Contacts of the helix formed by residues 146 - 161 (chain A) in PDB entry 1GV3
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 SER 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A ILE* 3.9 5.3 - - - +
141A ASN* 3.4 15.3 + - - +
144A PHE* 3.3 3.9 + - - +
145A GLY* 1.3 79.8 - - - +
147A PHE* 1.3 64.9 + - - +
148A GLU* 3.7 16.2 + - - +
149A GLU* 3.3 21.0 + - - +
150A PHE* 3.2 21.7 + - - +
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Residues in contact with PHE 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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130A GLY 4.7 5.8 - - - -
131A GLN* 4.1 21.5 - - + +
132A PRO* 3.4 44.0 - - + -
140A ILE* 4.2 8.3 - - + -
141A ASN* 3.7 7.0 + - - +
146A SER* 1.3 71.4 - - - +
148A GLU* 1.3 78.9 + - + +
150A PHE* 3.3 20.1 + + - -
151A LYS* 2.8 62.1 + - + +
222A TRP* 4.1 19.7 - + + -
227A TRP* 3.8 14.1 - + - -
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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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131A GLN* 3.7 23.6 + - - +
146A SER* 3.8 17.8 - - - +
147A PHE* 1.3 92.4 + - + +
149A GLU* 1.3 56.4 + - - +
151A LYS* 3.7 8.4 - - + +
152A LYS* 3.1 44.0 + - - +
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Residues in contact with GLU 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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144A PHE 3.5 22.0 - - - +
146A SER* 3.3 14.4 + - - +
147A PHE 3.2 0.2 - - - -
148A GLU* 1.3 78.1 - - - +
150A PHE* 1.3 64.9 + - - +
152A LYS* 3.3 26.0 + - - +
153A GLN* 3.0 56.5 + - - +
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Residues in contact with PHE 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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140A ILE* 3.7 27.1 - - + -
144A PHE* 3.8 35.3 - + + +
146A SER 3.2 14.8 + - - +
147A PHE* 3.3 24.7 + + - +
149A GLU* 1.3 74.7 - - - +
151A LYS* 1.3 60.0 + - - +
153A GLN* 3.2 3.7 + - - +
154A PHE* 2.8 48.2 + + - +
169A LEU* 3.9 41.1 - - + -
179A VAL* 4.1 12.3 - - + -
197A MET* 4.5 4.7 - - - -
222A TRP* 3.7 25.4 - + - -
227A TRP* 4.5 4.3 - + - -
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Residues in contact with LYS 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 PHE* 2.8 46.5 + - + +
148A GLU* 3.7 8.3 - - + +
150A PHE* 1.3 82.4 - - - +
152A LYS* 1.3 60.6 + - + +
154A PHE* 3.6 4.8 - - - +
155A ASN* 3.0 36.0 + - - +
219A ASN* 4.3 18.1 + - - +
222A TRP* 3.5 48.4 - - + +
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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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148A GLU* 3.1 30.6 + - - +
149A GLU* 3.6 30.5 + - - +
151A LYS* 1.3 78.5 - - + +
153A GLN* 1.3 57.4 + - + +
155A ASN* 3.5 5.4 + - - +
156A GLN* 2.9 31.2 + - - +
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Residues in contact with GLN 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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144A PHE* 3.8 28.9 + - + +
149A GLU* 3.0 51.7 + - - +
150A PHE* 3.7 4.3 - - - +
152A LYS* 1.3 76.7 - - + +
154A PHE* 1.3 57.9 + - - +
156A GLN* 3.6 18.3 + - - +
157A ALA* 3.0 29.5 + - - +
179A VAL* 4.2 13.0 - - + +
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Residues in contact with PHE 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 PHE* 2.8 39.4 + + + +
151A LYS* 3.6 4.5 - - - +
