Contacts of the helix formed by residues 144 - 160 (chain B) in PDB entry 1VE3
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 144 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B PHE* 3.6 12.9 + - + -
143B THR* 1.3 71.7 - - - +
145B LEU* 1.3 69.1 + - - +
146B ARG* 2.7 59.0 + - - +
147B GLU* 2.8 16.9 + - + +
148B LEU 2.9 10.0 + - - -
194B TRP 4.7 9.5 - - - +
195B GLY* 5.5 2.8 - - - -
196B LYS 5.7 1.6 + - - -
218B TYR* 3.3 41.5 - - + +
219B SER* 3.0 9.8 + - - +
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Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B PHE* 5.7 0.4 - - - -
143B THR 3.4 3.6 + - - -
144B ASP* 1.3 74.1 - - - +
146B ARG* 1.3 66.1 + - + +
147B GLU 3.0 1.4 + - - -
148B LEU* 3.1 23.4 + - + -
149B LEU* 3.1 46.3 + - + +
167B VAL* 5.9 1.6 - - + -
176B VAL* 4.1 27.8 - - + -
178B ILE* 4.7 0.2 - - + -
191B PHE* 4.5 21.3 - - + -
193B VAL* 4.4 21.5 - - + -
194B TRP 5.7 1.8 + - - -
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Residues in contact with ARG 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ASP* 2.7 41.2 + - - +
145B LEU* 1.3 78.5 - - + +
147B GLU* 1.3 57.2 + - - +
149B LEU* 4.8 3.8 - - - +
150B PRO* 3.1 22.0 - - - +
218B TYR* 3.4 54.1 + - + +
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Residues in contact with GLU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B THR* 4.0 10.5 - - + -
144B ASP 2.8 8.5 + - - +
146B ARG* 1.3 77.5 - - - +
148B LEU* 1.3 61.6 + - - +
150B PRO* 3.2 13.4 - - - +
151B ARG* 3.6 22.2 + - - +
215B VAL 3.6 0.4 - - - +
216B GLY* 3.4 10.4 - - - -
217B ASN* 3.0 18.1 + - + +
218B TYR* 2.7 48.4 + - + -
219B SER* 2.8 26.3 + - - -
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Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B TYR* 4.2 11.9 - - - +
13B TYR* 3.6 24.2 - - - +
114B VAL* 5.0 11.9 - - + -
143B THR* 3.7 26.4 - - + +
144B ASP 2.9 13.2 + - - +
145B LEU* 3.1 15.9 + - + +
147B GLU* 1.3 76.5 - - - +
149B LEU* 1.3 65.9 + - - +
151B ARG* 3.2 13.5 + - + +
152B LEU* 2.9 50.9 + - + +
191B PHE* 4.5 15.0 - - + -
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Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LEU* 3.1 36.6 + - + +
146B ARG* 5.3 3.4 - - - -
148B LEU* 1.3 76.8 - - - +
150B PRO* 1.3 68.7 - - + +
152B LEU* 3.2 10.3 + - + +
153B LYS* 3.0 41.7 + - - +
164B ILE* 4.3 11.6 - - + +
167B VAL* 4.7 21.3 - - + -
178B ILE* 3.2 36.1 - - + -
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Residues in contact with PRO 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B ARG 3.1 26.2 - - - +
147B GLU* 3.2 12.3 - - - +
149B LEU* 1.3 95.4 - - + +
151B ARG* 1.3 60.8 - - + +
153B LYS* 3.4 12.8 + - + +
154B GLU* 3.1 31.5 + - - +
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Residues in contact with ARG 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B THR* 3.9 12.5 - - - +
13B TYR* 4.6 6.3 + - - -
20B GLU 5.4 0.2 + - - -
24B ARG* 3.5 36.1 - - - +
111B ASP* 5.4 1.4 + - - -
141B TYR* 4.7 5.1 + - - -
143B THR* 3.6 29.0 + - - +
147B GLU* 3.6 18.6 + - - +
148B LEU* 3.2 16.9 + - + +
149B LEU 3.2 0.4 - - - -
150B PRO* 1.3 80.4 - - + +
152B LEU* 1.3 63.3 + - + +
154B GLU* 3.3 18.1 + - - +
155B SER* 3.2 23.5 + - - -
