* 3.3 12.8 + - - +
148A ILE* 3.1 34.5 + - - +
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Residues in contact with SER 145 (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 TRP* 2.8 50.1 + - - -
142A ALA* 3.5 7.3 + - - -
144A ALA* 1.3 71.7 - - - +
146A ARG* 1.3 60.0 + - - +
148A ILE* 4.3 7.7 - - - +
149A ASN* 3.0 39.6 + - - -
164A PHE* 4.1 19.1 - - - -
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Residues in contact with ARG 146 (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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142A ALA* 3.2 25.3 + - - +
143A THR* 3.1 39.3 + - - +
145A SER* 1.3 80.0 + - - +
147A GLN* 1.3 61.3 + - - +
149A ASN* 3.6 4.5 + - - +
150A SER* 3.0 30.7 + - - -
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Residues in contact with GLN 147 (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 PHE* 4.1 23.6 - - + -
134A LEU* 4.8 4.9 - - - +
135A ALA 3.2 23.1 + - - +
136A MET* 4.0 21.7 - - - +
137A ASN 5.2 0.2 + - - -
143A THR* 2.8 16.7 + - + +
144A ALA* 3.4 13.8 - - - +
146A ARG* 1.3 77.6 - - - +
148A ILE* 1.3 60.0 + - - +
150A SER* 3.0 18.2 + - - -
151A TYR* 3.2 13.7 + - - +
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Residues in contact with ILE 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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110A PHE* 3.8 44.9 - - + -
136A MET* 4.6 10.5 - - + -
141A TRP* 4.7 3.6 - - + -
144A ALA 3.1 19.4 + - - +
145A SER* 4.3 3.8 - - - +
146A ARG 3.4 0.2 - - - -
147A GLN* 1.3 75.3 - - - +
149A ASN* 1.3 65.4 + - - +
151A TYR* 3.3 1.7 + - - +
152A VAL* 3.1 29.2 + - + +
163A LEU* 5.3 0.2 - - + -
164A PHE* 3.6 30.3 - - + -
174A VAL* 4.1 30.7 - - + -
176A VAL* 4.1 12.6 - - + -
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Residues in contact with ASN 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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145A SER* 3.0 27.5 + - - +
146A ARG* 4.0 5.3 - - - +
147A GLN 3.4 0.2 - - - -
148A ILE* 1.3 76.9 - - - +
150A SER* 1.3 57.2 + - - +
152A VAL* 3.5 5.5 + - - +
153A LYS* 2.9 46.9 + - - +
160A ILE 4.6 0.9 - - - +
162A ASP* 3.9 12.1 + - - +
163A LEU* 3.1 16.1 + - - +
164A PHE* 2.7 54.9 + - - +
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Residues in contact with SER 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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146A ARG* 3.0 15.8 + - - -
147A GLN* 3.0 18.5 + - - -
149A ASN* 1.3 73.9 - - - +
151A TYR* 1.3 64.3 + - - +
153A LYS* 3.3 15.0 + - - +
154A ASN* 3.0 34.0 + - - +
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Residues in contact with TYR 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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107A ASN 4.2 3.1 + - - -
108A ALA* 3.5 30.5 - - + +
110A PHE* 3.7 19.5 - + + -
132A GLU* 2.7 30.6 + - - -
134A LEU* 3.9 20.0 - - + -
147A GLN* 3.2 14.5 + - + +
148A ILE 3.5 4.3 - - - +
150A SER* 1.3 82.7 + - - +
152A VAL* 1.3 71.2 + - + +
154A ASN* 3.5 3.5 + - - +
155A LYS* 3.2 56.4 + - + +
176A VAL* 5.0 2.7 - - + -
178A TYR* 4.1 19.4 + + - -
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Residues in contact with VAL 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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148A ILE* 3.1 19.9 + - + +
149A ASN* 3.9 4.5 - - - +
151A TYR* 1.3 79.6 - - + +
153A LYS* 1.3 63.6 + - - +
155A LYS* 3.4 4.6 + - - +
156A THR* 2.9 34.2 + - + +
160A ILE* 3.8 31.4 - - + +
163A LEU* 3.8 24.5 - - + -
176A VAL* 3.8 22.2 - - + -
178A TYR* 4.9 5.4 - - + -
341A ALA* 3.8 15.9 - - + -
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Residues in contact with LYS 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 ASN* 2.9 33.2 + - - +
150A SER* 3.3 13.0 - - - +
152A VAL* 1.3 77.5 - - - +
154A ASN* 1.3 58.5 + - - +
156A THR* 3.4 1.6 + - - -
157A GLN 3.4 1.9 + - - -
158A GLY* 2.7 42.0 + - - -
160A ILE 3.4 15.4 + - - +
161A VAL* 3.7 20.5 - - + +
162A ASP* 3.4 41.0 + - - +
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Residues in contact with ASN 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 SER* 3.0 22.8 + - - +
151A TYR* 4.0 4.5 - - - +
153A LYS* 1.3 75.7 - - - +
155A LYS* 1.3 62.1 + - + +
157A GLN* 3.0 25.9 + - - +
158A GLY 4.7 1.1 - - - +
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Residues in contact with LYS 155 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A THR* 3.9 22.0 - - - +
132A GLU* 4.0 8.9 + - - -
151A TYR* 3.2 50.0 + - + +
152A VAL 3.4 3.8 + - - +
154A ASN* 1.3 78.9 - - + +
156A THR* 1.3 57.7 + - - +
157A GLN* 3.3 4.9 + - - +
178A TYR* 3.4 49.6 + - + +
180A PHE* 4.5 0.2 - - - +
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Residues in contact with THR 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 VAL* 2.9 22.4 + - + +
153A LYS 3.4 3.5 + - - -
154A ASN 3.3 0.2 - - - -
155A LYS* 1.3 75.3 - - - +
157A GLN* 1.3 69.6 + - - +
159A LYS* 3.1 19.2 + - - +
160A ILE* 3.1 43.5 + - + +
178A TYR* 3.9 27.8 - - + -
179A ILE 3.9 16.8 - - - +
180A PHE* 3.3 13.7 - - - -
339A ALA* 4.4 3.4 - - - -
340A GLY 4.3 0.9 - - - +
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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