Contacts of the helix formed by residues 137 - 151 (chain A) in PDB entry 2VLA
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 GLN 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A PHE* 3.3 30.7 + - - -
114A GLN* 3.4 25.5 + - - -
115A PHE* 3.5 18.8 + - + -
135A ILE* 3.6 16.0 - - + -
136A ARG* 1.3 72.3 - - - +
138A PHE* 1.3 77.7 + - + +
140A TYR* 3.3 7.2 + - - +
141A ILE* 2.8 34.6 + - + +
164A VAL* 5.7 0.6 - - + +
165A LEU* 3.9 20.0 - - + -
171A LEU* 5.5 0.4 - - + -
213A GLN* 3.0 29.2 + - - +
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Residues in contact with PHE 138 (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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109A ILE* 5.5 0.2 - - + -
110A CYS* 3.4 52.3 - - + +
113A PHE* 3.7 34.3 + + + -
137A GLN* 1.3 86.8 - - + +
139A PRO* 1.4 69.9 - - + +
140A TYR 3.2 0.2 + - - -
141A ILE* 3.3 16.7 + - + +
142A LEU* 3.0 31.1 + - - +
213A GLN* 3.1 53.6 - - + -
214A LEU* 5.1 0.2 - - - -
216A TYR* 4.7 6.3 - + + -
217A LEU* 3.9 24.0 - - + -
243A ILE* 5.1 1.6 - - + -
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Residues in contact with PRO 139 (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 CYS 4.1 9.6 - - - +
111A PHE* 5.0 7.2 - - + +
113A PHE 5.4 0.4 - - - +
136A ARG* 3.4 25.6 - - + +
138A PHE* 1.4 94.5 - - + +
140A TYR* 1.3 61.7 + - - +
142A LEU* 3.4 2.3 + - + +
143A GLN* 3.0 24.3 + - - +
243A ILE* 3.1 38.6 - - + +
244A ALA* 3.7 3.9 - - - -
246A PHE* 3.7 12.6 - - + -
247A TRP* 3.6 23.2 - - - +
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Residues in contact with TYR 140 (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 ILE* 3.9 23.3 - - + -
136A ARG 3.2 15.6 + - - +
137A GLN* 3.5 8.1 - - - +
138A PHE 3.1 0.4 - - - -
139A PRO* 1.3 79.8 - - - +
141A ILE* 1.3 58.0 + - - +
143A GLN* 3.2 3.5 + - - +
144A VAL* 2.9 52.4 + - + +
164A VAL* 4.0 15.5 - - + -
170A VAL* 3.6 22.2 - - + +
175A ILE* 2.7 35.0 + - - +
176A LYS 3.5 1.6 - - - -
177A PRO* 3.5 27.0 - - + +
180A VAL* 3.7 14.6 - - + +
247A TRP* 3.8 25.8 - + + +
1281A PG6 4.3 4.9 - - - -
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Residues in contact with ILE 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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137A GLN* 2.8 25.9 + - + +
138A PHE* 3.3 27.1 + - + +
140A TYR* 1.3 72.0 - - - +
142A LEU* 1.3 64.5 + - - +
144A VAL* 3.2 9.3 + - + +
145A LEU* 2.9 37.4 + - + +
160A ILE* 4.5 11.7 - - + -
164A VAL* 4.3 18.6 - - + -
165A LEU* 3.9 31.0 - - + -
214A LEU* 4.4 18.2 - - + -
217A LEU* 3.9 18.8 - - + -
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Residues in contact with LEU 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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138A PHE 3.0 17.0 + - - +
139A PRO 3.7 3.4 - - - +
141A ILE* 1.3 77.0 - - - +
143A GLN* 1.3 57.8 + - - +
145A LEU* 3.3 5.5 + - + +
146A LEU* 2.9 30.7 + - - +
217A LEU* 3.7 30.3 - - + -
222A LEU* 4.1 22.4 - - + -
223A ILE* 4.2 4.5 - - + -
232A LEU* 3.6 26.2 - - + +
240A ILE* 4.1 16.4 - - + +
243A ILE* 3.7 37.7 - - + -
244A ALA* 3.9 11.9 - - + -
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Residues in contact with GLN 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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139A PRO 3.0 16.9 + - - +
140A TYR 3.2 4.0 + - - +
142A LEU* 1.3 72.6 - - - +
144A VAL* 1.3 61.5 + - - +
146A LEU* 3.3 13.8 + - - +
147A THR* 2.8 46.5 + - - +
150A ASN* 6.1 0.8 - - - +
177A PRO* 3.6 19.3 - - + +
244A ALA* 3.7 16.8 - - - +
245A GLN* 5.3 1.2 - - - +
247A TRP* 3.4 43.7 - - + +