152A LYS 3.2 0.2 - - - -
153A GLN* 1.3 73.7 - - - +
155A ASN* 1.3 65.6 + - - +
157A ALA 3.3 1.4 + - - -
158A GLY* 3.0 23.0 + - - -
167A VAL* 3.5 35.3 - - + +
168A TRP 4.1 25.4 - - - -
169A LEU* 4.2 4.3 - - + -
179A VAL* 4.3 10.5 - - + -
197A MET* 4.0 23.3 - - + -
198A GLY* 4.2 1.1 - - - -
199A ASN* 3.9 28.9 - - + -
218A LEU* 5.4 2.9 - - + -
221A TRP* 4.2 4.5 - + - -
222A TRP* 3.4 27.4 - + + -
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Residues in contact with ASN 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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151A LYS* 3.0 25.5 + - - +
152A LYS* 3.9 5.0 - - - +
154A PHE* 1.3 76.1 - - - +
156A GLN* 1.3 61.5 + - - +
158A GLY* 3.2 1.0 + - - +
159A GLY* 2.9 25.1 + - - -
215A PRO 5.6 0.2 + - - -
218A LEU* 3.5 33.6 + - + +
219A ASN* 3.8 24.4 - - - +
222A TRP* 3.0 33.6 + - - +
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Residues in contact with GLN 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 2.9 19.1 + - - +
153A GLN* 3.6 19.7 + - - +
155A ASN* 1.3 77.0 - - - +
157A ALA* 1.3 58.8 + - - +
159A GLY* 3.0 3.8 + - - -
160A ASP* 2.8 49.6 + - - +
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Residues in contact with ALA 157 (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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153A GLN 3.0 18.5 + - - +
154A PHE 3.3 4.7 + - - +
156A GLN* 1.3 76.6 - - - +
158A GLY* 1.3 61.6 + - - +
160A ASP* 3.4 9.2 + - - +
161A ARG* 3.3 22.9 + - - +
167A VAL* 3.8 8.1 - - + -
179A VAL* 3.7 22.9 - - + -
180A VAL* 5.7 0.2 - - - -
181A SER* 4.1 13.7 + - - +
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Residues in contact with GLY 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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154A PHE 3.0 11.9 + - - -
155A ASN 3.6 4.0 - - - -
156A GLN 3.1 0.4 - - - -
157A ALA* 1.3 78.4 - - - +
159A GLY* 1.3 57.7 - - - +
161A ARG* 3.6 5.0 + - - +
167A VAL* 3.1 29.3 - - - +
201A VAL* 3.8 5.0 - - - +
214A ARG* 2.9 25.1 + - - -
218A LEU* 3.9 11.7 - - - -
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Residues in contact with GLY 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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155A ASN 2.9 14.1 + - - -
156A GLN* 3.0 3.5 + - - -
158A GLY* 1.3 77.3 - - - +
160A ASP* 1.3 63.1 + - - +
161A ARG 3.4 1.9 + - - +
162A PHE* 5.4 0.7 - - - -
214A ARG* 3.8 15.8 + - - -
215A PRO* 6.3 2.2 - - - -
218A LEU* 3.8 8.4 - - - +
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Residues in contact with ASP 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 GLN* 2.8 36.9 + - - +
157A ALA* 3.9 10.0 + - - +
158A GLY 3.3 0.2 - - - -
159A GLY* 1.3 77.1 - - - +
161A ARG* 1.3 58.5 + - - +
162A PHE* 3.1 11.2 + - - +
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Residues in contact with ARG 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 3.3 14.6 + - - +
158A GLY* 3.9 8.1 - - - +
159A GLY 3.3 2.3 - - - -
160A ASP* 1.3 73.1 - - - +
162A PHE* 1.3 71.8 + - - +
163A GLY 3.7 0.3 - - - +
164A SER 4.1 7.2 + - - -
165A GLY* 4.0 9.0 - - - +
166A TRP 4.4 1.8 - - - +
181A SER* 2.9 48.0 + - - +
182A THR 3.6 17.6 + - - +
183A PRO* 3.4 31.5 - - - +
201A VAL* 3.9 20.4 - - + -
214A ARG* 2.7 29.2 + - - -
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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