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Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B TYR* 3.6 35.2 - - + +
10B PHE* 3.3 39.0 - - + -
12B THR* 5.5 3.1 - - - +
13B TYR* 5.3 4.3 - - + -
148B LEU* 2.9 40.8 + - + +
149B LEU* 3.5 20.0 - - + +
151B ARG* 1.3 78.1 - - + +
153B LYS* 1.3 57.7 + - - +
155B SER* 3.1 3.2 + - - +
156B LEU* 2.7 34.1 + - + +
164B ILE* 4.5 5.4 - - + -
178B ILE* 4.9 0.4 - - + -
180B PHE* 4.7 10.3 - - + -
191B PHE* 4.7 5.6 - - + -
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Residues in contact with LYS 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B LEU* 3.0 31.3 + - - +
150B PRO* 3.7 11.4 - - + +
151B ARG 3.3 0.2 - - - -
152B LEU* 1.3 75.2 - - - +
154B GLU* 1.3 62.5 + - + +
156B LEU* 3.2 12.3 + - - +
157B VAL* 3.1 27.4 + - + +
164B ILE* 3.6 36.1 - - + +
167B VAL* 5.9 4.6 - - - +
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Residues in contact with GLU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B PRO* 3.1 23.0 + - - +
151B ARG* 3.5 21.9 - - - +
153B LYS* 1.3 77.0 - - + +
155B SER* 1.3 61.6 + - - +
157B VAL* 3.3 18.2 + - - +
158B VAL* 3.4 17.9 + - - +
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Residues in contact with SER 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL 5.9 0.4 - - - -
10B PHE* 3.6 23.6 - - - -
11B PRO* 5.3 7.6 - - - -
12B THR* 4.2 5.6 + - - -
20B GLU* 4.2 24.8 + - - +
151B ARG 3.2 10.3 + - - -
152B LEU* 3.1 10.2 + - - +
154B GLU* 1.3 77.1 - - - +
156B LEU* 1.3 64.7 + - - +
158B VAL* 3.0 13.1 + - - +
159B GLY* 2.9 17.7 + - - -
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Residues in contact with LEU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 4.0 15.7 - - + -
10B PHE* 3.3 30.5 - - + -
152B LEU 2.7 38.3 + - - +
153B LYS* 3.2 10.5 + - - +
155B SER* 1.3 75.1 - - - +
157B VAL* 1.3 66.1 + - + +
159B GLY* 2.9 4.9 + - - +
160B GLN* 2.9 19.4 + - - -
161B LYS 4.1 0.5 + - - -
162B TYR* 3.1 50.5 + - + +
163B TRP* 4.4 5.8 - - - +
164B ILE* 4.3 6.3 - - + +
180B PHE* 4.2 15.5 - - + -
187B PHE* 5.9 0.2 - - + -
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Residues in contact with VAL 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B LYS* 3.1 19.8 + - + +
154B GLU* 3.5 10.8 - - - +
155B SER 3.2 0.4 - - - -
156B LEU* 1.3 75.1 - - + +
158B VAL* 1.3 65.5 + - + +
160B GLN* 3.0 23.5 + - - +
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLU* 5.0 11.7 - - - +
154B GLU 3.4 14.6 - - - +
155B SER* 3.0 12.3 + - - +
157B VAL* 1.3 79.8 - - + +
159B GLY* 1.3 63.3 + - - +
160B GLN* 3.4 12.6 + - - +
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Residues in contact with GLY 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B SER 2.9 9.8 + - - -
156B LEU* 2.9 10.4 + - - -
158B VAL* 1.3 76.8 - - - +
160B GLN* 1.3 69.5 + - - +
161B LYS* 3.1 11.9 + - - +
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Residues in contact with GLN 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B LEU 2.9 8.5 + - - -
157B VAL* 3.0 19.5 + - - +
158B VAL* 3.6 11.2 + - - +
159B GLY* 1.3 77.7 - - - +
161B LYS* 1.3 57.8 + - - +
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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