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Residues in contact with VAL 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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140A TYR* 2.9 45.4 + - + +
141A ILE* 3.5 10.1 - - + +
143A GLN* 1.3 74.3 - - - +
145A LEU* 1.3 59.6 + - + +
147A THR* 3.3 3.1 + - - -
148A ALA* 2.8 28.6 + - - +
155A LEU* 3.6 25.8 - - + -
160A ILE* 5.6 2.2 - - + -
164A VAL* 4.3 20.6 - - + -
177A PRO* 3.9 19.1 - - + -
180A VAL* 4.6 7.4 - - + -
181A ILE* 3.8 12.2 - - + +
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Residues in contact with LEU 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 ILE* 2.9 36.9 + - + +
142A LEU* 3.7 4.9 - - - +
143A GLN 3.3 0.2 - - - -
144A VAL* 1.3 74.8 - - + +
146A LEU* 1.3 65.7 + - - +
148A ALA* 3.3 6.5 + - + +
149A ASP* 3.0 27.4 + - - +
155A LEU* 4.3 17.9 - - + +
160A ILE* 4.2 12.1 - - + -
223A ILE* 3.9 28.0 - - + -
230A VAL* 3.6 37.7 - - + +
231A LYS* 5.3 1.1 - - - -
232A LEU* 3.8 22.2 - - + +
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Residues in contact with LEU 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 LEU 2.9 15.9 + - - +
143A GLN* 3.7 16.6 - - - +
145A LEU* 1.3 74.8 - - - +
147A THR* 1.3 58.9 + - - +
149A ASP* 3.2 4.3 + - - +
150A ASN* 2.9 41.3 + - - +
232A LEU* 3.6 21.3 - - + +
234A TYR* 3.8 21.3 + - + +
240A ILE* 4.2 13.5 - - + -
241A ASN* 3.9 22.2 - - - +
244A ALA* 3.7 29.4 - - + -
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Residues in contact with THR 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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143A GLN* 2.8 33.4 + - - -
144A VAL* 3.7 5.4 - - - -
146A LEU* 1.3 73.6 - - - +
148A ALA* 1.3 64.6 + - - +
150A ASN* 3.2 11.1 + - + +
151A ASN* 2.9 34.0 + - - +
177A PRO* 4.1 7.6 - - - +
178A ILE* 3.7 40.4 - - + +
181A ILE* 3.7 14.4 - - + -
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Residues in contact with ALA 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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144A VAL 2.8 17.8 + - - +
145A LEU* 3.5 8.3 - - + +
146A LEU 3.3 0.2 - - - -
147A THR* 1.3 74.8 - - - +
149A ASP* 1.3 62.8 + - - +
151A ASN* 3.0 4.2 + - - +
152A ASN 3.0 17.0 + - - -
153A ILE* 3.1 31.9 + - + +
154A GLN* 5.0 0.9 - - - -
155A LEU* 4.0 19.3 - - + -
181A ILE* 3.8 21.0 - - + +
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Residues in contact with ASP 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 LEU 3.0 13.8 + - - +
146A LEU 3.6 6.1 - - - +
148A ALA* 1.3 77.2 - - - +
150A ASN* 1.3 66.0 + - - +
152A ASN* 3.0 20.5 + - - +
153A ILE 3.9 10.5 - - - +
154A GLN* 4.6 11.3 + - - +
232A LEU* 3.9 10.3 + - - +
234A TYR* 2.5 43.0 + - - +
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Residues in contact with ASN 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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143A GLN* 6.1 1.0 - - - +
146A LEU* 2.9 30.6 + - - +
147A THR* 3.6 12.2 + - + +
148A ALA 3.2 0.2 - - - -
149A ASP* 1.3 78.8 - - - +
151A ASN* 1.3 63.9 - - - +
152A ASN* 3.4 9.1 + - - -
234A TYR* 5.7 0.2 + - - -
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Residues in contact with ASN 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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147A THR* 2.9 39.5 + - - +
148A ALA 3.0 4.9 + - - +
150A ASN* 1.3 82.7 - - - +
152A ASN* 1.3 73.0 + - - +
153A ILE* 3.2 12.0 + - + +
178A ILE* 3.7 15.3 - - - +
181A ILE* 4.1 17.9 - - + +
185A ILE* 4.6 12.5 - - + +
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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